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!