Query gi|254780591|ref|YP_003065004.1| aminomethyltransferase protein (glycine cleavage) [Candidatus Liberibacter asiaticus str. psy62] Match_columns 273 No_of_seqs 105 out of 5937 Neff 10.5 Searched_HMMs 39220 Date Sun May 29 22:05:42 2011 Command /home/congqian_1/programs/hhpred/hhsearch -i 254780591.hhm -d /home/congqian_1/database/cdd/Cdd.hhm No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM 1 PRK00389 gcvT glycine cleavage 100.0 1.4E-45 0 286.5 17.2 267 4-273 47-357 (362) 2 COG0404 GcvT Glycine cleavage 100.0 1.3E-41 0 262.1 18.3 270 4-273 51-371 (379) 3 PRK12486 dmdA putative dimethy 100.0 3.7E-42 0 265.2 15.2 265 4-271 56-366 (367) 4 PRK13579 gcvT glycine cleavage 100.0 1.5E-41 0 261.6 14.5 264 4-273 56-366 (371) 5 TIGR00528 gcvT glycine cleavag 100.0 4.1E-39 1.1E-43 247.4 14.5 268 5-273 49-393 (394) 6 COG0354 Predicted aminomethylt 100.0 1.8E-36 4.6E-41 231.9 15.3 265 1-272 14-295 (305) 7 PRK09559 putative global regul 100.0 6.9E-34 1.7E-38 216.9 18.7 261 2-270 20-322 (327) 8 TIGR01372 soxA sarcosine oxida 100.0 6.5E-35 1.7E-39 222.9 8.8 266 7-272 686-1017(1026) 9 KOG2929 consensus 100.0 9.8E-33 2.5E-37 210.2 13.8 270 3-273 32-338 (348) 10 KOG2770 consensus 100.0 6.4E-31 1.6E-35 199.6 15.0 268 3-272 71-393 (401) 11 KOG2844 consensus 100.0 3.5E-30 8.8E-35 195.3 14.9 241 3-244 520-810 (856) 12 pfam01571 GCV_T Aminomethyltra 99.9 3E-23 7.8E-28 154.7 8.4 113 4-116 2-114 (212) 13 pfam08669 GCV_T_C Glycine clea 99.3 8E-12 2E-16 88.1 6.6 86 183-270 1-94 (95) 14 TIGR03317 ygfZ_signature folat 98.2 6.4E-07 1.6E-11 59.4 2.5 65 143-208 2-66 (67) 15 pfam04268 SoxG Sarcosine oxida 97.0 0.0024 6.2E-08 38.5 6.1 69 8-82 73-143 (148) 16 COG0486 ThdF Predicted GTPase 96.9 0.0024 6.1E-08 38.6 5.7 58 8-66 18-76 (454) 17 pfam10396 TrmE_N GTP-binding p 96.7 0.0078 2E-07 35.6 6.8 51 8-61 13-63 (114) 18 COG4583 Sarcosine oxidase gamm 96.7 0.0064 1.6E-07 36.1 6.3 73 4-82 106-181 (189) 19 PRK05291 trmE tRNA modificatio 96.4 0.0088 2.2E-07 35.3 5.6 56 8-65 18-74 (445) 20 TIGR01375 soxG sarcosine oxida 96.3 0.0033 8.5E-08 37.7 3.2 75 3-83 73-150 (154) 21 TIGR00450 thdF tRNA modificati 90.7 0.072 1.8E-06 29.9 0.3 59 8-66 12-75 (473) 22 TIGR02860 spore_IV_B stage IV 54.1 15 0.00037 16.5 3.1 54 181-234 339-401 (423) 23 pfam11834 DUF3354 Domain of un 50.9 16 0.00041 16.2 2.9 45 17-67 25-69 (69) 24 TIGR02876 spore_yqfD sporulati 49.7 12 0.00031 17.0 2.1 76 5-83 4-84 (406) 25 pfam02743 Cache_1 Cache domain 48.7 14 0.00035 16.6 2.3 28 27-54 41-68 (81) 26 pfam06898 YqfD Putative stage 45.4 13 0.00034 16.7 1.8 31 3-33 5-35 (383) 27 pfam07932 DAP_C D-aminopeptida 38.1 27 0.00069 14.9 3.5 55 180-234 29-83 (97) 28 KOG1191 consensus 29.9 30 0.00076 14.7 1.5 56 9-66 57-123 (531) 29 TIGR02082 metH methionine synt 25.0 40 0.001 13.9 1.5 16 20-35 408-424 (1265) 30 PRK10807 paraquat-inducible pr 23.4 49 0.0013 13.4 5.3 60 12-71 45-110 (546) 31 TIGR01755 flav_wrbA flavoprote 23.3 49 0.0013 13.4 2.4 41 220-260 105-166 (205) 32 pfam09863 DUF2090 Uncharacteri 23.1 25 0.00064 15.1 0.1 11 19-29 20-30 (310) 33 pfam00673 Ribosomal_L5_C ribos 22.1 33 0.00085 14.4 0.6 39 11-49 5-43 (95) 34 TIGR00380 cobD cobalamin biosy 22.0 32 0.00083 14.5 0.5 24 17-40 120-143 (322) 35 PRK05054 exoribonuclease II; P 20.8 56 0.0014 13.1 4.1 49 2-59 251-303 (644) 36 pfam05580 Peptidase_S55 SpoIVB 20.3 57 0.0015 13.0 2.7 20 216-235 183-202 (219) No 1 >PRK00389 gcvT glycine cleavage system aminomethyltransferase T; Reviewed Probab=100.00 E-value=1.4e-45 Score=286.51 Aligned_cols=267 Identities=18% Similarity=0.162 Sum_probs=204.1 Q ss_pred EECCCCEEEEEECCCHHHHHHCCCCCCHHHCCCCCEEEEEEECCCCCEEEEEEEEEECCCCCCEEHHHHHHHHHHHHHHH Q ss_conf 76179407999875878786321326731089982689999979998899899997045552000033333456777643 Q gi|254780591|r 4 VYLSNQSFIKVCGKSAIPFLQAIITADVLTLPYKIARGSAILTPQGKILLYFLISKIEEDTFILEIDRSKRDSLIDKLLF 83 (273) Q Consensus 4 ~~L~~~~~i~i~G~DA~~fL~~l~t~di~~l~~g~~~yt~~ln~~G~i~~D~~i~r~~~~~~~~~~~~~~~~~~~~~~~~ 83 (273) +=+|+++.|+|+||||.+|||+++|||++++++|+++||+|||++|+|++|++|+|+++++|+++.++........|+.. T Consensus 47 ~D~S~~~ki~I~G~Da~~~L~~l~t~di~~l~~G~~~yt~~ln~~G~i~~D~~v~rl~e~~~~lv~~a~~~~~~~~wl~~ 126 (362) T PRK00389 47 FDVSHMGEVDVTGPDALAFLQYLLANDVAKLKPGKALYTAMLNEDGGVIDDLIVYKLSEDEYLLVVNAANREKDLAWILE 126 (362) T ss_pred EECCCCEEEEEECCCHHHHHHHHHCCCCCCCCCCCEEEEEEECCCCCEEEEEEEEEECCCCEEEECCCCHHHHHHHHHHH T ss_conf 96887489999888999999886113534479986999987879987887677888637604762372048899999996 Q ss_pred HHHCCCCCCCCCCCCEEEEEECCCCCCCCCCCCCCCCCCC-CCHH----------HHH----------HCCCCCC----- Q ss_conf 2100012235688436999971854322211123456644-4101----------222----------1013555----- Q gi|254780591|r 84 YKLRSNVIIEIQPINGVVLSWNQEHTFSNSSFIDERFSIA-DVLL----------HRT----------WGHNEKI----- 137 (273) Q Consensus 84 ~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~~-~~~~----------~~~----------~~~~~~~----- 137 (273) +....++.+.+.+++++.+++|||+|+..+.......... .... ... ++...+. T Consensus 127 ~~~~~dv~i~d~t~~~a~l~vqGPkS~~vL~~l~~~~~~~l~~~~~~~~~i~g~~~~i~R~g~tGE~G~Ei~~~~~~~~~ 206 (362) T PRK00389 127 HAEGFGVEVTDRSDDLALLAVQGPKAREKLQKLTPADLSELKPFEFAQAGFAGVDVFVARTGYTGEDGFEIYLPAEDAEA 206 (362) T ss_pred HCCCCCCEEEECCCCEEEEEEECHHHHHHHHHHCCCCHHHCCCCCEEEEEECCCEEEEEECCCCCCCEEEEEECHHHHHH T ss_conf 37779829998776465643018479999998677386568744206998679769999457578976999966999999 Q ss_pred -----------CCCHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCEEEECCC-CCCCCCCCCCCCCCCCCCCEEEE Q ss_conf -----------579678888887520133456543221233100111220133147-52133101321001244434788 Q gi|254780591|r 138 -----------ASDIKTYHELRINHGIVDPNTDFLPSTIFPHDALMDLLNGISLTK-GCYIGQEVVSRIQHRNIIRKRPM 205 (273) Q Consensus 138 -----------~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~k-~~f~G~e~~~~~~~~~~~~~~~~ 205 (273) +.+..+.+..+.+.+... .+.+......+....+.+.+++.| +||+||+++.+++..+..+++++ T Consensus 207 lw~~l~~~Gi~p~G~~A~dsLRiE~G~~~---~G~D~~~~~tP~E~gL~~~v~~~k~~~FiGkeal~~~~~~g~~~~lvg 283 (362) T PRK00389 207 LWDALLEAGVKPCGLGARDTLRLEAGMPL---YGQDMDETTTPLEAGLGWTVKLEKERDFIGREALEAQKEEGVERKLVG 283 (362) T ss_pred HHHHHHHCCCEECCCCCCHHHHHHCCCCC---CCCCCCCCCCHHHCCCCCEEECCCCCCCCCHHHHHHHHHCCCCEEEEE T ss_conf 99999985991026554314588669887---786557789855758523785388888674899999984199819999 Q ss_pred EEECCCCCCCCCCEEEECCEEEEEEEEEECC------EEEEEEEHHHCCCCCCCCCEEEECCEEEEEECCCCCC Q ss_conf 7401345667898872467796799983478------3368998131036656786488688899997488769 Q gi|254780591|r 206 IITGTDDLPPSGSPILTDDIEIGTLGVVVGK------KALAIARIDKVDHAIKKGMALTVHGVRVKASFPHWYK 273 (273) Q Consensus 206 ~~~~~~~~~~~g~~i~~~g~~VG~vtS~~~~------~gla~i~~~~~~~~~~~~~~l~~~~~~~~i~~P~w~~ 273 (273) +..+.+..++.|++|+.+|++||.|||+++| +||||++.++...+.+..+++.++..+++|.++|||+ T Consensus 284 l~~~~~~~~~~g~~v~~~g~~VG~vTS~~~sp~l~k~Iala~v~~~~~~~G~~l~V~i~g~~~~a~V~~~PF~~ 357 (362) T PRK00389 284 LVLEERGIPRHGYPVLFDGGEIGEVTSGTFSPTLGKSIALAYVPAEYAKIGTEVEVEIRGKRVPAKVVKPPFVR 357 (362) T ss_pred EEECCCCCCCCCCEEEECCCEEEEEEEEEECCCCCCEEEEEEECHHHCCCCCEEEEEECCEEEEEEEECCCCCC T ss_conf 99999867899998977992699981256863669468999988554689998999999959999996899768 No 2 >COG0404 GcvT Glycine cleavage system T protein (aminomethyltransferase) [Amino acid transport and metabolism] Probab=100.00 E-value=1.3e-41 Score=262.06 Aligned_cols=270 Identities=17% Similarity=0.123 Sum_probs=202.7 Q ss_pred EECCCCEEEEEECCCHHHHHHCCCCCCHHHCCCCCEEEEEEECCCCCEEEEEEEEEECCCCCCEEHHHHHHHHHHHHHHH Q ss_conf 76179407999875878786321326731089982689999979998899899997045552000033333456777643 Q gi|254780591|r 4 VYLSNQSFIKVCGKSAIPFLQAIITADVLTLPYKIARGSAILTPQGKILLYFLISKIEEDTFILEIDRSKRDSLIDKLLF 83 (273) Q Consensus 4 ~~L~~~~~i~i~G~DA~~fL~~l~t~di~~l~~g~~~yt~~ln~~G~i~~D~~i~r~~~~~~~~~~~~~~~~~~~~~~~~ 83 (273) |=+|+++.++|+||||.+|||+++|||++++++||++||+|||++|+|+||++|+|++++.|+++.++.+......|+.. T Consensus 51 fDvShmgk~~V~GpdA~~~L~~l~~ndv~kl~~Gr~~Yt~~lne~G~v~dD~~v~rl~~d~f~lv~~a~~~~~~~~~l~~ 130 (379) T COG0404 51 FDVSHMGKVEVSGPDAAAFLQRLLTNDVSKLKPGRARYTLMLNEDGGIIDDLIVYRLGEDRFFLVTNAATAEKDLAWLER 130 (379) T ss_pred EECCCCEEEEEECCCHHHHHHHHCCCCCCCCCCCCEEEEEEECCCCCEEEEEEEEEECCCEEEEEECCCCHHHHHHHHHH T ss_conf 86468569999898999999977056667677774887245879998874179997269869999476662889999987 Q ss_pred HH--HCCCCCCCCCCCCEEEEEECCCCCCCCCCCCCCCCC--CCCCH-----------HHHHHCCCCCCCCCH------- Q ss_conf 21--000122356884369999718543222111234566--44410-----------122210135555796------- Q gi|254780591|r 84 YK--LRSNVIIEIQPINGVVLSWNQEHTFSNSSFIDERFS--IADVL-----------LHRTWGHNEKIASDI------- 141 (273) Q Consensus 84 ~~--~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~--~~~~~-----------~~~~~~~~~~~~~~~------- 141 (273) +. ....+.+.+.+++++.+++|||++++....+..... ...+. ........++.+.+. T Consensus 131 ~~~~~~~~v~~~~~t~~~~~lalqGPkAr~il~~~~~~~~~~~l~~~~~~~~~i~g~~~~~i~R~gyTGE~G~Ei~~p~~ 210 (379) T COG0404 131 HQAGPDLDVTLTSVTEDLAVLALQGPKAREVLAKLVDGDLVEALPFFAFKEVTIGGGVPVRISRTGYTGELGFEIYVPAE 210 (379) T ss_pred HHCCCCCCEEEEECCCCEEEEEEECCCHHHHHHHHCCCCCCCCCCCEEEEEEEECCCCEEEEEECCCCCCCEEEEEECHH T ss_conf 51368860597653554899998786789999874465532358835788877057734999946634787589973689 Q ss_pred ---HHHHHHHHH-----------------HHCCCCCCCCCCCCCCCCCCCCCCCEEEECCCCCCCCCCCCCCCCCCCCCC Q ss_conf ---788888875-----------------201334565432212331001112201331475213310132100124443 Q gi|254780591|r 142 ---KTYHELRIN-----------------HGIVDPNTDFLPSTIFPHDALMDLLNGISLTKGCYIGQEVVSRIQHRNIIR 201 (273) Q Consensus 142 ---~~~~~~~~~-----------------~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~k~~f~G~e~~~~~~~~~~~~ 201 (273) ..|+....+ +....+...+.+......+....+.|.+...|.+|+|++++.+.+..+..+ T Consensus 211 ~a~~vw~aL~~aG~~~g~~P~Gl~A~dtLRlE~g~~l~g~d~~~~~~P~eagl~~~v~~~k~dFiGk~al~~~k~~g~~r 290 (379) T COG0404 211 DAAAVWDALLEAGEKFGVKPCGLGARDTLRLEAGLRLYGQDLDETITPLEAGLGWAVKLDKDDFIGKAALLREKAKGVRR 290 (379) T ss_pred HHHHHHHHHHHHHHHCCCEEEECCHHHHHHHHCCCCCCCCCCCCCCCHHHCCCCEEECCCCCCCCCHHHHHHHHHCCCCE T ss_conf 99999999997200238557600356675664576432643599989755676208227876776899999667417761 Q ss_pred EEEEEEECCCC-CCCCCCEEE-ECCEE-EEEEEEEECC------EEEEEEEHHHCCCCCCCCCEEEECCEEEEEECCCCC Q ss_conf 47887401345-667898872-46779-6799983478------336899813103665678648868889999748876 Q gi|254780591|r 202 KRPMIITGTDD-LPPSGSPIL-TDDIE-IGTLGVVVGK------KALAIARIDKVDHAIKKGMALTVHGVRVKASFPHWY 272 (273) Q Consensus 202 ~~~~~~~~~~~-~~~~g~~i~-~~g~~-VG~vtS~~~~------~gla~i~~~~~~~~~~~~~~l~~~~~~~~i~~P~w~ 272 (273) +++++...... .++++++|+ .+++. ||+|||+++| |+|||+..++...+....++++++..+++|.+||+| T Consensus 291 ~lVgl~~~~~~~~~~~g~~v~~~~g~~~vG~VTSg~~Sptlg~~IAla~v~~~~~~~G~~~~v~i~~~~~~a~V~~~pf~ 370 (379) T COG0404 291 KLVGLKLDDKGPVLRGGEPVLDADGEVEVGEVTSGTFSPTLGKSIALAYVDSDYAKPGTELEVEIRGKRVPARVVKPPFY 370 (379) T ss_pred EEEEEEECCCCCCCCCCCEEEECCCCEEEEEEEECCCCCCCCCEEEEEEECCHHCCCCCEEEEEECCEEEEEEEECCCCC T ss_conf 79989975887777788858845797767999605625667970699995503316886899997885887899557984 Q ss_pred C Q ss_conf 9 Q gi|254780591|r 273 K 273 (273) Q Consensus 273 ~ 273 (273) . T Consensus 371 d 371 (379) T COG0404 371 D 371 (379) T ss_pred C T ss_conf 8 No 3 >PRK12486 dmdA putative dimethyl sulfoniopropionate demethylase; Reviewed Probab=100.00 E-value=3.7e-42 Score=265.17 Aligned_cols=265 Identities=11% Similarity=0.001 Sum_probs=187.5 Q ss_pred EECCCCEEEEEECCCHHHHHHCCCCCCHHHCCCCCEEEEEEECCCCCEEEEEEEEEECCCCCCEEHHHHHHHHHHHHHHH Q ss_conf 76179407999875878786321326731089982689999979998899899997045552000033333456777643 Q gi|254780591|r 4 VYLSNQSFIKVCGKSAIPFLQAIITADVLTLPYKIARGSAILTPQGKILLYFLISKIEEDTFILEIDRSKRDSLIDKLLF 83 (273) Q Consensus 4 ~~L~~~~~i~i~G~DA~~fL~~l~t~di~~l~~g~~~yt~~ln~~G~i~~D~~i~r~~~~~~~~~~~~~~~~~~~~~~~~ 83 (273) +=+|+++.|+|+||||.+|||+++|||++++++|+++||+|||++|+|++|++|+|++++.|+++.++... ..|.+. T Consensus 56 fDvS~mgk~~v~G~dA~~fL~~l~t~d~~~l~~G~~~Yt~~lne~GgiidD~iv~rl~ed~f~i~~~~~~~---~~~~~~ 132 (367) T PRK12486 56 WDVACERQVEIRGPDAGRLMQLLTPRDLRGMLPGQCYYVPIVDETGGMLNDPVALKLAEDRWWISIADSDL---LLWVKG 132 (367) T ss_pred EECCCCEEEEEECCCHHHHHHHHCCCCCCCCCCCCEEEEEEECCCCCEEEEEEEEEECCCCEEEECCCHHH---HHHHHH T ss_conf 97887189999898999999875124766588897999888989998900048997058726653165359---999986 Q ss_pred HHHCCCCCCCCCCCCEEEEEECCCCCCCCCCCCCCCCCCC-CCHH----------HHHHCCCCCCCCC-----------H Q ss_conf 2100012235688436999971854322211123456644-4101----------2221013555579-----------6 Q gi|254780591|r 84 YKLRSNVIIEIQPINGVVLSWNQEHTFSNSSFIDERFSIA-DVLL----------HRTWGHNEKIASD-----------I 141 (273) Q Consensus 84 ~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~~-~~~~----------~~~~~~~~~~~~~-----------~ 141 (273) ......+.+.+.+.++..+++|||+|+............. .... .......++.+.+ . T Consensus 133 ~~~~~~~~v~~~~~~~~~lalqGP~a~~vl~~~~~~~~~~l~~~~~~~~~~~g~~~~i~RtgyTGE~G~EI~v~~~~~a~ 212 (367) T PRK12486 133 IANGRRLDVLIVEPDVSPLAVQGPKADDLMARVFGESIRDIRFFRFGYFDFEGHDLVVARSGYSKQGGFEIYVEGSDLGM 212 (367) T ss_pred HHCCCCCEEEECCCCEEEEEEECCCHHHHHHHHCCCCHHHCCCCCCCEEEECCEEEEEEEECCCCCCEEEEEECCHHHHH T ss_conf 43038817998668878898557084999976347874556445465799999179999522367887999953589999 Q ss_pred HHHHHHHHH---------------HHCCCCCCCCCCCCCCCCCCCCCCCEEEECCCC-CCCCCCCCCCCCCCCCCCEEEE Q ss_conf 788888875---------------201334565432212331001112201331475-2133101321001244434788 Q gi|254780591|r 142 KTYHELRIN---------------HGIVDPNTDFLPSTIFPHDALMDLLNGISLTKG-CYIGQEVVSRIQHRNIIRKRPM 205 (273) Q Consensus 142 ~~~~~~~~~---------------~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~k~-~f~G~e~~~~~~~~~~~~~~~~ 205 (273) ..|+....+ +....+...+.+......+....+.+.+...|+ +|+||+++.+++..+..+++++ T Consensus 213 ~lw~~L~~aG~~~~i~~g~~~~l~RlEaG~~l~G~Dl~~~~tP~EagL~~~v~~~k~~dFiGk~al~~~~~~g~~~~lvg 292 (367) T PRK12486 213 PLWNALFEAGADLNVRAGCPNLIERIESGLLSYGNDMTDDNTPHECGLGRFCNTQTAIGCIGRDALLRVAKEGPVQQIRA 292 (367) T ss_pred HHHHHHHHHCCCCCCCCCCCCHHHHHHCCCCCCCCCCCCCCCHHHCCCHHHCCCCCCCCCCCHHHHHHHHHCCCCEEEEE T ss_conf 99999998588888664766055677504300288789999866788841206898989869999999985098869999 Q ss_pred EEECCCCCCCC--CCEEEECCEEEEEEEEEECC------EEEEEEEHHHCCCCCCCCCEEEECCEEEEEECCCC Q ss_conf 74013456678--98872467796799983478------33689981310366567864886888999974887 Q gi|254780591|r 206 IITGTDDLPPS--GSPILTDDIEIGTLGVVVGK------KALAIARIDKVDHAIKKGMALTVHGVRVKASFPHW 271 (273) Q Consensus 206 ~~~~~~~~~~~--g~~i~~~g~~VG~vtS~~~~------~gla~i~~~~~~~~~~~~~~l~~~~~~~~i~~P~w 271 (273) +....+..++. +.++..+|++||+|||+++| +||||++.++...+....++++.+-.+++|++||| T Consensus 293 l~~~~~~~p~~~~~~~v~~~g~~vG~VTSg~~SP~l~~~Iala~v~~~~a~~G~~v~V~i~~~~~~a~V~~~p~ 366 (367) T PRK12486 293 IEIDGERIPLCDRAWPLLAGGRRVGQVTSAAWSPDFQTNVAIGMVRMTHWDPGTGLEVETPDGMRPATVREGFW 366 (367) T ss_pred EEECCCCCCCCCCCEEECCCCCEEEEECCCCHHHHCCCEEEEEEECHHHCCCCCEEEEEECCEEEEEEEECCCC T ss_conf 99878757888994259269988989072463275391389999997887999989999999368999966998 No 4 >PRK13579 gcvT glycine cleavage system aminomethyltransferase T; Provisional Probab=100.00 E-value=1.5e-41 Score=261.63 Aligned_cols=264 Identities=14% Similarity=0.065 Sum_probs=181.3 Q ss_pred EECCCCEEEEEECCCHHHHHHCCCCCCHHHCCCCCEEEEEEECCCCCEEEEEEEEEECCCCCCEEHHHHHHHHHHHHHHH Q ss_conf 76179407999875878786321326731089982689999979998899899997045552000033333456777643 Q gi|254780591|r 4 VYLSNQSFIKVCGKSAIPFLQAIITADVLTLPYKIARGSAILTPQGKILLYFLISKIEEDTFILEIDRSKRDSLIDKLLF 83 (273) Q Consensus 4 ~~L~~~~~i~i~G~DA~~fL~~l~t~di~~l~~g~~~yt~~ln~~G~i~~D~~i~r~~~~~~~~~~~~~~~~~~~~~~~~ 83 (273) +=+|+++.|+|+|+||.+|||+++|||++++++|+++||+|||++|+|++|++|+|++++.|+++.++ .......+++. T Consensus 56 ~D~S~~~ki~I~G~DA~~fL~~l~t~dv~~l~~G~~~Yt~~Ln~~Ggi~~D~~v~rl~d~~~l~~~~~-~~~~~~~~l~~ 134 (371) T PRK13579 56 FDVSHMGQIEVSGKDAAAALERLVPQDILALKEGRQRYTFFTNDQGGILDDLMVTNLGDHLFLVVNAA-CKDADIAHLRE 134 (371) T ss_pred EECCCCEEEEEECCCHHHHHHHHCCCCCCCCCCCCEEEEEEECCCCCEEEEEEEEEECCEEEEEECCC-HHHHHHHHHHH T ss_conf 95798489999878999999886153777789996899998879997877789998224167641212-28899999997 Q ss_pred HHHCCCCCCCCCCCCEEEEEECCCCCCCCCCCCCCCC-----------------------CCCCCHHHHHH--------- Q ss_conf 2100012235688436999971854322211123456-----------------------64441012221--------- Q gi|254780591|r 84 YKLRSNVIIEIQPINGVVLSWNQEHTFSNSSFIDERF-----------------------SIADVLLHRTW--------- 131 (273) Q Consensus 84 ~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~-----------------------~~~~~~~~~~~--------- 131 (273) +... ++.+.+.++ .+.++++||+|+..+....... ...++..+.++ T Consensus 135 ~~~~-~v~v~~~~~-~~~l~lqGP~S~~vL~~l~~~~~~~~~~~~~~~~i~g~~~~i~R~g~tGE~G~Ei~~~~~~a~~l 212 (371) T PRK13579 135 HLSD-ACEVNPLED-RALLALQGPKAEAVLADLCPPVAALRFMDGAEPRLHGVDCFVSRSGYTGEDGFEISVPADAAEAL 212 (371) T ss_pred HCCC-CCEEEECCC-HHHHHHHCCHHHHHHHHHCCCHHHCCCCCCEEEEECCEEEEEEECCCCCCCEEEEEECHHHHHHH T ss_conf 5788-877997865-42676629058999987489867775442149999997999993353689659999659999999 Q ss_pred -----CCCCCCCCCHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCEEEE---CCCCCCCCCCCCCCCCCCCCCCEE Q ss_conf -----013555579678888887520133456543221233100111220133---147521331013210012444347 Q gi|254780591|r 132 -----GHNEKIASDIKTYHELRINHGIVDPNTDFLPSTIFPHDALMDLLNGIS---LTKGCYIGQEVVSRIQHRNIIRKR 203 (273) Q Consensus 132 -----~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~---~~k~~f~G~e~~~~~~~~~~~~~~ 203 (273) ......+.+..+.+..+.+.+.. ..+.+......+....+.+.+. ..|+||+||+++.++...+..+++ T Consensus 213 ~~~l~~~~~~~p~G~~A~~~lRlE~G~~---~~G~Dl~~~~~P~EagL~~~v~~~k~~k~dFiGk~al~~~~~~g~~~kl 289 (371) T PRK13579 213 AEALLADPRVEPIGLGARDSLRLEAGLC---LYGHDIDTTTDPVEAALEWAIQKARREAGGFPGAKAILAALAKGASRRR 289 (371) T ss_pred HHHHHHCCCCCCCCCCCCHHHHHHCCCC---CCCCCCCCCCCHHHCCCCCCCCCCCCCCCCCHHHHHHHHHHHCCCCEEE T ss_conf 9999974898662246460014432866---6563469999945776421536663555571579999999855976699 Q ss_pred EEEEECCCCCCCCCCEEEEC-CEEEEEEEEEECC------EEEEEEEHHHCCCCCCCCCEEEECCEEEEEECCCCCC Q ss_conf 88740134566789887246-7796799983478------3368998131036656786488688899997488769 Q gi|254780591|r 204 PMIITGTDDLPPSGSPILTD-DIEIGTLGVVVGK------KALAIARIDKVDHAIKKGMALTVHGVRVKASFPHWYK 273 (273) Q Consensus 204 ~~~~~~~~~~~~~g~~i~~~-g~~VG~vtS~~~~------~gla~i~~~~~~~~~~~~~~l~~~~~~~~i~~P~w~~ 273 (273) +++....+.+.+.+++++.+ |+.||.|||+++| +||||++.++...+....+++.++..+++|+++||++ T Consensus 290 vgl~~~~~~~~~~g~~v~~~~g~~VG~vTS~~~sp~l~k~Iala~v~~~~~~~G~~v~V~i~g~~~~a~V~~~PF~~ 366 (371) T PRK13579 290 VGLKPEGRAPVREGADLFDDAGTPIGTVTSGGFGPSLGGPVAMGYVPASLAAPGTAVFAEVRGKRLPVTVHALPFVP 366 (371) T ss_pred EEEEECCCCCCCCCCEEECCCCCEEEEECEEEEHHHCCEEEEEEEECHHHCCCCCEEEEEECCEEEEEEEECCCCCC T ss_conf 99998688468999968938992599918151726488089999999778799988999999989999996889889 No 5 >TIGR00528 gcvT glycine cleavage system T protein; InterPro: IPR006223 This is a subfamily of glycine cleavage T proteins, part of the glycine cleavage multienzyme complex (GCV) found in bacteria and the mitochondria of eukaryotes. GCV catalyses the catabolism of glycine in eukaryotes. The T-protein is an aminomethyl transferase 2.1.2.10 from EC that catalyses the following reaction:(6S)-tetrahydrofolate + S-aminomethyldihydrolipoylprotein = (6R)-5,10-methylenetetrahydrofolate + NH_3 + dihydrolipoylprotein ; GO: 0004047 aminomethyltransferase activity, 0006546 glycine catabolic process. Probab=100.00 E-value=4.1e-39 Score=247.36 Aligned_cols=268 Identities=15% Similarity=0.088 Sum_probs=202.4 Q ss_pred ECCCCEEEEEECCCHHHHHHCCCCCCHHHCCC-CCEEEEEEECCCCCEEEEEEEEEECCC-----CCCEEHHHHHHHHHH Q ss_conf 61794079998758787863213267310899-826899999799988998999970455-----520000333334567 Q gi|254780591|r 5 YLSNQSFIKVCGKSAIPFLQAIITADVLTLPY-KIARGSAILTPQGKILLYFLISKIEED-----TFILEIDRSKRDSLI 78 (273) Q Consensus 5 ~L~~~~~i~i~G~DA~~fL~~l~t~di~~l~~-g~~~yt~~ln~~G~i~~D~~i~r~~~~-----~~~~~~~~~~~~~~~ 78 (273) =.||++.++++|+++.+|||++++||+++|++ |++.||.|||++|||+||++||..++| .|+++.++++...+. T Consensus 49 DvSHM~~~~l~G~~~~~fLq~l~~~D~~~Lt~sG~A~ys~lLna~GGvvDD~ivy~~~~dPeG~e~f~LvvNAa~~~kD~ 128 (394) T TIGR00528 49 DVSHMGKVKLSGSKSLKFLQRLLPNDVDALTPSGKAQYSVLLNAQGGVVDDLIVYKEGEDPEGNERFLLVVNAATAEKDL 128 (394) T ss_pred EEEECEEEEECCHHHHHHHHHHHHHHHHHCCCCCCEEEEEEECCCCCEEEEEEEECCCCCCCCCCEEEEEECCCCHHHHH T ss_conf 34203268982058998886332445864488784678898807978781278851488987450799998165416679 Q ss_pred HHHHHHHHCCCCCCCCCCCCE---EEEEECCC----CCCCCCCCC-----------CCCCCCCCCH--------HHHH-- Q ss_conf 776432100012235688436---99997185----432221112-----------3456644410--------1222-- Q gi|254780591|r 79 DKLLFYKLRSNVIIEIQPING---VVLSWNQE----HTFSNSSFI-----------DERFSIADVL--------LHRT-- 130 (273) Q Consensus 79 ~~~~~~~~~~~~~~~~~~~~~---~~~~~~g~----~~~~~~~~~-----------~~~~~~~~~~--------~~~~-- 130 (273) .|+..+...... +++.+++. +++++||| ++.....-. .+.+.....+ .+.+ T Consensus 129 ~w~~~hl~~~~~-~~~~~~~~eGr~LlAlQGPnaqakA~~~L~~l~~~~~~~kdLk~f~~~q~~e~~~~kaslv~IArtG 207 (394) T TIGR00528 129 EWLKEHLEEEVT-LDTQSDEIEGRSLLALQGPNAQAKAKTILEPLLDQAVEGKDLKPFFFVQEAEFALKKASLVFIARTG 207 (394) T ss_pred HHHHHHCCCCCE-EEHHHHHHCCEEEEEEECCCHHHHHHHHHHHHHHCCCCCCCCCCCCCCCHHHHHHCCCCEEEEECCC T ss_conf 999986268760-2011253357078886287657899999888873005644674002533356410465489982577 Q ss_pred ------HCCCCCCCCCHHHHHHHHHH-----------------HHCCCCCCCCCCCCCCCCCCCCCCCEEEEC------- Q ss_conf ------10135555796788888875-----------------201334565432212331001112201331------- Q gi|254780591|r 131 ------WGHNEKIASDIKTYHELRIN-----------------HGIVDPNTDFLPSTIFPHDALMDLLNGISL------- 180 (273) Q Consensus 131 ------~~~~~~~~~~~~~~~~~~~~-----------------~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~------- 180 (273) +++....+.....|...... +..+....++.+......+....+.|.|.. T Consensus 208 YTGEdGfEI~~~~e~A~~~w~~l~~~Gda~g~~PcGLgARDtLRLEAGm~LYGqel~~~itP~eA~lgw~v~~~~rdlvd 287 (394) T TIGR00528 208 YTGEDGFEIAVANEKAVEFWKKLVEAGDAYGVKPCGLGARDTLRLEAGMGLYGQELDEEITPLEAGLGWVVKKERRDLVD 287 (394) T ss_pred CCCCCCEEEECCCHHHHHHHHHHHHCCCCCCCCCCCCCCCCHHHHHCCCCCCCCCCCCCCCHHHHCCCCEEEECCCCCCC T ss_conf 76645415861873689999999862788631103553230135445888767466775285865067668606432335 Q ss_pred CCCCCCCCCCCCCCCCCCCCCE-EEEEEECCCC-CCCCCCEEEE---CC-EEEEEEEEEEC-------CEEEEEEEHHHC Q ss_conf 4752133101321001244434-7887401345-6678988724---67-79679998347-------833689981310 Q gi|254780591|r 181 TKGCYIGQEVVSRIQHRNIIRK-RPMIITGTDD-LPPSGSPILT---DD-IEIGTLGVVVG-------KKALAIARIDKV 247 (273) Q Consensus 181 ~k~~f~G~e~~~~~~~~~~~~~-~~~~~~~~~~-~~~~g~~i~~---~g-~~VG~vtS~~~-------~~gla~i~~~~~ 247 (273) .+.+|.|++.+..++..+..+| ++++....+. +++++-+|+. +| +.+|.||||+. +||||||..++. T Consensus 288 ~~~DF~G~~~L~~Q~~ng~~~kvlVGL~m~~KGP~~R~~~~v~~~da~g~~~~G~vTSGt~SPTL~n~~ialA~v~~e~~ 367 (394) T TIGR00528 288 KKSDFIGRAVLEEQKENGTEKKVLVGLEMLEKGPIARNGYPVFLTDANGEKEVGIVTSGTLSPTLGNKNIALAYVPKELE 367 (394) T ss_pred CCCCCCCHHHHHHHHHCCCEEEEEEEEEEECCCCCCCCCCEEECCCCCCCEEEEEEEECCCCCCCCCCCEEEEECCCCCC T ss_conf 56763547899999865953467630334205740427824650367866043248807778320132122420333300 Q ss_pred CCCCCCCCEEEECCEEEEEECCCCCC Q ss_conf 36656786488688899997488769 Q gi|254780591|r 248 DHAIKKGMALTVHGVRVKASFPHWYK 273 (273) Q Consensus 248 ~~~~~~~~~l~~~~~~~~i~~P~w~~ 273 (273) ..+....+++|.+-.+|++.|+|||| T Consensus 368 ~~G~~~~V~vR~k~~~ikv~K~~f~~ 393 (394) T TIGR00528 368 KIGTKLEVEVRNKLYPIKVVKKPFVR 393 (394) T ss_pred CCCCEEEEEECCEEEEEEEEECCCCC T ss_conf 04878999981716623887146568 No 6 >COG0354 Predicted aminomethyltransferase related to GcvT [General function prediction only] Probab=100.00 E-value=1.8e-36 Score=231.94 Aligned_cols=265 Identities=27% Similarity=0.414 Sum_probs=192.8 Q ss_pred CCEEECCCCEEEEEECCCHHHHHHCCCCCCHHHCCCCCEEEEEEECCCCCEEEEEEEEEECCCCCCEEHHHHHHHHHHHH Q ss_conf 94176179407999875878786321326731089982689999979998899899997045552000033333456777 Q gi|254780591|r 1 MSSVYLSNQSFIKVCGKSAIPFLQAIITADVLTLPYKIARGSAILTPQGKILLYFLISKIEEDTFILEIDRSKRDSLIDK 80 (273) Q Consensus 1 m~~~~L~~~~~i~i~G~DA~~fL~~l~t~di~~l~~g~~~yt~~ln~~G~i~~D~~i~r~~~~~~~~~~~~~~~~~~~~~ 80 (273) |.-+.|++|++|+|+|+||.+|||+|+||||.++.+|+.+|+.+||++|||++++++|+.++..++++..+.......++ T Consensus 14 ~~l~~l~~~~li~V~G~D~~kfLq~q~T~dv~~l~~g~~~~~a~l~~qGrv~~~~~~~~~~d~~~l~~~~~~~~~~l~~L 93 (305) T COG0354 14 LTLVLLSDRALIRVSGADAEKFLQGQLTNDVSALAEGQSTLAALLTPQGRVLFDFRLYRRGDGLYLDTDKSVLEALLKRL 93 (305) T ss_pred CEEEECCCCEEEEEECCCHHHHHHHHHHHHHHHCCCCCEEEEEEECCCCEEEEEEEEEEECCEEEEECCHHHCHHHHHHH T ss_conf 37886587306999877789987677777676445575546668778722889889998688489971600047999998 Q ss_pred HHHHHHCCCCCCCCCCCCEEEEEECCCCCCCCCCCCCC----------CCCCCCC-----HHHHHHCCCCCCCCCHHHHH Q ss_conf 64321000122356884369999718543222111234----------5664441-----01222101355557967888 Q gi|254780591|r 81 LLFYKLRSNVIIEIQPINGVVLSWNQEHTFSNSSFIDE----------RFSIADV-----LLHRTWGHNEKIASDIKTYH 145 (273) Q Consensus 81 ~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~----------~~~~~~~-----~~~~~~~~~~~~~~~~~~~~ 145 (273) .++.++. ++.+.+.+ ...+.+.++.+......... ....... ..................|. T Consensus 94 ~kY~~~s-kv~i~~~~--~~~i~v~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~w~ 170 (305) T COG0354 94 KKYALRS-KVTIAPSD--LVLIGVAGEEAAEALAVDFPALPKQWRAAGRFLLDLPVPRLLQLVPKLALPQALEASLDQWL 170 (305) T ss_pred HHCEECC-CCEEECCC--CEEEEEEECCCCCHHHCCCCCCCCCCCCCCCCEECCCHHHHHHHHHHCCCCCCCCCCHHHHH T ss_conf 7410000-12574277--42688750332211211353456434556641222451455543212035533335688999 Q ss_pred HHHHHHHCCCCCCCCCCCCCCCCCCCCCCCEEEECCCCCCCCCCCCCCCCCCCCCCEEEEEEECCCCCCCCCCEEEECCE Q ss_conf 88875201334565432212331001112201331475213310132100124443478874013456678988724677 Q gi|254780591|r 146 ELRINHGIVDPNTDFLPSTIFPHDALMDLLNGISLTKGCYIGQEVVSRIQHRNIIRKRPMIITGTDDLPPSGSPILTDDI 225 (273) Q Consensus 146 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~k~~f~G~e~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~i~~~g~ 225 (273) ....+.+.+... ....+...+.........+++++||||+|||.++|++++|..+|++.........+..|+.|..+++ T Consensus 171 ~lri~~G~p~~~-~~~~~~~iPqevnl~~~~gISF~KGCYvGQE~VAR~~~rG~~kRrl~~l~~d~~~p~~g~~i~a~~~ 249 (305) T COG0354 171 ALRIRAGIPGID-DATSEDFIPQEVNLDALGGISFKKGCYVGQETVARAKYRGTNKRRLVLLALDASLPEAGEEILAGGE 249 (305) T ss_pred HHHHHCCCCCCC-CHHCCCCCHHHHCCCCCCCEECCCCCCCCHHHHHHHHHCCCCCEEEEEEEECCCCCCCCCEEECCCC T ss_conf 999980898643-0002566822417110284711586636687766887628775169999817878999874422887 Q ss_pred E--EEEEEEEECCEEEEEEEHHHCCCCCCCCCEEEECCEEEEEECCCCC Q ss_conf 9--6799983478336899813103665678648868889999748876 Q gi|254780591|r 226 E--IGTLGVVVGKKALAIARIDKVDHAIKKGMALTVHGVRVKASFPHWY 272 (273) Q Consensus 226 ~--VG~vtS~~~~~gla~i~~~~~~~~~~~~~~l~~~~~~~~i~~P~w~ 272 (273) . +|.|+|.....++|+++++.+ ...+..+.+++..+.+..|+|. T Consensus 250 ~~~~G~v~s~~~~~~~~l~~l~~~---l~~~~~~~v~~~~~~~~~~~~~ 295 (305) T COG0354 250 EVGLGTVLSAVGLGPVALIRLKVV---LDNGLAIDVGGRIANLALPPWV 295 (305) T ss_pred CCEEEEEEECCCCCCHHHHHHHHH---HCCCCHHHHCCCCCCCCCCCCC T ss_conf 530466886356740257899876---2255312214521246666210 No 7 >PRK09559 putative global regulator; Reviewed Probab=100.00 E-value=6.9e-34 Score=216.89 Aligned_cols=261 Identities=18% Similarity=0.217 Sum_probs=172.5 Q ss_pred CEEECCCCEEEEEECCCHHHHHHCCCCCCHHHCCCCCEEEEEEECCCCCEEEEEEEEEECCCCCCEEHHHHHHHHHHHHH Q ss_conf 41761794079998758787863213267310899826899999799988998999970455520000333334567776 Q gi|254780591|r 2 SSVYLSNQSFIKVCGKSAIPFLQAIITADVLTLPYKIARGSAILTPQGKILLYFLISKIEEDTFILEIDRSKRDSLIDKL 81 (273) Q Consensus 2 ~~~~L~~~~~i~i~G~DA~~fL~~l~t~di~~l~~g~~~yt~~ln~~G~i~~D~~i~r~~~~~~~~~~~~~~~~~~~~~~ 81 (273) .-+.|++|++|+|+|+||.+|||+|+||||.+|++++++|+++||+||||+.++.+++.++..++++..+.......+ + T Consensus 20 tl~~L~~~~lI~vsG~Da~~FLQGQlT~Dv~~L~~~~~~~~a~c~pKGRvla~f~l~~~~d~~~L~~~~~~~~~~l~~-L 98 (327) T PRK09559 20 TLISLDDWALATITGADSEKYLQGQVTADVSQLTEDQHLLAAHCDAKGKMWSNLRLFRRGDGFAWIERRSVRENQLTE-L 98 (327) T ss_pred EEEECCCCEEEEEECCCHHHHHCHHHHHHHHHCCCCCEEEEEEECCCCCEEEEEEEEEECCEEEEEECCHHHHHHHHH-H T ss_conf 365357743899988887897553646656414888768997998786789999999989979999260457999999-8 Q ss_pred HHHHHCCCCCCCCCCCCEEEEEECCCCCCCCCCCCCCCC--------C----------CCCCHHHH---------HHC-- Q ss_conf 432100012235688436999971854322211123456--------6----------44410122---------210-- Q gi|254780591|r 82 LFYKLRSNVIIEIQPINGVVLSWNQEHTFSNSSFIDERF--------S----------IADVLLHR---------TWG-- 132 (273) Q Consensus 82 ~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~--------~----------~~~~~~~~---------~~~-- 132 (273) +++..+.++.+.+.+ +.+++.+.|+.+........... . ....+... ... T Consensus 99 kkY~lfsKV~i~~~~-~~~~~g~~G~~a~~~l~~~~~~~p~~~~~~~~~~~~~~~~~~~p~~r~lli~~~~~~~~l~~~l 177 (327) T PRK09559 99 KKYAVFSKVTIAPDD-ERVLLGVAGFQARAALANLFSELPSAEKPVVQEGATTLLWFEHPAERFLLVTDEATANMLTEKL 177 (327) T ss_pred HHHHCCCCEEEECCC-CCEEEEEECCCHHHHHHHHCCCCCCCCCCEEECCCCEEEEECCCCCCEEEEECHHHHHHHHHHH T ss_conf 745342220896178-7189998451067887653013776568435358844998348887469971788889999863 Q ss_pred CCCCCCCCHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCEEEECCCCCCCCCCCCCCCCCCCCCCEEEEEEECCCC Q ss_conf 13555579678888887520133456543221233100111220133147521331013210012444347887401345 Q gi|254780591|r 133 HNEKIASDIKTYHELRINHGIVDPNTDFLPSTIFPHDALMDLLNGISLTKGCYIGQEVVSRIQHRNIIRKRPMIITGTDD 212 (273) Q Consensus 133 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~k~~f~G~e~~~~~~~~~~~~~~~~~~~~~~~ 212 (273) .......+...|....++.+.+.... .......+..........|+|+||||+|||.++|++++|..+|++++...... T Consensus 178 ~~~~~~~~~~~W~~l~I~aG~p~i~~-~~~e~fiPQ~lNld~l~gIsF~KGCY~GQEiVAR~~YrG~~KRrly~l~~~~~ 256 (327) T PRK09559 178 RGEAELNNSQQWLALDIEAGFPVIDA-ANSGQFIPQATNLQALGGISFKKGCYTGQEMVARAKFRGANKRALWLLAGKAS 256 (327) T ss_pred HCCCCCCCHHHHHHHHHHCCCCCCCC-CCCHHCCHHHCCCHHHCCCCCCCCCCCCHHHHHHHHHCCCCCEEEEEEECCCC T ss_conf 22345578888999898749953166-53022578671946339894158885769999999873855301799854667 Q ss_pred -CCCCCCEEE----ECCEEEEEEEEEECC-----EEEEEEEHHHCCCCCCCCCEEEEC---CEEEEEECCC Q ss_conf -667898872----467796799983478-----336899813103665678648868---8899997488 Q gi|254780591|r 213 -LPPSGSPIL----TDDIEIGTLGVVVGK-----KALAIARIDKVDHAIKKGMALTVH---GVRVKASFPH 270 (273) Q Consensus 213 -~~~~g~~i~----~~g~~VG~vtS~~~~-----~gla~i~~~~~~~~~~~~~~l~~~---~~~~~i~~P~ 270 (273) .+..|+.|. .+.+.+|.|.+++.- ..++.++.+. ..+..++++ +..+++...| T Consensus 257 ~~p~~g~~le~~~~~~~~~~G~v~~a~~~~~g~~~~l~vl~~~~-----~~~~~lrl~~~~~~~l~~~~LP 322 (327) T PRK09559 257 RVPEAGEDLELQMGENWRRTGTVLAAVQLEDGQVWVQVVMNNDL-----EADSVFRVRDDATNTLHIQPLP 322 (327) T ss_pred CCCCCCCEEEECCCCCCCCCEEEEEEEECCCCCEEEEEEECCCC-----CCCCEEEECCCCCCEEEECCCC T ss_conf 79999972163247787422199998985899399999966776-----7787058548999734751899 No 8 >TIGR01372 soxA sarcosine oxidase, alpha subunit family; InterPro: IPR006277 This set of sequences describe the alpha subunit of a family of known and putative heterotetrameric sarcosine oxidases. Five operons of such oxidases are found in Mesorhizobium loti and three in Agrobacterium tumefaciens, a high enough copy number to suggest that not all members share the same function. Sarcosine oxidase catalyzes the oxidative demethylation of sarcosine to glycine. The reaction converts tetrahydrofolate to 5,10-methylene-tetrahydrofolate . Bacterial sarcosine oxidases have been isolated from over a dozen different organisms and fall into two major classes (1) monomeric form that contains only covalent flavin and (2) heterotetrameric (alpha, beta, gamma, delta) form that contain a covalent and noncovalent flavin, this entry represents the heterotetrameric form. ; GO: 0008115 sarcosine oxidase activity, 0046653 tetrahydrofolate metabolic process. Probab=100.00 E-value=6.5e-35 Score=222.87 Aligned_cols=266 Identities=15% Similarity=0.067 Sum_probs=196.8 Q ss_pred CCCEEEEEECCCHHHHHHCCCCCCHHHCCCCCEEEEEEECCCCCEEEEEEEEEECCCCCCEEHHHHHHHHHHHHHH---- Q ss_conf 7940799987587878632132673108998268999997999889989999704555200003333345677764---- Q gi|254780591|r 7 SNQSFIKVCGKSAIPFLQAIITADVLTLPYKIARGSAILTPQGKILLYFLISKIEEDTFILEIDRSKRDSLIDKLL---- 82 (273) Q Consensus 7 ~~~~~i~i~G~DA~~fL~~l~t~di~~l~~g~~~yt~~ln~~G~i~~D~~i~r~~~~~~~~~~~~~~~~~~~~~~~---- 82 (273) |..|+|+|.||||.+|||+++||-.++|+||+|+|.+||.++|-|-||.++.|++||+|++++.++.......|++ T Consensus 686 STLGKIev~GPDAaeFLnRvYtN~~~kL~vGkaRYGlMLreDG~vfDDGvt~RL~EdrF~mTTTTg~Aa~Vl~~LE~~~Q 765 (1026) T TIGR01372 686 STLGKIEVVGPDAAEFLNRVYTNAFSKLKVGKARYGLMLREDGMVFDDGVTSRLAEDRFLMTTTTGGAARVLQHLEEYLQ 765 (1026) T ss_pred CCCCCEEEECCCHHHHCCHHHCCCCCCCCCCCEECCCCCCCCCEEECCCEEEEECCCCEEEECCCHHHHHHHHHHHHHHH T ss_conf 34660430078779862511128777878864302641246855871866887437873787244025689999898751 Q ss_pred HHHHCCCCCCCCCCCCEEEEEECCCCCCCCCCCCCC-CCCCCCCHH---------------HHHH----------CCCCC Q ss_conf 321000122356884369999718543222111234-566444101---------------2221----------01355 Q gi|254780591|r 83 FYKLRSNVIIEIQPINGVVLSWNQEHTFSNSSFIDE-RFSIADVLL---------------HRTW----------GHNEK 136 (273) Q Consensus 83 ~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~-~~~~~~~~~---------------~~~~----------~~~~~ 136 (273) ..++..+|.+...|++++.++++||++++++..+.. .+..+..++ -+++ +...+ T Consensus 766 ~~wP~L~V~lTSvTdqwAt~a~~GPkaR~lLa~~v~G~dlsneaFPfM~~~eg~~~GGq~~aRlfRiSFsGElayEv~vp 845 (1026) T TIGR01372 766 TEWPELDVYLTSVTDQWATLAVSGPKARDLLAELVDGLDLSNEAFPFMSIKEGSLAGGQVPARLFRISFSGELAYEVNVP 845 (1026) T ss_pred HCCCCCCEEEEECHHHHHHHHCCCCCHHHHHHHHCCCCCCCCCCCCCCEEEEEEEECCCEEEEEEEEEEECCEEEEEECC T ss_conf 01786540787401345465216842689988535885356122774515631353682027899877405401575045 Q ss_pred CCCCHHHHH-----------------HHHHHHHCCCCCCCCCCCCCCCCCCCCCCCEEEECCCCC-CCCCCCCCCCCCCC Q ss_conf 557967888-----------------888752013345654322123310011122013314752-13310132100124 Q gi|254780591|r 137 IASDIKTYH-----------------ELRINHGIVDPNTDFLPSTIFPHDALMDLLNGISLTKGC-YIGQEVVSRIQHRN 198 (273) Q Consensus 137 ~~~~~~~~~-----------------~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~k~~-f~G~e~~~~~~~~~ 198 (273) ...+...|+ .+...+..-.++..+.+......+....+.|.++..|.+ |+|+....|..... T Consensus 846 A~yG~~vw~~L~~AG~~fg~~pYGtEalhVLRaEKGfiivG~dtDGTvtP~Dlg~~w~vsk~K~dsFvG~R~~~Redl~~ 925 (1026) T TIGR01372 846 ADYGEAVWEALMEAGQPFGITPYGTEALHVLRAEKGFIIVGQDTDGTVTPADLGLGWAVSKKKKDSFVGRRGLAREDLVA 925 (1026) T ss_pred HHHHHHHHHHHHHHCCCCCCEEECHHHHHHHHHHCCCEEECCCCCCCHHHHHCCCCCCCCCCCCCCCEEEECCCCHHHHH T ss_conf 04578999999984424686210422432662115637842588853107553788754466897431531257712332 Q ss_pred CCCEEEEEEE-CC-CCCCCCCCEEEECC--------EEEEEEEEEECC------EEEEEEEHHHCCCCCCCCCEE--EEC Q ss_conf 4434788740-13-45667898872467--------796799983478------336899813103665678648--868 Q gi|254780591|r 199 IIRKRPMIIT-GT-DDLPPSGSPILTDD--------IEIGTLGVVVGK------KALAIARIDKVDHAIKKGMAL--TVH 260 (273) Q Consensus 199 ~~~~~~~~~~-~~-~~~~~~g~~i~~~g--------~~VG~vtS~~~~------~gla~i~~~~~~~~~~~~~~l--~~~ 260 (273) ..|+.++... .+ ...++.|..|..+. +-+|+|||+++| ||||+|+--..-.+....+.. +.+ T Consensus 926 ~dR~~LVGl~p~D~~~~L~~GAhiv~~~~~~~PGC~~~~GhVTSSy~SP~lG~~IaLALV~gG~~R~Ge~v~v~~~~Rgr 1005 (1026) T TIGR01372 926 EDRKQLVGLLPLDPQRRLEEGAHIVADGAEATPGCMKMQGHVTSSYFSPALGRTIALALVKGGRARHGETVYVPDALRGR 1005 (1026) T ss_pred CCCCEEEEEEECCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEEEEECCCCCCCHHHHHHHCHHHCCCCEEEEECCCCCC T ss_conf 58844345774788863754211112436688787785032873551423277110441222032478789950178885 Q ss_pred CEEEEEECCCCC Q ss_conf 889999748876 Q gi|254780591|r 261 GVRVKASFPHWY 272 (273) Q Consensus 261 ~~~~~i~~P~w~ 272 (273) -++++|+.|-|| T Consensus 1006 ~~~v~i~~~Vff 1017 (1026) T TIGR01372 1006 FIAVEICSPVFF 1017 (1026) T ss_pred EEEEEEECCEEE T ss_conf 366898134417 No 9 >KOG2929 consensus Probab=100.00 E-value=9.8e-33 Score=210.16 Aligned_cols=270 Identities=25% Similarity=0.380 Sum_probs=194.4 Q ss_pred EEECCCCEEEEEECCCHHHHHHCCCCCCHHH--------CCCCCEEEEEEECCCCCEEEEEEEEEECCC----CCCEEHH Q ss_conf 1761794079998758787863213267310--------899826899999799988998999970455----5200003 Q gi|254780591|r 3 SVYLSNQSFIKVCGKSAIPFLQAIITADVLT--------LPYKIARGSAILTPQGKILLYFLISKIEED----TFILEID 70 (273) Q Consensus 3 ~~~L~~~~~i~i~G~DA~~fL~~l~t~di~~--------l~~g~~~yt~~ln~~G~i~~D~~i~r~~~~----~~~~~~~ 70 (273) .+.|++|++|+|+|||+.+|||+++||||.. .......|+.+||.+||++.|.++|+.... .+++.+. T Consensus 32 ~~~L~~RsliRv~GpDtvkFLqGL~TNdv~~~~p~~~~a~~t~~~~Ya~fLN~qGR~LyD~iLY~~~~~~~~~~~llE~d 111 (348) T KOG2929 32 LSLLESRSLIRVRGPDTVKFLQGLLTNDVTRHFPGIQGAPITRNGLYAAFLNTQGRLLYDTILYPTPVPVSEPELLLECD 111 (348) T ss_pred EEECCCCEEEEEECCCHHHHHHHHHCCCCCCCCCCCCCCCCCCCHHHHHHHCCCCCEEEEEEEECCCCCCCCCCEEEEEC T ss_conf 45248824999858627888765421553456766456877773566664056763799999835888888875699814 Q ss_pred HHHHHHHHHHHHHHHHCCCCCCCCCCCCEEEEEEC-CC-CCCCC----------CCCCCCCCCCCCCHHH----HHHCCC Q ss_conf 33334567776432100012235688436999971-85-43222----------1112345664441012----221013 Q gi|254780591|r 71 RSKRDSLIDKLLFYKLRSNVIIEIQPINGVVLSWN-QE-HTFSN----------SSFIDERFSIADVLLH----RTWGHN 134 (273) Q Consensus 71 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-g~-~~~~~----------~~~~~~~~~~~~~~~~----~~~~~~ 134 (273) .........++..+..+..+.++..++..-.+.+- -| +..+. ......++...++... ...... T Consensus 112 ~~~~~~~~khl~~yrLr~kv~v~~id~el~tw~v~~~p~~~~d~~~~~~~~~~~~~~rdpr~s~~~~~~l~~~f~~~~~~ 191 (348) T KOG2929 112 GSVVGDFLKHLQKYRLRRKVEVEKIDHELKTWKVEVLPKNSIDANVFEENVLNVLYNRDPRFSGMGWRLLPQDFAVPTSE 191 (348) T ss_pred CCCCHHHHHHHHHHHHHHCCEEEECCHHHCEEEEEECCCCCCCHHHCCHHHHHHHHCCCCCCCCCCCCCCCEEECCCCCC T ss_conf 76636778777775165204054176133103666346656300100002245665258851235421253220476664 Q ss_pred CCCCCCHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCEEEECCCCCCCCCCCCCCCCCCCCCCEEEEEEEC----C Q ss_conf 555579678888887520133456543221233100111220133147521331013210012444347887401----3 Q gi|254780591|r 135 EKIASDIKTYHELRINHGIVDPNTDFLPSTIFPHDALMDLLNGISLTKGCYIGQEVVSRIQHRNIIRKRPMIITG----T 210 (273) Q Consensus 135 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~k~~f~G~e~~~~~~~~~~~~~~~~~~~~----~ 210 (273) .....+...|...+...+.+.-..........+.+.+......++++||||+|||..+|.++.|+.+||++.+.. . T Consensus 192 ~~~~~d~~~Y~~~Ry~~Gv~EG~~el~pg~~lPLE~N~d~lngISf~KGCYVGQELTARThhtGViRKRl~P~r~~~~e~ 271 (348) T KOG2929 192 QVSEGDESDYRLLRYQQGVAEGSQELIPGTLLPLESNFDFLNGISFDKGCYVGQELTARTHHTGVIRKRLFPFRLDLAEN 271 (348) T ss_pred CCCCCCHHHHHHHHHHCCCCCCHHHCCCCCCCCEECCCCCCCCCCCCCCCEECHHHEEHHHHCCEEEEEEEEEEECCCCC T ss_conf 44444466899999872766661232865410300033402340026761204223000020333353354178336678 Q ss_pred CCCCCC-----CCEEEECCEEEEEEEEEECCEEEEEEEHHHCCCCCCCCCEEEECCEEEEEECCCCCC Q ss_conf 456678-----988724677967999834783368998131036656786488688899997488769 Q gi|254780591|r 211 DDLPPS-----GSPILTDDIEIGTLGVVVGKKALAIARIDKVDHAIKKGMALTVHGVRVKASFPHWYK 273 (273) Q Consensus 211 ~~~~~~-----g~~i~~~g~~VG~vtS~~~~~gla~i~~~~~~~~~~~~~~l~~~~~~~~i~~P~w~~ 273 (273) ++.+-. -+.....|+.||.+.|+.+..|||+++++...... ....+.+.+++++..+|.||- T Consensus 272 ~p~~~~~~~~~~~v~~~~g~kvG~~~~~~g~~glgllr~e~~~~~~-~~l~~~g~~i~i~~~~p~W~p 338 (348) T KOG2929 272 EPLLVGFTNAPPEVEKKKGRKVGRVISGEGLRGLGLLRLEKFKAQF-YKLTTKGENIKIKPQKPEWWP 338 (348) T ss_pred CCCCCCCCCCCCCEECCCCCEEEEEECCCCCEEEEEEEHHHHHCCC-HHHHCCCCCCEECCCCCCCCC T ss_conf 8543577888600000158610466316751353310066652521-243126765232247985352 No 10 >KOG2770 consensus Probab=99.97 E-value=6.4e-31 Score=199.56 Aligned_cols=268 Identities=15% Similarity=0.064 Sum_probs=200.0 Q ss_pred EEECCCCEEEEEECCCHHHHHHCCCCCCHHHCCCCCEEEEEEECCCCCEEEEEEEEEECCCCCCEEHHHHHHHHHHHHHH Q ss_conf 17617940799987587878632132673108998268999997999889989999704555200003333345677764 Q gi|254780591|r 3 SVYLSNQSFIKVCGKSAIPFLQAIITADVLTLPYKIARGSAILTPQGKILLYFLISKIEEDTFILEIDRSKRDSLIDKLL 82 (273) Q Consensus 3 ~~~L~~~~~i~i~G~DA~~fL~~l~t~di~~l~~g~~~yt~~ln~~G~i~~D~~i~r~~~~~~~~~~~~~~~~~~~~~~~ 82 (273) -|=+||+.-++|+|+|+.+||++++|.|+..|++|+...|.++||+||++||.+|.+.++++++++.++.+.+.+..+.+ T Consensus 71 lfDVSHmlq~~v~G~d~v~fLes~ttad~~~L~~g~GtlsvFtne~ggiiDd~ii~k~~~~~ly~VsnAgC~ekd~~~~k 150 (401) T KOG2770 71 LFDVSHMLQSRVSGKDRVAFLESLTTADFEGLPEGSGTLSVFTNETGGIIDDLIITKVDENELYIVSNAGCQEKDEALLK 150 (401) T ss_pred EEEEHHHEEEEECCCCHHHHHHHCCCCCHHCCCCCCCEEEEEECCCCCEEEEEEEEEECCCEEEEEECCCHHHHHHHHHH T ss_conf 88621400434116626677653262013105899850488875877614335787303777999725315777888899 Q ss_pred HHHHCCCCCCCCCCC----CEEEEEECCCCCCCCCCCCCC---------------------------CCCCCCCHHH--- Q ss_conf 321000122356884----369999718543222111234---------------------------5664441012--- Q gi|254780591|r 83 FYKLRSNVIIEIQPI----NGVVLSWNQEHTFSNSSFIDE---------------------------RFSIADVLLH--- 128 (273) Q Consensus 83 ~~~~~~~~~~~~~~~----~~~~~~~~g~~~~~~~~~~~~---------------------------~~~~~~~~~~--- 128 (273) .++........|.+. ...+.++|||.+-..+..... +....++..+ T Consensus 151 ~~~~a~ks~gkDv~~~~~~~r~l~A~Qgp~~akvlq~l~~k~~DL~~l~fg~~~~~~~~G~~~~~vtr~gytgEDGfeis 230 (401) T KOG2770 151 DHFFAWKSKGKDVSWETLDGRSLLALQGPEAAKVLQKLLSKLGDLSKLPFGQSQVYDFKGGPGCRVTRGGYTGEDGFEIS 230 (401) T ss_pred HHHHHHHHCCCEEEEEEECCCCHHHHCCHHHHHHHHHHHCCCCCHHCCCCCCEEEEEECCCCCEEEECCCCCCCCCEEEE T ss_conf 99973221264024787246641321273789999976313565100644546899863888558961453267864996 Q ss_pred -----------HHHCCCCCCCCCHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCEEEECCCC--CCCCCCCCCCCC Q ss_conf -----------2210135555796788888875201334565432212331001112201331475--213310132100 Q gi|254780591|r 129 -----------RTWGHNEKIASDIKTYHELRINHGIVDPNTDFLPSTIFPHDALMDLLNGISLTKG--CYIGQEVVSRIQ 195 (273) Q Consensus 129 -----------~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~k~--~f~G~e~~~~~~ 195 (273) .+.........+..+++..+.+.+.+.+.-+.. ....+.+..+.+......++ ||.|++.+.++. T Consensus 231 v~~~~Av~la~~LLa~~~vkp~Gl~ArDsLRLeaGlclyg~did--~~~tpvEa~L~W~i~krrR~~~~f~Ga~~I~~qL 308 (401) T KOG2770 231 VPPEGAVDLAETLLANPVVKPAGLGARDSLRLEAGLCLYGSDID--EETTPVEAGLSWVIGKRRRGTYDFPGAEVILKQL 308 (401) T ss_pred CCCCHHHHHHHHHHHCCCEEECCCCHHHHHHHHCCCCCCCCCCC--CCCCHHHHEEEEEEEECCCCCCCCCCHHHHHHHH T ss_conf 48730579999986187602314112555455327765675334--4567001010022111014556778289999986 Q ss_pred CCC-CCCEEEEEEECCCCCCCCCCEEEEC-CEEEEEEEEEEC------CEEEEEEEHHHCCCCCCCCCEEEECCEEEEEE Q ss_conf 124-4434788740134566789887246-779679998347------83368998131036656786488688899997 Q gi|254780591|r 196 HRN-IIRKRPMIITGTDDLPPSGSPILTD-DIEIGTLGVVVG------KKALAIARIDKVDHAIKKGMALTVHGVRVKAS 267 (273) Q Consensus 196 ~~~-~~~~~~~~~~~~~~~~~~g~~i~~~-g~~VG~vtS~~~------~~gla~i~~~~~~~~~~~~~~l~~~~~~~~i~ 267 (273) +.+ ..+||+++.....++.+.|.+|+.+ |++||.|||++. ++|+|||+..+...++...+.++.+.+++.++ T Consensus 309 k~~~~~~RrvGl~~~~~p~ar~gs~I~~~~g~kVG~vTSg~~sptl~kniamgYV~k~~~~~Gtkv~v~vr~k~~~~~Vs 388 (401) T KOG2770 309 KDGGISRRRVGLNLSAKPPARSGSAIFVDDGTKVGQVTSGCPSPTLGKNIAMGYVKKGYHKIGTKVLVKVRNKLYPAEVS 388 (401) T ss_pred HCCCCCEEEEEEECCCCCCCCCCCEEECCCCCEEEEECCCCCCCCCCCCEEEEEEECCCCCCCCEEEEEECCCCCCEEEE T ss_conf 05886337874442678877899736757885673670489898766615678840355678877999852752425888 Q ss_pred CCCCC Q ss_conf 48876 Q gi|254780591|r 268 FPHWY 272 (273) Q Consensus 268 ~P~w~ 272 (273) |=||- T Consensus 389 kmPfV 393 (401) T KOG2770 389 KMPFV 393 (401) T ss_pred ECCCC T ss_conf 54532 No 11 >KOG2844 consensus Probab=99.97 E-value=3.5e-30 Score=195.28 Aligned_cols=241 Identities=13% Similarity=0.053 Sum_probs=178.8 Q ss_pred EEECCCCEEEEEECCCHHHHHHCCCCCCHHHCCCCCEEEEEEECCCCCEEEEEEEEEECCCCCCEEHHHHHHHHHHHHHH Q ss_conf 17617940799987587878632132673108998268999997999889989999704555200003333345677764 Q gi|254780591|r 3 SVYLSNQSFIKVCGKSAIPFLQAIITADVLTLPYKIARGSAILTPQGKILLYFLISKIEEDTFILEIDRSKRDSLIDKLL 82 (273) Q Consensus 3 ~~~L~~~~~i~i~G~DA~~fL~~l~t~di~~l~~g~~~yt~~ln~~G~i~~D~~i~r~~~~~~~~~~~~~~~~~~~~~~~ 82 (273) .+=+|.|+.+.|+|+||.+.||+++++|++. ++|..+||+|||++||+.+|++|.|+++..|+++.++........|++ T Consensus 520 v~DmS~F~Kf~i~G~da~e~ld~LfSanv~~-~vg~tv~T~mln~~Gg~e~D~tvsrl~~~~f~mia~t~qq~~~~~wi~ 598 (856) T KOG2844 520 VFDMSSFGKFDITGQDAVELLDYLFSANVDV-PVGSTVYTGMLNPKGGYEADCTVSRLSPRGFFMIAGTIQQLHDLSWIK 598 (856) T ss_pred EEECCCCCEEEECCHHHHHHHHHHHHCCCCC-CCCCEEEEEEECCCCCEEEEEEEEEECCCCEEEECCCHHHHHHHHHHH T ss_conf 7641532036510678999999886327788-987346663554899757555666306873599816314412199999 Q ss_pred HHHHC--CCCCCCCCCCCEEEEEECCCCCCCCCCCCCCCCCCCCCHHHH-------------HHCCCCCCCCCH------ Q ss_conf 32100--012235688436999971854322211123456644410122-------------210135555796------ Q gi|254780591|r 83 FYKLR--SNVIIEIQPINGVVLSWNQEHTFSNSSFIDERFSIADVLLHR-------------TWGHNEKIASDI------ 141 (273) Q Consensus 83 ~~~~~--~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~-------------~~~~~~~~~~~~------ 141 (273) ..... ..+.+.|.++.+-.+.++||.++..+..+...+.....+... ......+.+.+. T Consensus 599 k~~~~~~~~v~l~DvT~~~~~l~i~GP~sR~vLqelt~~dls~~~fp~~~~k~l~vg~~girairis~~GELG~~Lyip~ 678 (856) T KOG2844 599 KEMPKGGSNVELKDVTDELGALSIIGPQSRKVLQELTDADLSDDHFPFLTTKELKVGNAGIRAIRISHTGELGWELYIPN 678 (856) T ss_pred HHHHCCCCCEEEEECHHHHCEEEECCCHHHHHHHHCCCCCCCCCCCCCCEEEEEECCCCCEEEEEEEECCCCCEEEEECH T ss_conf 98633687446634130204154218358888874257888845467523433303566248999885066414998112 Q ss_pred ----HHHHH-----------------HHHHHHCCCCCCCCCCCCCCCCCCCCCCCEEEECC-CCCCCCCCCCCCCCCCCC Q ss_conf ----78888-----------------88752013345654322123310011122013314-752133101321001244 Q gi|254780591|r 142 ----KTYHE-----------------LRINHGIVDPNTDFLPSTIFPHDALMDLLNGISLT-KGCYIGQEVVSRIQHRNI 199 (273) Q Consensus 142 ----~~~~~-----------------~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-k~~f~G~e~~~~~~~~~~ 199 (273) ..|.. .......-.+.....+...+..+......+.+.++ .-+|+|++++..++.+|. T Consensus 679 e~~~~vY~~im~AG~~~~l~naGyya~~aLriEK~y~~Wg~dl~~d~tPlEaGl~f~vk~k~p~dFiGk~ALeqqra~Gl 758 (856) T KOG2844 679 EDAVAVYRAIMNAGQEEGLQNAGYYALRALRIEKFYRAWGQDLNPDTTPLEAGLEFRVKLKKPADFIGKQALEQQKAEGL 758 (856) T ss_pred HHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHCCCCCCCCCHHHCCCEEEEECCCCCCCHHHHHHHHHHHHHH T ss_conf 77789999998531120542210677777777787876223368889803336036873378866221899999997625 Q ss_pred CCEEEEEEECCCCC-CCCCCEEEECCEEEEEEEEEECC------EEEEEEEH Q ss_conf 43478874013456-67898872467796799983478------33689981 Q gi|254780591|r 200 IRKRPMIITGTDDL-PPSGSPILTDDIEIGTLGVVVGK------KALAIARI 244 (273) Q Consensus 200 ~~~~~~~~~~~~~~-~~~g~~i~~~g~~VG~vtS~~~~------~gla~i~~ 244 (273) ++|.+.+.....+. +..+++|+.||+.||.+||+.|+ +++||+.. T Consensus 759 kkrlV~l~l~d~d~~~~G~E~I~rnG~~VG~ttsa~Y~ytl~k~v~~gyV~n 810 (856) T KOG2844 759 KKRLVCLTLDDHDPDPWGGEPIYRNGQVVGNTTSAAYGYTLGKSVCLGYVHN 810 (856) T ss_pred HHEEEEEEECCCCCCCCCCCCEEECCEEEEEEEECCCEEEECCEEEEEEECC T ss_conf 4327899933888876678612268889724630100044033378987516 No 12 >pfam01571 GCV_T Aminomethyltransferase folate-binding domain. This is a family of glycine cleavage T-proteins, part of the glycine cleavage multienzyme complex (GCV) found in bacteria and the mitochondria of eukaryotes. GCV catalyses the catabolism of glycine in eukaryotes. The T-protein is an aminomethyl transferase. Probab=99.89 E-value=3e-23 Score=154.73 Aligned_cols=113 Identities=23% Similarity=0.247 Sum_probs=103.0 Q ss_pred EECCCCEEEEEECCCHHHHHHCCCCCCHHHCCCCCEEEEEEECCCCCEEEEEEEEEECCCCCCEEHHHHHHHHHHHHHHH Q ss_conf 76179407999875878786321326731089982689999979998899899997045552000033333456777643 Q gi|254780591|r 4 VYLSNQSFIKVCGKSAIPFLQAIITADVLTLPYKIARGSAILTPQGKILLYFLISKIEEDTFILEIDRSKRDSLIDKLLF 83 (273) Q Consensus 4 ~~L~~~~~i~i~G~DA~~fL~~l~t~di~~l~~g~~~yt~~ln~~G~i~~D~~i~r~~~~~~~~~~~~~~~~~~~~~~~~ 83 (273) +-+|++++|+|+|+||.+|||+++||||+++++|+++||++||++|+|++|++|+|.+++.|+++.++........++.. T Consensus 2 ~D~S~~~~i~v~G~Da~~fL~~l~t~di~~l~~g~~~~~~~ln~~G~i~~d~~v~~~~e~~~~l~~~~~~~~~~~~~L~~ 81 (212) T pfam01571 2 FDVSHMGKIEVSGPDAAAFLQRLLTNDVSKLKPGQATYTLLLNEKGGIIDDLTVYRLGEDEFLLVVNAANAEKDLAWLRK 81 (212) T ss_pred CCCCCCEEEEEECCCHHHHHHHHCCCCCCCCCCCCEEEEEEECCCCCEEEEEEEEECCCCCEEEECCHHHHHHHHHHHHH T ss_conf 83788079999888999999784224645489995987340255678777310023157704785167579999999996 Q ss_pred HHHCCCCCCCCCCCCEEEEEECCCCCCCCCCCC Q ss_conf 210001223568843699997185432221112 Q gi|254780591|r 84 YKLRSNVIIEIQPINGVVLSWNQEHTFSNSSFI 116 (273) Q Consensus 84 ~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~ 116 (273) +....++.+.+.++++..+.++||++....... T Consensus 82 ~~~~~~V~i~d~t~~~~~l~v~GP~a~~~l~~~ 114 (212) T pfam01571 82 YAVFSKVTVADVTDELAVLALQGPKARELLQEL 114 (212) T ss_pred HCCCCCEEEEEEECCCEEEECCCCCHHHHHHHH T ss_conf 467786199996041224530188489999985 No 13 >pfam08669 GCV_T_C Glycine cleavage T-protein C-terminal barrel domain. This is a family of glycine cleavage T-proteins, part of the glycine cleavage multienzyme complex (GCV) found in bacteria and the mitochondria of eukaryotes. GCV catalyses the catabolism of glycine in eukaryotes. The T-protein is an aminomethyl transferase. Probab=99.28 E-value=8e-12 Score=88.06 Aligned_cols=86 Identities=24% Similarity=0.448 Sum_probs=65.8 Q ss_pred CCCCCCCCCCCCCCCCCC-CEEEEEEECCCCCCCCCCEEEE-CCEEEEEEEEEEC------CEEEEEEEHHHCCCCCCCC Q ss_conf 521331013210012444-3478874013456678988724-6779679998347------8336899813103665678 Q gi|254780591|r 183 GCYIGQEVVSRIQHRNII-RKRPMIITGTDDLPPSGSPILT-DDIEIGTLGVVVG------KKALAIARIDKVDHAIKKG 254 (273) Q Consensus 183 ~~f~G~e~~~~~~~~~~~-~~~~~~~~~~~~~~~~g~~i~~-~g~~VG~vtS~~~------~~gla~i~~~~~~~~~~~~ 254 (273) +||+|||++.+++..+.. ++++++.......++.+++++. +++.||+|||+++ ++||||++.++.+.+.. T Consensus 1 g~FiGkeal~~~~~~g~~~k~lv~l~~~~~~~~~~g~~i~~~~g~~vG~vTS~~~s~~~~~~iala~v~~~~~~~g~~-- 78 (95) T pfam08669 1 GDFIGKEALARQKAKGVVRRRLVGLLLDGDGPPREGEPVLAADGEVVGEVTSGTYSPTLGKNIALAYVRTEAAEPGTE-- 78 (95) T ss_pred CCCCCHHHHHHHHHHCCCCEEEEEEEECCCCCCCCCCEEECCCCEEEEEEEEEEECCCCCCEEEEEEECHHHCCCCCE-- T ss_conf 997459999999972997248999962377788999988818997997986666987579738999986889799999-- Q ss_pred CEEEECCEEEEEECCC Q ss_conf 6488688899997488 Q gi|254780591|r 255 MALTVHGVRVKASFPH 270 (273) Q Consensus 255 ~~l~~~~~~~~i~~P~ 270 (273) +.+.+++..+.++.++ T Consensus 79 ~~V~i~g~~~~a~v~~ 94 (95) T pfam08669 79 VEVEIRGKRVPATVVK 94 (95) T ss_pred EEEEECCEEEEEEEEE T ss_conf 9999999799899998 No 14 >TIGR03317 ygfZ_signature folate-binding protein YgfZ. YgfZ is a protein from Escherichia coli, homologous to the glycine cleavage system T protein, or aminomethyltransferase, GcvT (TIGR00528). Homologs of YgfZ other than members of the GcvT family share a well-conserved signature region that includes the motif, KGCYxGQE. Elsewhere, sequence diverge and length variation are substantial. Members of this family are mostly bacterial, largely absent from the Firmicutes and otherwise usually present. A few eukaryotic examples are found among the Apicomplexa, and a few archaeal sequences are found. Two functions implicated for this folate-binding protein are RNA modification (a function likely to be conserved) and replication initiation (a function likely to be highly variable). Many members of this family are, at the time of construction of this model, misnamed as the glycine cleavage system T protein. Probab=98.22 E-value=6.4e-07 Score=59.42 Aligned_cols=65 Identities=34% Similarity=0.684 Sum_probs=46.8 Q ss_pred HHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCEEEECCCCCCCCCCCCCCCCCCCCCCEEEEEEE Q ss_conf 888888752013345654322123310011122013314752133101321001244434788740 Q gi|254780591|r 143 TYHELRINHGIVDPNTDFLPSTIFPHDALMDLLNGISLTKGCYIGQEVVSRIQHRNIIRKRPMIIT 208 (273) Q Consensus 143 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~k~~f~G~e~~~~~~~~~~~~~~~~~~~ 208 (273) .|...+...+.+....... ....+.........+++++||||+|||.++|++++|..+++++... T Consensus 2 ~~~~~ri~~gip~~~~e~~-~~~~P~e~~l~~~~~Isf~KGCY~GQEvvaR~~~rg~~kk~L~~l~ 66 (67) T TIGR03317 2 AWELLRIAAGIPEGGAETS-GEFLPQELNLDALGGVSFKKGCYVGQEVVARMHYRGKVKRRLVRLR 66 (67) T ss_pred HHHHHHHHCCCCCCCCCCC-CCCCHHHCCHHHHCCCCCCCCCCCCHHHHHHHHHCCCCCCEEEEEE T ss_conf 5899999859862575578-7754535686661975146774243679999987388860378866 No 15 >pfam04268 SoxG Sarcosine oxidase, gamma subunit family. Sarcosine oxidase is a hetero-tetrameric enzyme that contains both covalently bound FMN and non-covalently bound FAD and NAD(+). This enzyme catalyses the oxidative demethylation of sarcosine to yield glycine, H2O2, and 5,10-CH2-tetrahydrofolate (H4folate) in a reaction requiring H4folate and O2. Probab=96.97 E-value=0.0024 Score=38.54 Aligned_cols=69 Identities=26% Similarity=0.294 Sum_probs=44.5 Q ss_pred CCEEEEEECCCHHHHHHCCCCCCHH--HCCCCCEEEEEEECCCCCEEEEEEEEEECCCCCCEEHHHHHHHHHHHHHH Q ss_conf 9407999875878786321326731--08998268999997999889989999704555200003333345677764 Q gi|254780591|r 8 NQSFIKVCGKSAIPFLQAIITADVL--TLPYKIARGSAILTPQGKILLYFLISKIEEDTFILEIDRSKRDSLIDKLL 82 (273) Q Consensus 8 ~~~~i~i~G~DA~~fL~~l~t~di~--~l~~g~~~yt~~ln~~G~i~~D~~i~r~~~~~~~~~~~~~~~~~~~~~~~ 82 (273) .|.+|+|+|+.+.+.|.+.++-|+. .+++|++..|.+ +++ ..+++|.+++.|.+....+.......++. T Consensus 73 ~~~~~~lsG~~~~~vL~k~~piDl~~~~f~~g~~a~T~~----~~v--~v~l~r~~~~~f~l~~~RSfa~~l~~~L~ 143 (148) T pfam04268 73 GRVAIRISGPAAEAVLAKGTAIDLHADAFPVGAAATTIL----GHI--AAVIWRTGSDSFELLVFRSFAESLWHWLT 143 (148) T ss_pred CEEEEEECCHHHHHHHHHHCCCCCCHHCCCCCCEEEECC----CCE--EEEEEECCCCEEEEEEECCHHHHHHHHHH T ss_conf 789999749669999980398876620089997999804----857--99999779992999997857999999999 No 16 >COG0486 ThdF Predicted GTPase [General function prediction only] Probab=96.92 E-value=0.0024 Score=38.58 Aligned_cols=58 Identities=16% Similarity=0.240 Sum_probs=49.0 Q ss_pred CCEEEEEECCCHHHHHHCCCCCCHHHCCCCCEEEEEEECCCCCEEEEEEEEEE-CCCCCC Q ss_conf 94079998758787863213267310899826899999799988998999970-455520 Q gi|254780591|r 8 NQSFIKVCGKSAIPFLQAIITADVLTLPYKIARGSAILTPQGKILLYFLISKI-EEDTFI 66 (273) Q Consensus 8 ~~~~i~i~G~DA~~fL~~l~t~di~~l~~g~~~yt~~ln~~G~i~~D~~i~r~-~~~~~~ 66 (273) .-++||+|||+|...++.++.. +...++..+.|+.+.+++|.++|+.++..+ +++.|- T Consensus 18 aI~IvRiSGp~a~~ia~~i~~~-~~~~~~r~a~y~~i~d~~~~~iDe~lvl~f~aP~SFT 76 (454) T COG0486 18 AIGIVRISGPDALEIAQKLFGG-LKLPKPRTAHYGHIKDENGEIIDEVLVLYFKAPNSFT 76 (454) T ss_pred EEEEEECCCHHHHHHHHHHHCC-CCCCCCCEEEEEEEECCCCCEEEEEEEEEEECCCCCC T ss_conf 3899990277499999998477-7778871899998986997575225378870898746 No 17 >pfam10396 TrmE_N GTP-binding protein TrmE N-terminus. This family represents the shorter, B, chain of the homo-dimeric structure which is a guanine nucleotide-binding protein that binds and hydrolyses GTP. TrmE is homologous to the tetrahydrofolate-binding domain of N,N-dimethylglycine oxidase and indeed binds formyl-tetrahydrofolate. TrmE actively participates in the formylation reaction of uridine and regulates the ensuing hydrogenation reaction of a Schiff's base intermediate. This B chain is the N-terminal portion of the protein consisting of five beta-strands and three alpha helices and is necessary for mediating dimer formation within the protein. Probab=96.67 E-value=0.0078 Score=35.58 Aligned_cols=51 Identities=16% Similarity=0.247 Sum_probs=44.0 Q ss_pred CCEEEEEECCCHHHHHHCCCCCCHHHCCCCCEEEEEEECCCCCEEEEEEEEEEC Q ss_conf 940799987587878632132673108998268999997999889989999704 Q gi|254780591|r 8 NQSFIKVCGKSAIPFLQAIITADVLTLPYKIARGSAILTPQGKILLYFLISKIE 61 (273) Q Consensus 8 ~~~~i~i~G~DA~~fL~~l~t~di~~l~~g~~~yt~~ln~~G~i~~D~~i~r~~ 61 (273) -.++|||+||+|.+.++.++..+ +++.+..|.-+.|.+|.++|+.++.... T Consensus 13 aiaVIRvSG~~a~~~~~~l~~~~---~~~r~~~~~~~~d~~~~~iD~~lv~~f~ 63 (114) T pfam10396 13 GIAIIRISGPDALEIAKKLFGKL---PKPRTAHYGTIRDPNGEVIDEVLVLYFP 63 (114) T ss_pred EEEEEEEECCCHHHHHHHHCCCC---CCCCEEEEEEEECCCCCEEEEEEEEEEC T ss_conf 69999987844899999973679---9998899999988999884178998606 No 18 >COG4583 Sarcosine oxidase gamma subunit [Amino acid transport and metabolism] Probab=96.67 E-value=0.0064 Score=36.07 Aligned_cols=73 Identities=29% Similarity=0.365 Sum_probs=57.8 Q ss_pred EECCC-CEEEEEECCCHHHHHHCCCCCCH--HHCCCCCEEEEEEECCCCCEEEEEEEEEECCCCCCEEHHHHHHHHHHHH Q ss_conf 76179-40799987587878632132673--1089982689999979998899899997045552000033333456777 Q gi|254780591|r 4 VYLSN-QSFIKVCGKSAIPFLQAIITADV--LTLPYKIARGSAILTPQGKILLYFLISKIEEDTFILEIDRSKRDSLIDK 80 (273) Q Consensus 4 ~~L~~-~~~i~i~G~DA~~fL~~l~t~di--~~l~~g~~~yt~~ln~~G~i~~D~~i~r~~~~~~~~~~~~~~~~~~~~~ 80 (273) +=.|+ +..|+|+|+.|+..|+.-|+.|+ +..++|++.-|.+ |++ ..++.|.+++.|.++...+.......+ T Consensus 106 VDvShg~t~I~IsG~~Ae~~L~kg~~~DL~~~~FpvG~~a~T~~----~~~--~vvl~r~g~d~fei~V~RSFAe~~w~~ 179 (189) T COG4583 106 VDVSHGRTAIRISGPKAEAVLAKGCALDLSLEAFPVGAAARTIF----GKA--AVVLTRTGADTFEIEVWRSFAESLWHL 179 (189) T ss_pred EECCCCEEEEEECCHHHHHHHHCCCCCCCCHHHCCCCCCEEEEE----CCE--EEEEEEECCCEEEEEEEHHHHHHHHHH T ss_conf 62158759999517859999863785434852277751001230----545--899996057738998616569999999 Q ss_pred HH Q ss_conf 64 Q gi|254780591|r 81 LL 82 (273) Q Consensus 81 ~~ 82 (273) +. T Consensus 180 L~ 181 (189) T COG4583 180 LL 181 (189) T ss_pred HH T ss_conf 99 No 19 >PRK05291 trmE tRNA modification GTPase TrmE; Reviewed Probab=96.39 E-value=0.0088 Score=35.28 Aligned_cols=56 Identities=18% Similarity=0.317 Sum_probs=45.7 Q ss_pred CCEEEEEECCCHHHHHHCCCCCCHHHCCCCCEEEEEEECCCCCEEEEEEEEEE-CCCCC Q ss_conf 94079998758787863213267310899826899999799988998999970-45552 Q gi|254780591|r 8 NQSFIKVCGKSAIPFLQAIITADVLTLPYKIARGSAILTPQGKILLYFLISKI-EEDTF 65 (273) Q Consensus 8 ~~~~i~i~G~DA~~fL~~l~t~di~~l~~g~~~yt~~ln~~G~i~~D~~i~r~-~~~~~ 65 (273) -.++|||+||+|.+.++.++... ..+|.++.|+-+.+++|.++|+.++..+ +++.| T Consensus 18 aiavIRiSG~~a~~i~~~l~~~~--~~~~r~~~~~~~~d~~~~~iD~~l~~~f~~P~Sy 74 (445) T PRK05291 18 GIGIIRISGPDALEIAQKLFGKK--LPKPRTAHYGHIYDPDGEVIDEVLVLYFPAPNSF 74 (445) T ss_pred EEEEEEEECHHHHHHHHHHHCCC--CCCCCEEEEEEEECCCCCCCCEEEEEEECCCCCC T ss_conf 69999830660999999995689--9999789999998899888326999995599988 No 20 >TIGR01375 soxG sarcosine oxidase, gamma subunit family; InterPro: IPR006280 These sequences represent the gamma subunit of a family of known and putative heterotetrameric sarcosine oxidases. Five operons of such oxidases are found in Mesorhizobium loti and three in Agrobacterium tumefaciens, a high enough copy number to suggest that not all members share the same function. The gamma subunit is the most divergent between operons of the four subunits. Sarcosine oxidase catalyzes the oxidative demethylation of sarcosine to glycine. The reaction converts tetrahydrofolate to 5,10-methylene-tetrahydrofolate . Bacterial sarcosine oxidases have been isolated from over a dozen different organisms and fall into two major classes (1) monomeric form that contains only covalent flavin and (2) heterotetrameric (alpha, beta, gamma, delta) form that contain a covalent and noncovalent flavin, this entry represents the heterotetrameric form.. Probab=96.34 E-value=0.0033 Score=37.73 Aligned_cols=75 Identities=27% Similarity=0.319 Sum_probs=61.3 Q ss_pred EEECC-CCEEEEEECCCHHHHHHCCCCCCHHH--CCCCCEEEEEEECCCCCEEEEEEEEEECCCCCCEEHHHHHHHHHHH Q ss_conf 17617-94079998758787863213267310--8998268999997999889989999704555200003333345677 Q gi|254780591|r 3 SVYLS-NQSFIKVCGKSAIPFLQAIITADVLT--LPYKIARGSAILTPQGKILLYFLISKIEEDTFILEIDRSKRDSLID 79 (273) Q Consensus 3 ~~~L~-~~~~i~i~G~DA~~fL~~l~t~di~~--l~~g~~~yt~~ln~~G~i~~D~~i~r~~~~~~~~~~~~~~~~~~~~ 79 (273) .+=+| .+..|+|+||.|...|+.=|+.|++- .++|+++-|.+ |+| ...|.|.+++.|.+..-.+-...... T Consensus 73 ~vD~S~~~t~l~i~Gp~a~~vL~kg~a~Dl~l~~FpVG~~~~T~~----~~~--~~~l~Rtge~~F~i~v~rSFa~~~~~ 146 (154) T TIGR01375 73 VVDLSGGRTALRISGPKAEEVLAKGCAVDLSLSAFPVGAARRTIF----AKV--EVVLWRTGEDTFEILVRRSFAESLWH 146 (154) T ss_pred EEEECCCEEEEEEECHHHHHHHHCCCCCCCCCCCCCHHHHHHHHH----CCC--EEEEEECCCCEEEEEEEECCHHHHHH T ss_conf 786338748999808458989871697155656564034566564----492--69999735573689996373568999 Q ss_pred HHHH Q ss_conf 7643 Q gi|254780591|r 80 KLLF 83 (273) Q Consensus 80 ~~~~ 83 (273) ++.. T Consensus 147 ~L~~ 150 (154) T TIGR01375 147 LLVD 150 (154) T ss_pred HHHH T ss_conf 9999 No 21 >TIGR00450 thdF tRNA modification GTPase TrmE; InterPro: IPR004520 The GTP-binding domain of all TrmE/ThdF orthologues is found in the C-terminal portion of the molecule. The N-terminal half can be removed without affecting the GTP-binding/hydrolysis function of the GTP-binding domain. The last four amino acids of all orthologues of ThdF/TrmE are highly conserved, being either CIGK or CLGK. This matches the Caax (where 'a' represents an aliphatic amino acid, and 'x' represents any amino acid) motif for isoprenylation that anchors small GTP-binding proteins to cell membranes in eukaryotic cells. However, protein isoprenylation has never been shown to occur in bacteria. Interestingly, biochemical experiments have shown that the Escherichia coli TrmE protein peripherally associates with the membrane fraction . Although the biochemical properties of TrmE have been investigated for the E. coli and Thermotoga maritima proteins, nothing is known about the relationship of this protein to tRNA modification. Orthologues of TrmE are present in eukaryotes and bacteria, but are not present in archaea. In Saccharomyces cerevisiae, Mss1p is a nuclear-encoded mitochondrial protein that is the yeast orthologue of TrmE. Mss1p interacts with the 15S rRNA of the yeast mitochondria, which is equivalent to the 16S rRNA of bacteria. Subsequent analysis of the S. cerevisiae MTO1 gene suggests that MSS1 and MTO1 act together in a pathway involved in optimizing mitochondrial protein synthesis. TrmE may play a role in tRNA processing and may be directly or indirectly involved in regulating ribosome function.; GO: 0003924 GTPase activity, 0005525 GTP binding, 0006400 tRNA modification, 0005622 intracellular. Probab=90.68 E-value=0.072 Score=29.94 Aligned_cols=59 Identities=19% Similarity=0.207 Sum_probs=47.3 Q ss_pred CCEEEEEECCCHHHHHHCCCCC---CHHHCCCCCEEEEEEECCCCCEEEEEEEEEEC--CCCCC Q ss_conf 9407999875878786321326---73108998268999997999889989999704--55520 Q gi|254780591|r 8 NQSFIKVCGKSAIPFLQAIITA---DVLTLPYKIARGSAILTPQGKILLYFLISKIE--EDTFI 66 (273) Q Consensus 8 ~~~~i~i~G~DA~~fL~~l~t~---di~~l~~g~~~yt~~ln~~G~i~~D~~i~r~~--~~~~~ 66 (273) --++||+||||+..-++.++.+ .-.+-...|..|+..++++++-.+|..++++- ++.|- T Consensus 12 Ai~iir~SG~~~~~i~~~it~~Ph~~~~~~~g~ri~y~~~~~~~~~~~~d~ll~~l~~AP~SyT 75 (473) T TIGR00450 12 AIHIIRLSGPDSLSILKKITDAPHNKKKTAEGMRIQYGHIIDSNNKALDDELLLKLVAAPNSYT 75 (473) T ss_pred CEEEEEECCHHHHHHHHHHHCCCCCCCCCCCCCEEEEEEEEECCCCCHHHHHHHHHHHCCCCCC T ss_conf 6179970547899999986247111001457761789999716864028888988875679878 No 22 >TIGR02860 spore_IV_B stage IV sporulation protein B; InterPro: IPR014219 Proteolytic enzymes that exploit serine in their catalytic activity are ubiquitous, being found in viruses, bacteria and eukaryotes . They include a wide range of peptidase activity, including exopeptidase, endopeptidase, oligopeptidase and omega-peptidase activity. Over 20 families (denoted S1 - S66) of serine protease have been identified, these being grouped into clans on the basis of structural similarity and other functional evidence . Structures are known for members of the clans and the structures indicate that some appear to be totally unrelated, suggesting different evolutionary origins for the serine peptidases . Not withstanding their different evolutionary origins, there are similarities in the reaction mechanisms of several peptidases. Chymotrypsin, subtilisin and carboxypeptidase C have a catalytic triad of serine, aspartate and histidine in common: serine acts as a nucleophile, aspartate as an electrophile, and histidine as a base . The geometric orientations of the catalytic residues are similar between families, despite different protein folds . The linear arrangements of the catalytic residues commonly reflect clan relationships. For example the catalytic triad in the chymotrypsin clan (PA) is ordered HDS, but is ordered DHS in the subtilisin clan (SB) and SDH in the carboxypeptidase clan (SC) , . Peptidases are grouped into clans and families. Clans are groups of families for which there is evidence of common ancestry. Each clan is identified with two letters, the first representing the catalytic type of the families included in the clan (with the letter 'P' being used for a clan containing families of more than one of the catalytic types serine, threonine and cysteine). Some families cannot yet be assigned to clans, and when a formal assignment is required, such a family is described as belonging to clan A-, C-, M-, S-, T- or U-, according to the catalytic type. Some clans are divided into subclans because there is evidence of a very ancient divergence within the clan, for example MA(E), the gluzincins, and MA(M), the metzincins. Families are grouped by their catalytic type, the first character representing the catalytic type: A, aspartic; C, cysteine; G, glutamic acid; M, metallo; S, serine; T, threonine; and U, unknown. The serine, threonine and cysteine peptidases utilise the amino acid as a nucleophile and form an acyl intermediate - these peptidases can also readily act as transferases. In the case of aspartic, glutamic and metallopeptidases, the nucleophile is an activated water molecule. SpoIVB, the stage IV sporulation protein B of endospore-forming bacteria such as Bacillus subtilis, is a serine proteinase expressed in the spore (rather than mother cell) compartment, that participates in a proteolytic activation cascade for Sigma-K. It appears to be universal among endospore-forming bacteria and occurs nowhere else. The members of this entry belong to MEROPS peptidase family S55 (SpoIVB peptidase, clan PA).. Probab=54.06 E-value=15 Score=16.48 Aligned_cols=54 Identities=26% Similarity=0.286 Sum_probs=33.1 Q ss_pred CCCCCCCCCCCCCCCCCCCCCEEEEEEECCCCCCC---------CCCEEEECCEEEEEEEEEE Q ss_conf 47521331013210012444347887401345667---------8988724677967999834 Q gi|254780591|r 181 TKGCYIGQEVVSRIQHRNIIRKRPMIITGTDDLPP---------SGSPILTDDIEIGTLGVVV 234 (273) Q Consensus 181 ~k~~f~G~e~~~~~~~~~~~~~~~~~~~~~~~~~~---------~g~~i~~~g~~VG~vtS~~ 234 (273) .+..--==|.+....+..+..|-+...+....++. -|.||-=|||.||.||++- T Consensus 339 ~~~e~FdieIVk~~~Q~~p~tKgMvikiTD~rLL~~TGGIVQGMSGSPIIQngKviGAVTHVF 401 (423) T TIGR02860 339 EKVEKFDIEIVKLVPQKSPATKGMVIKITDKRLLEKTGGIVQGMSGSPIIQNGKVIGAVTHVF 401 (423) T ss_pred CEEEEEEEEEEEEEECCCCCCCCCEEEEECHHHHHHCCCEEECCCCCCEEECCCEEEEEEEEE T ss_conf 712788989998565689898620799507699642498898642897578892999999899 No 23 >pfam11834 DUF3354 Domain of unknown function (DUF3354). This domain is functionally uncharacterized. This domain is found in eukaryotes. This presumed domain is about 60 amino acids in length. Probab=50.89 E-value=16 Score=16.21 Aligned_cols=45 Identities=9% Similarity=0.101 Sum_probs=29.5 Q ss_pred CCHHHHHHCCCCCCHHHCCCCCEEEEEEECCCCCEEEEEEEEEECCCCCCE Q ss_conf 587878632132673108998268999997999889989999704555200 Q gi|254780591|r 17 KSAIPFLQAIITADVLTLPYKIARGSAILTPQGKILLYFLISKIEEDTFIL 67 (273) Q Consensus 17 ~DA~~fL~~l~t~di~~l~~g~~~yt~~ln~~G~i~~D~~i~r~~~~~~~~ 67 (273) |+..+=|=.+.+..+.. .-+.++|++|.=++|.-+.|.++..|++ T Consensus 25 P~sleeLl~ia~~Kfg~------~~~~v~~~dgaeIddi~~IRDgD~L~~v 69 (69) T pfam11834 25 PDSLEELLEIAGKKFGF------SPTKVLNEDGAEIDDIEVIRDGDHLYLV 69 (69) T ss_pred CCCHHHHHHHHHHHCCC------CCCEEECCCCCEEEEEEEEECCCEEEEC T ss_conf 85799999999998099------8518982798586035369829999979 No 24 >TIGR02876 spore_yqfD sporulation protein YqfD; InterPro: IPR010690 This family consists of several putative bacterial stage IV sporulation (SpoIV) proteins. YqfD of Bacillus subtilis (P54469 from SWISSPROT) is known to be essential for efficient sporulation although its exact function is unknown .. Probab=49.70 E-value=12 Score=16.98 Aligned_cols=76 Identities=13% Similarity=0.004 Sum_probs=50.3 Q ss_pred ECCCCEEEEEECCCHHHHHHCCCCCC-----HHHCCCCCEEEEEEECCCCCEEEEEEEEEECCCCCCEEHHHHHHHHHHH Q ss_conf 61794079998758787863213267-----3108998268999997999889989999704555200003333345677 Q gi|254780591|r 5 YLSNQSFIKVCGKSAIPFLQAIITAD-----VLTLPYKIARGSAILTPQGKILLYFLISKIEEDTFILEIDRSKRDSLID 79 (273) Q Consensus 5 ~L~~~~~i~i~G~DA~~fL~~l~t~d-----i~~l~~g~~~yt~~ln~~G~i~~D~~i~r~~~~~~~~~~~~~~~~~~~~ 79 (273) +|-..-.|+|+|.+.++|||.+..|- +.+.+..+++....|.+=.++. .+.|-......++...+..=.+.+ T Consensus 4 ~l~G~v~v~v~G~~iErFlN~~~~~gi~vwdv~k~~~~~l~~~~~L~d~~~~~---~~~r~~~~Kv~i~~r~G~pF~~~r 80 (406) T TIGR02876 4 YLRGYVKVEVEGEDIERFLNLCWRNGILVWDVKKINAETLTFKVSLKDFKKLK---QIARKTGCKVKIIARKGLPFLIKR 80 (406) T ss_pred CEEEEEEEEEEECCCHHHHHHHHHCCEEEEEEEEECCCEEEEEEEHHHHHHHH---HHHHHCCCEEEEEEECCCHHHHHH T ss_conf 03548999998167027888988787579987871664489996145677766---441021856999986181478889 Q ss_pred HHHH Q ss_conf 7643 Q gi|254780591|r 80 KLLF 83 (273) Q Consensus 80 ~~~~ 83 (273) ..++ T Consensus 81 ~~kr 84 (406) T TIGR02876 81 LRKR 84 (406) T ss_pred HHHC T ss_conf 8855 No 25 >pfam02743 Cache_1 Cache domain. Probab=48.67 E-value=14 Score=16.62 Aligned_cols=28 Identities=14% Similarity=0.112 Sum_probs=20.4 Q ss_pred CCCCHHHCCCCCEEEEEEECCCCCEEEE Q ss_conf 3267310899826899999799988998 Q gi|254780591|r 27 ITADVLTLPYKIARGSAILTPQGKILLY 54 (273) Q Consensus 27 ~t~di~~l~~g~~~yt~~ln~~G~i~~D 54 (273) ++..+.++..|+.-|+.++|.+|.++.. T Consensus 41 l~~~v~~~~~g~~Gy~flvd~~G~ii~H 68 (81) T pfam02743 41 LLKITKSIKLGKTGYAFIVDNNGKVLAH 68 (81) T ss_pred HHHHHHHCCCCCCEEEEEECCCCCEEEE T ss_conf 9988874502896099999399999990 No 26 >pfam06898 YqfD Putative stage IV sporulation protein YqfD. This family consists of several putative bacterial stage IV sporulation (SpoIV) proteins. YqfD of Bacillus subtilis is known to be essential for efficient sporulation although its exact function is unknown. Probab=45.41 E-value=13 Score=16.70 Aligned_cols=31 Identities=10% Similarity=0.138 Sum_probs=27.2 Q ss_pred EEECCCCEEEEEECCCHHHHHHCCCCCCHHH Q ss_conf 1761794079998758787863213267310 Q gi|254780591|r 3 SVYLSNQSFIKVCGKSAIPFLQAIITADVLT 33 (273) Q Consensus 3 ~~~L~~~~~i~i~G~DA~~fL~~l~t~di~~ 33 (273) +-|+..+-.|+|+|...++|||.+..|+|.- T Consensus 5 ~~~~~G~v~i~v~G~~~ErflN~~~~~gI~l 35 (383) T pfam06898 5 EKFKRGYVTVEISGLGIEKFLNLCWRNGIEV 35 (383) T ss_pred HEEEEEEEEEEEEECCHHHHHHHHHHCCCEE T ss_conf 2351589999999678899999999789789 No 27 >pfam07932 DAP_C D-aminopeptidase, domain C. D-aminopeptidase is a dimeric enzyme with each monomer being composed of three domains. Domain C is organized to form a beta barrel made up of eight antiparallel beta strands. It is connected to domain B by a short linker sequence, and interacts extensively with the domain A, the catalytic domain. The gamma loop of domain C forms part of the wall of the catalytic pocket; domain C is in fact thought to confer substrate and inhibitor specificity to the enzyme. Probab=38.14 E-value=27 Score=14.90 Aligned_cols=55 Identities=11% Similarity=-0.004 Sum_probs=41.0 Q ss_pred CCCCCCCCCCCCCCCCCCCCCCEEEEEEECCCCCCCCCCEEEECCEEEEEEEEEE Q ss_conf 1475213310132100124443478874013456678988724677967999834 Q gi|254780591|r 180 LTKGCYIGQEVVSRIQHRNIIRKRPMIITGTDDLPPSGSPILTDDIEIGTLGVVV 234 (273) Q Consensus 180 ~~k~~f~G~e~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~i~~~g~~VG~vtS~~ 234 (273) -.-..|+|+....+++..+...+.+.....-+.+.++...+...-..-|.||... T Consensus 29 g~F~G~LG~g~~e~m~~~g~DvW~l~~~R~mDApaPGdWTlvf~Rd~~G~VtG~t 83 (97) T pfam07932 29 GAFEGFLGKGPMELMRYLGPDVWLLACRRSMDAPAPGNWTLVFQRDEAGRVTGVT 83 (97) T ss_pred EEEECCCCCCCHHHHHHCCCCEEEEECCCCCCCCCCCCEEEEEEECCCCCEEEEE T ss_conf 9876012689325544238946998645547998898659999964799688888 No 28 >KOG1191 consensus Probab=29.91 E-value=30 Score=14.68 Aligned_cols=56 Identities=13% Similarity=0.099 Sum_probs=35.6 Q ss_pred CEEEEEECCCHHHHHHCCCCCC-HHHCCCCCEEEEEEECC--CCC-------EEEEE-EEEEECCCCCC Q ss_conf 4079998758787863213267-31089982689999979--998-------89989-99970455520 Q gi|254780591|r 9 QSFIKVCGKSAIPFLQAIITAD-VLTLPYKIARGSAILTP--QGK-------ILLYF-LISKIEEDTFI 66 (273) Q Consensus 9 ~~~i~i~G~DA~~fL~~l~t~d-i~~l~~g~~~yt~~ln~--~G~-------i~~D~-~i~r~~~~~~~ 66 (273) -++|+++||++.+.+.+++-.- +.+ +-.+-+..+-|+ .+. ++|-. .+|..++..|. T Consensus 57 iai~R~sG~~a~kv~r~L~~s~~v~~--~~~~~~~~l~~~~~r~~~~~e~~v~~D~~l~l~~~gp~sFt 123 (531) T KOG1191 57 IAIFRISGPDATKVARRLLRSVMVPK--RRNAGLRALYNPEVRVYVVDEDGVTRDRALGLYFLGPQSFT 123 (531) T ss_pred EEEEEECCCHHHHHHHHHCCCCCCCC--CCCCCCCCCCCHHHCCCCCCCCCCCHHHHHHCCCCCCCEEE T ss_conf 25998148317799998602132578--87545010148555122468887422133410035882234 No 29 >TIGR02082 metH methionine synthase; InterPro: IPR011822 Vitamin B12 dependent methionine synthase 2.1.1.13 from EC (5-methyltetrahydrofolate--homocysteine S-methyltransferase) catalyses the conversion of 5-methyltetrahydrofolate and L-homocysteine to tetrahydrofolate and L-methionine as the final step in de novo methionine biosynthesis. The enzyme requires methylcobalamin as a cofactor. In humans, defects in this enzyme are the cause of autosomal recessive inherited methylcobalamin deficiency (CBLG), which causes mental retardation, macrocytic anemia and homocystinuria. Mild deficiencies in activity may result in mild hyperhomocysteinemia, and mutations in the enzyme may be involved in tumorigenesis. Vitamin B12 dependent methionine synthase is found in prokaryotes and eukaryotes, but in prokaryotes the cofactor is cobalamin. This enzyme is a large protein composed of four structurally and functionally distinct modules: the first two modules bind homocysteine and tetrahydrofolate , the third module binds the B12 cofactor , and the C-terminal module (activation domain) binds S-adenosylmethionine. The activation domain is essential for the reductive activation of the enzyme. During the catalytic cycle, the highly reactive cob(I)alamin intermediate can be oxidised to produce an inactive cob(II)alamin enzyme; the enzyme is then reactivated via reductive methylation by the activation domain . The activation domain adopts an unusual alpha/beta fold.Recent studies suggest that this enzyme exists as an ensemble of conformations with equilibria dependent on the oxidation and methylation state of the cobalamin and on the concentrations of substrates or products .; GO: 0008705 methionine synthase activity, 0031419 cobalamin binding, 0050897 cobalt ion binding, 0009086 methionine biosynthetic process. Probab=25.02 E-value=40 Score=13.90 Aligned_cols=16 Identities=25% Similarity=0.565 Sum_probs=9.0 Q ss_pred HHHHHCCCCC-CHHHCC Q ss_conf 8786321326-731089 Q gi|254780591|r 20 IPFLQAIITA-DVLTLP 35 (273) Q Consensus 20 ~~fL~~l~t~-di~~l~ 35 (273) .+||+.|.++ ||++++ T Consensus 408 ~~f~~llA~ePdia~vP 424 (1265) T TIGR02082 408 KRFLNLLASEPDIAKVP 424 (1265) T ss_pred HHHHHHHCCCCCCCCCC T ss_conf 99999626898602136 No 30 >PRK10807 paraquat-inducible protein B; Provisional Probab=23.43 E-value=49 Score=13.40 Aligned_cols=60 Identities=5% Similarity=0.008 Sum_probs=36.7 Q ss_pred EEEECCCHHHHHHCCCCCCHHHCCCCCEEEEEEECCCCCEEEEEEEEEEC------CCCCCEEHHH Q ss_conf 99987587878632132673108998268999997999889989999704------5552000033 Q gi|254780591|r 12 IKVCGKSAIPFLQAIITADVLTLPYKIARGSAILTPQGKILLYFLISKIE------EDTFILEIDR 71 (273) Q Consensus 12 i~i~G~DA~~fL~~l~t~di~~l~~g~~~yt~~ln~~G~i~~D~~i~r~~------~~~~~~~~~~ 71 (273) |.|+=++|.-.--+-+.-....+..|+..---+-++..+|+....+.+.. +-.||++.+. T Consensus 45 Iti~f~~a~Gi~aGkT~ikyr~V~VG~V~~v~ls~d~~~V~v~a~l~~~~~~~l~~dtrFWvV~Pr 110 (546) T PRK10807 45 VTLITTNAEGIEGGKTTIKSRSVDVGVVESATLTDDLTHVEIKARLNSGMEKLLHKDTVFWVVKPQ 110 (546) T ss_pred EEEEECCCCCCCCCCEEEEECCCCEEEEEEEEECCCCCEEEEEEEECHHHHHHHHCCCEEEEEECE T ss_conf 999976878865696468975861789979998887672899999887688774238769998020 No 31 >TIGR01755 flav_wrbA flavoprotein WrbA; InterPro: IPR010089 This entry represents a protein, WrbA, related to and slightly larger than flavodoxin. In Escherichia coli, this protein is produced during stationary phase, binds to the trp repressor, and makes trp operon repression more efficient. WrbA does not interact with the trp operator by itself. Three copies are found in Sinorhizobium meliloti, and members are found in species in which homologs of the Escherichia coli trp operon repressor TrpR (P03032 from SWISSPROT) are not detected.; GO: 0010181 FMN binding, 0016481 negative regulation of transcription. Probab=23.32 E-value=49 Score=13.39 Aligned_cols=41 Identities=10% Similarity=0.135 Sum_probs=27.5 Q ss_pred EEECCEEEEEEEEEEC---------------------CEEEEEEEHHHCCCCCCCCCEEEEC Q ss_conf 7246779679998347---------------------8336899813103665678648868 Q gi|254780591|r 220 ILTDDIEIGTLGVVVG---------------------KKALAIARIDKVDHAIKKGMALTVH 260 (273) Q Consensus 220 i~~~g~~VG~vtS~~~---------------------~~gla~i~~~~~~~~~~~~~~l~~~ 260 (273) +|..|+-||+|-|+-- .+|+.+|-+.|+....-..-+++++ T Consensus 105 LW~~gaL~GKvGSvf~SsaTqHGGqE~ti~~~~~tl~HhGMi~VgL~YA~~~q~~~d~v~GG 166 (205) T TIGR01755 105 LWASGALVGKVGSVFTSSATQHGGQESTILSFIVTLLHHGMIIVGLPYAEQEQMGVDEVRGG 166 (205) T ss_pred CCCCCCCCCCEEEEEEECCCCCCHHHHHHHHHHHHHHHCCEEEECCCHHHHHHCCCCEEECC T ss_conf 02015402122557642574744167899999999976586774666243532477766325 No 32 >pfam09863 DUF2090 Uncharacterized protein conserved in bacteria (DUF2090). This domain, found in various prokaryotic carbohydrate kinases, has no known function. Probab=23.07 E-value=25 Score=15.11 Aligned_cols=11 Identities=18% Similarity=0.341 Sum_probs=5.0 Q ss_pred HHHHHHCCCCC Q ss_conf 78786321326 Q gi|254780591|r 19 AIPFLQAIITA 29 (273) Q Consensus 19 A~~fL~~l~t~ 29 (273) +..-||+.+|+ T Consensus 20 ~L~~lH~~T~r 30 (310) T pfam09863 20 ELEHLHRVTTR 30 (310) T ss_pred HHHHHHHCCCC T ss_conf 89877621468 No 33 >pfam00673 Ribosomal_L5_C ribosomal L5P family C-terminus. This region is found associated with pfam00281. Probab=22.06 E-value=33 Score=14.39 Aligned_cols=39 Identities=13% Similarity=0.160 Sum_probs=27.0 Q ss_pred EEEEECCCHHHHHHCCCCCCHHHCCCCCEEEEEEECCCC Q ss_conf 799987587878632132673108998268999997999 Q gi|254780591|r 11 FIKVCGKSAIPFLQAIITADVLTLPYKIARGSAILTPQG 49 (273) Q Consensus 11 ~i~i~G~DA~~fL~~l~t~di~~l~~g~~~yt~~ln~~G 49 (273) .+.+.|+.+.+||+++++--++++.+-+....---|..| T Consensus 5 kVTLRg~~m~~FL~~li~ivlPrirdf~gi~~~sfD~~G 43 (95) T pfam00673 5 KVTLRGEKMYEFLDRLINIVLPRIRDFRGLSPKSFDGRG 43 (95) T ss_pred EEEECCHHHHHHHHHHHHHHCCCEECCCCCCCCCCCCCC T ss_conf 999771989999999998735200036657864347873 No 34 >TIGR00380 cobD cobalamin biosynthesis protein CobD; InterPro: IPR004485 Cobalamin (vitamin B12) is a structurally complex cofactor, consisting of a modified tetrapyrrole with a centrally chelated cobalt. Cobalamin is usually found in one of two biologically active forms: methylcobalamin and adocobalamin. Most prokaryotes, as well as animals, have cobalamin-dependent enzymes, whereas plants and fungi do not appear to use it. In bacteria and archaea, these include methionine synthase, ribonucleotide reductase, glutamate and methylmalonyl-CoA mutases, ethanolamine ammonia lyase, and diol dehydratase . In mammals, cobalamin is obtained through the diet, and is required for methionine synthase and methylmalonyl-CoA mutase . There are at least two distinct cobalamin biosynthetic pathways in bacteria : Aerobic pathway that requires oxygen and in which cobalt is inserted late in the pathway ; found in Pseudomonas denitrificans and Rhodobacter capsulatus. Anaerobic pathway in which cobalt insertion is the first committed step towards cobalamin synthesis ; found in Salmonella typhimurium, Bacillus megaterium, and Propionibacterium freudenreichii shermanii. Either pathway can be divided into two parts: (1) corrin ring synthesis (differs in aerobic and anaerobic pathways) and (2) adenosylation of corrin ring, attachment of aminopropanol arm, and assembly of the nucleotide loop (common to both pathways) . There are about 30 enzymes involved in either pathway, where those involved in the aerobic pathway are prefixed Cob and those of the anaerobic pathway Cbi. Several of these enzymes are pathway-specific: CbiD, CbiG, and CbiK are specific to the anaerobic route of S. typhimurium, whereas CobE, CobF, CobG, CobN, CobS, CobT, and CobW are unique to the aerobic pathway of P. denitrificans. This entry represents the CbiB protein, which is involved in cobalamin biosynthesis and porphyrin biosynthesis. It converts cobyric acid to cobinamide by the addition of aminopropanol on the F carboxylic group. It is part of the cob operon .; GO: 0009236 cobalamin biosynthetic process, 0016021 integral to membrane. Probab=22.03 E-value=32 Score=14.46 Aligned_cols=24 Identities=25% Similarity=0.163 Sum_probs=12.6 Q ss_pred CCHHHHHHCCCCCCHHHCCCCCEE Q ss_conf 587878632132673108998268 Q gi|254780591|r 17 KSAIPFLQAIITADVLTLPYKIAR 40 (273) Q Consensus 17 ~DA~~fL~~l~t~di~~l~~g~~~ 40 (273) |||.+-||.+++||-++|++.+.. T Consensus 120 e~AR~~l~~~VSRdt~~Ls~e~i~ 143 (322) T TIGR00380 120 EDARKKLQMIVSRDTEELSEEQIL 143 (322) T ss_pred HHHHHHHHHHHCCCCCCCCHHHHH T ss_conf 678999876422475534535677 No 35 >PRK05054 exoribonuclease II; Provisional Probab=20.80 E-value=56 Score=13.08 Aligned_cols=49 Identities=20% Similarity=0.234 Sum_probs=35.2 Q ss_pred CEEECCCCEEEEEECCCHHHHHHCCCCCCHHHCCCCCEEEE----EEECCCCCEEEEEEEEE Q ss_conf 41761794079998758787863213267310899826899----99979998899899997 Q gi|254780591|r 2 SSVYLSNQSFIKVCGKSAIPFLQAIITADVLTLPYKIARGS----AILTPQGKILLYFLISK 59 (273) Q Consensus 2 ~~~~L~~~~~i~i~G~DA~~fL~~l~t~di~~l~~g~~~yt----~~ln~~G~i~~D~~i~r 59 (273) .++||+++. ...|=..++|++=+|.||.-++| +-+|.+|.+..+..+++ T Consensus 251 tSvYlp~~v---------iPMLPe~LSn~lCSL~P~~dRlalsv~~~id~~G~i~~~~~~~~ 303 (644) T PRK05054 251 FTNYLPGFN---------IPMLPRELSDDLCSLRENEVRPALACRITIDADGTIEDDIEFFA 303 (644) T ss_pred EEEECCCCC---------CCCCCHHHHCCCCCCCCCCCCEEEEEEEEECCCCCEEEEEEEEE T ss_conf 169789984---------48999688077562489996427999999958987865159999 No 36 >pfam05580 Peptidase_S55 SpoIVB peptidase S55. The protein SpoIVB plays a key role in signalling in the final sigma-K checkpoint of Bacillus subtilis. Probab=20.28 E-value=57 Score=13.02 Aligned_cols=20 Identities=40% Similarity=0.551 Sum_probs=17.4 Q ss_pred CCCEEEECCEEEEEEEEEEC Q ss_conf 89887246779679998347 Q gi|254780591|r 216 SGSPILTDDIEIGTLGVVVG 235 (273) Q Consensus 216 ~g~~i~~~g~~VG~vtS~~~ 235 (273) .|.||.-|||.||.||.+-- T Consensus 183 SGSPIIQngKlIGAVTHVfv 202 (219) T pfam05580 183 SGSPIIQNGKIIGAVTHVFV 202 (219) T ss_pred CCCCEEECCEEEEEEEEEEE T ss_conf 78967658908989989996 Done!