Query         gi|254780509|ref|YP_003064922.1| hypothetical protein CLIBASIA_01980 [Candidatus Liberibacter asiaticus str. psy62]
Match_columns 112
No_of_seqs    141 out of 240
Neff          5.0 
Searched_HMMs 39220
Date          Sun May 29 23:04:49 2011
Command       /home/congqian_1/programs/hhpred/hhsearch -i 254780509.hhm -d /home/congqian_1/database/cdd/Cdd.hhm 

 No Hit                             Prob E-value P-value  Score    SS Cols Query HMM  Template HMM
  1 PRK05684 flgJ peptidoglycan hy  99.9 1.1E-23 2.9E-28  149.6   8.3   84   22-106     5-90  (313)
  2 PRK12709 flgJ peptidoglycan hy  99.9 2.1E-23 5.2E-28  148.2   8.3   82   23-106    12-93  (318)
  3 TIGR02541 flagell_FlgJ flagell  99.9 2.5E-23 6.3E-28  147.8   6.9   79   27-106     3-87  (332)
  4 PRK12712 flgJ peptidoglycan hy  99.9 1.2E-22 3.2E-27  143.9   8.8   92    8-106     5-96  (344)
  5 PRK12710 flgJ peptidoglycan hy  99.9 1.5E-22 3.7E-27  143.5   8.2   82   24-106     6-90  (291)
  6 PRK12713 flgJ peptidoglycan hy  99.9 3.3E-22 8.5E-27  141.6   8.5   84   22-106    12-96  (339)
  7 PRK12711 flgJ peptidoglycan hy  99.8 2.2E-21 5.6E-26  137.1   6.9   65   41-106    14-78  (392)
  8 PRK12790 chemotactic signal-re  99.8   1E-20 2.6E-25  133.5   7.6   68   39-106    31-99  (115)
  9 COG3951 Rod binding protein [C  99.8 2.4E-20   6E-25  131.5   8.1   81   25-106     9-91  (166)
 10 PRK12708 flgJ peptidoglycan hy  99.8 5.8E-19 1.5E-23  123.9   7.2   82   25-106     5-90  (134)
 11 pfam10135 Rod-binding Rod bind  99.0 2.2E-10 5.6E-15   77.0   3.3   42   65-106     1-43  (49)
 12 TIGR01371 met_syn_B12ind 5-met  51.0      18 0.00046   17.4   3.2   30   78-107   473-502 (778)
 13 PRK05222 5-methyltetrahydropte  43.5      24  0.0006   16.8   2.8   31   78-108   450-480 (756)
 14 TIGR02506 NrdE_NrdA ribonucleo  32.5      25 0.00065   16.6   1.6   20   91-110   100-119 (685)
 15 COG0307 RibC Riboflavin syntha  23.0     5.6 0.00014   20.2  -3.2   29   79-107   113-141 (204)
 16 PRK00448 polC DNA polymerase I  20.2      34 0.00086   16.0   0.3   37   53-89   1147-1186(1436)

No 1  
>PRK05684 flgJ peptidoglycan hydrolase; Validated
Probab=99.90  E-value=1.1e-23  Score=149.58  Aligned_cols=84  Identities=18%  Similarity=0.296  Sum_probs=75.3

Q ss_pred             HHHHHHHHCCHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHCCC--CCCCCCCCHHHHHHHHHHHHHHHHHHH
Q ss_conf             544323120789999987022855479999999999999999999951021--123357533368999999999999998
Q gi|254780509|r   22 ISQDDSSFQSFLQLKDVQEACDKSKSVPEMTQKLQGIMFQYFIKSILPEET--VKSLGGGFNGDFWQEILAENISDVIVK   99 (112)
Q Consensus        22 is~~~~s~q~~~~Lk~~~~~~~~~~~l~~~a~~fEa~fl~~~lksmr~~~~--~~~lggg~a~d~~~sMl~ee~a~~iAk   99 (112)
                      .+....+++++++||. ++..|+.++|++||+|||++|+||||||||.+.+  +++++++.++++|++|+|+|+|+.|++
T Consensus         5 ~~~~a~D~~~L~~Lk~-~a~~d~~~al~~vA~QFEalF~q~mlKsMR~A~~~~~d~l~~s~~~~~y~~M~DqQla~~ls~   83 (313)
T PRK05684          5 LSGAALDLQSLNSLKA-KAGKDPAANLRKVAQQFEGIFVQMMLKSMRDANPVFKDGLMNSQQTKLYTSMYDQQIAQQLSA   83 (313)
T ss_pred             HHHHHCCHHHHHHHHH-HHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHC
T ss_conf             0022218788999998-854292999999999999999999999998445523588878806779999999999999860


Q ss_pred             CCCCCCC
Q ss_conf             0798756
Q gi|254780509|r  100 QQRITLD  106 (112)
Q Consensus       100 ~ggiGL~  106 (112)
                      +|||||-
T Consensus        84 ~~glGla   90 (313)
T PRK05684         84 GGGLGLA   90 (313)
T ss_pred             CCCCCHH
T ss_conf             7998499


No 2  
>PRK12709 flgJ peptidoglycan hydrolase; Provisional
Probab=99.89  E-value=2.1e-23  Score=148.20  Aligned_cols=82  Identities=12%  Similarity=0.216  Sum_probs=75.0

Q ss_pred             HHHHHHHCCHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHCCC
Q ss_conf             44323120789999987022855479999999999999999999951021123357533368999999999999998079
Q gi|254780509|r   23 SQDDSSFQSFLQLKDVQEACDKSKSVPEMTQKLQGIMFQYFIKSILPEETVKSLGGGFNGDFWQEILAENISDVIVKQQR  102 (112)
Q Consensus        23 s~~~~s~q~~~~Lk~~~~~~~~~~~l~~~a~~fEa~fl~~~lksmr~~~~~~~lggg~a~d~~~sMl~ee~a~~iAk~gg  102 (112)
                      ++...+++++++||. .+..++.++|++||+|||++|+||||||||.+.++++++++.+.++|++|+|+|+|..|+++ |
T Consensus        12 ~~~a~D~~~L~~Lk~-~a~~~~~~al~~vA~QFEalF~qmmlKsMR~a~~~~~l~~s~~~~~y~~M~DqQla~~ls~~-G   89 (318)
T PRK12709         12 QRFALDVQGFDALRA-QAKASPQAGAKMVAGQFDAMFTQMMLKSMRDATPSDGLFDSHTSKMYTSMLDQQLAQQMSSK-G   89 (318)
T ss_pred             HHHHHHHHHHHHHHH-HHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHC-C
T ss_conf             677745776999999-87419399999999999999999999999846767888787067899999999999998537-8


Q ss_pred             CCCC
Q ss_conf             8756
Q gi|254780509|r  103 ITLD  106 (112)
Q Consensus       103 iGL~  106 (112)
                      |||-
T Consensus        90 ~Gla   93 (318)
T PRK12709         90 IGVA   93 (318)
T ss_pred             CCHH
T ss_conf             7799


No 3  
>TIGR02541 flagell_FlgJ flagellar rod assembly protein/muramidase FlgJ; InterPro: IPR013377    The N-terminal region of this protein acts directly in flagellar rod assembly, while the C-terminal region is a flagellum-specific muramidase (peptidoglycan hydrolase) required for formation of the outer membrane L ring .; GO: 0016798 hydrolase activity acting on glycosyl bonds, 0001539 ciliary or flagellar motility, 0009296 flagellum biogenesis, 0009288 flagellin-based flagellum.
Probab=99.89  E-value=2.5e-23  Score=147.75  Aligned_cols=79  Identities=18%  Similarity=0.307  Sum_probs=72.1

Q ss_pred             HHHCCHHHHHHHHCCCCHH--HHHH--HHHHHHHHHHHHHHHHHHHHCCCCCCC--CCCCHHHHHHHHHHHHHHHHHHHC
Q ss_conf             3120789999987022855--4799--999999999999999999510211233--575333689999999999999980
Q gi|254780509|r   27 SSFQSFLQLKDVQEACDKS--KSVP--EMTQKLQGIMFQYFIKSILPEETVKSL--GGGFNGDFWQEILAENISDVIVKQ  100 (112)
Q Consensus        27 ~s~q~~~~Lk~~~~~~~~~--~~l~--~~a~~fEa~fl~~~lksmr~~~~~~~l--ggg~a~d~~~sMl~ee~a~~iAk~  100 (112)
                      .+.+++++||. ++..||.  ++.+  +||+||||||++||||+||++.+++++  +.+..+++|++|+|||++++|+.+
T Consensus         3 ~D~~~L~~Lk~-kA~~dP~dG~~~~~~~~ArQFEalF~~mMLKsMReAt~k~glni~~S~~~~~y~~m~DqQ~a~~L~~~   81 (332)
T TIGR02541         3 IDAQSLDELKA-KAVKDPKDGEAAKLTEAARQFEALFLNMMLKSMREATPKDGLNIFDSQQTRFYQQMLDQQLAQQLSAR   81 (332)
T ss_pred             CCHHHHHHHHH-HHHCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHCC
T ss_conf             16467999998-85028810799886688889999998624455440478887653255316788635489999998458


Q ss_pred             CCCCCC
Q ss_conf             798756
Q gi|254780509|r  101 QRITLD  106 (112)
Q Consensus       101 ggiGL~  106 (112)
                      +||||-
T Consensus        82 ~GiGLA   87 (332)
T TIGR02541        82 KGIGLA   87 (332)
T ss_pred             CCCCHH
T ss_conf             997689


No 4  
>PRK12712 flgJ peptidoglycan hydrolase; Provisional
Probab=99.88  E-value=1.2e-22  Score=143.93  Aligned_cols=92  Identities=12%  Similarity=0.209  Sum_probs=76.1

Q ss_pred             CCHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCHHHHHHH
Q ss_conf             61135543336887544323120789999987022855479999999999999999999951021123357533368999
Q gi|254780509|r    8 NISHSQSMGGNLAKISQDDSSFQSFLQLKDVQEACDKSKSVPEMTQKLQGIMFQYFIKSILPEETVKSLGGGFNGDFWQE   87 (112)
Q Consensus         8 ~is~~~~M~gnla~is~~~~s~q~~~~Lk~~~~~~~~~~~l~~~a~~fEa~fl~~~lksmr~~~~~~~lggg~a~d~~~s   87 (112)
                      +++....+++      +...++++++.||......++.++|++||+|||++|+||||||||.+.++++++++..+++|++
T Consensus         5 ~~~~~~dls~------~~a~D~~~l~~Lk~~a~~~~~~~al~~va~qFEalF~q~mlKsMR~a~~~~~~~~s~~~~~y~~   78 (344)
T PRK12712          5 TLSAQADLSQ------RFALDTQGFEALKHSARGGADAGTLQAAARQFEAVFTQMVLKSMRDATPQDGLFDNEQSKLYMS   78 (344)
T ss_pred             CCCCCCCHHH------HHHHCHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCHHHHHHHH
T ss_conf             8786433034------5562677799999998539817899999999999999999999984677788878716789999


Q ss_pred             HHHHHHHHHHHHCCCCCCC
Q ss_conf             9999999999980798756
Q gi|254780509|r   88 ILAENISDVIVKQQRITLD  106 (112)
Q Consensus        88 Ml~ee~a~~iAk~ggiGL~  106 (112)
                      |+|+|++..|+++ ||||-
T Consensus        79 m~DqQla~~ls~~-G~GLa   96 (344)
T PRK12712         79 MMDQQLAQQMSSR-GIGLA   96 (344)
T ss_pred             HHHHHHHHHHHHC-CCCHH
T ss_conf             9999999998546-88899


No 5  
>PRK12710 flgJ peptidoglycan hydrolase; Provisional
Probab=99.88  E-value=1.5e-22  Score=143.53  Aligned_cols=82  Identities=27%  Similarity=0.376  Sum_probs=72.7

Q ss_pred             HHHHHHCCHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHCC---CCCCCCCCCHHHHHHHHHHHHHHHHHHHC
Q ss_conf             432312078999998702285547999999999999999999995102---11233575333689999999999999980
Q gi|254780509|r   24 QDDSSFQSFLQLKDVQEACDKSKSVPEMTQKLQGIMFQYFIKSILPEE---TVKSLGGGFNGDFWQEILAENISDVIVKQ  100 (112)
Q Consensus        24 ~~~~s~q~~~~Lk~~~~~~~~~~~l~~~a~~fEa~fl~~~lksmr~~~---~~~~lggg~a~d~~~sMl~ee~a~~iAk~  100 (112)
                      ....+++++++||. .+..++.++|++||+|||++|+||||||||.+.   .+++++.+..+++|++|+|+|+|..|+++
T Consensus         6 ~~~~D~~~L~~Lk~-~A~~~~~~al~~vA~QFEalF~qmmLKsMR~A~~~~~~~~~~~s~~~~~y~~M~DqQlA~~ls~~   84 (291)
T PRK12710          6 IATSDFQGLNELKI-QAKNNAKEALPEVAKQFEGIFLQSMLKSMRMGQHFLDESSPFSGKNEATFQEMLDAQYASTIAES   84 (291)
T ss_pred             HHHHCHHHHHHHHH-HHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHCC
T ss_conf             00415778999999-86229499999999999999999999998724466766898786167899999899999998428


Q ss_pred             CCCCCC
Q ss_conf             798756
Q gi|254780509|r  101 QRITLD  106 (112)
Q Consensus       101 ggiGL~  106 (112)
                      +||||-
T Consensus        85 ~g~GLA   90 (291)
T PRK12710         85 KGIGLA   90 (291)
T ss_pred             CCCCHH
T ss_conf             998599


No 6  
>PRK12713 flgJ peptidoglycan hydrolase; Provisional
Probab=99.87  E-value=3.3e-22  Score=141.58  Aligned_cols=84  Identities=14%  Similarity=0.209  Sum_probs=73.2

Q ss_pred             HHHHHHHHCCHHHHHHHHC-CCCHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHC
Q ss_conf             5443231207899999870-228554799999999999999999999510211233575333689999999999999980
Q gi|254780509|r   22 ISQDDSSFQSFLQLKDVQE-ACDKSKSVPEMTQKLQGIMFQYFIKSILPEETVKSLGGGFNGDFWQEILAENISDVIVKQ  100 (112)
Q Consensus        22 is~~~~s~q~~~~Lk~~~~-~~~~~~~l~~~a~~fEa~fl~~~lksmr~~~~~~~lggg~a~d~~~sMl~ee~a~~iAk~  100 (112)
                      ++.+..++++++.||.... .++...++++||+|||++|+||||||||.+.++++++++..+++|++|+|+|+|..|+++
T Consensus        12 ~q~~a~D~~~L~~Lk~~A~~~~~~~~~~r~vA~QFEalF~q~mlKsMR~a~~~~~l~~s~~~~~y~~m~DqQla~~ls~~   91 (339)
T PRK12713         12 VQESVFDLGRLADLKRDAVKAPDGQRQQTEVARQFEALFLQMMLKRMREATPKEGLFDSQQTEMLQGMADEQLALQLASP   91 (339)
T ss_pred             CCHHHHCHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHC
T ss_conf             31323066569999999851952567799999999999999999999846777888887177899999999999998346


Q ss_pred             CCCCCC
Q ss_conf             798756
Q gi|254780509|r  101 QRITLD  106 (112)
Q Consensus       101 ggiGL~  106 (112)
                       ||||-
T Consensus        92 -G~Gla   96 (339)
T PRK12713         92 -GIGLA   96 (339)
T ss_pred             -CCCHH
T ss_conf             -87799


No 7  
>PRK12711 flgJ peptidoglycan hydrolase; Reviewed
Probab=99.84  E-value=2.2e-21  Score=137.12  Aligned_cols=65  Identities=12%  Similarity=0.296  Sum_probs=59.0

Q ss_pred             CCCHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHCCCCCCC
Q ss_conf             228554799999999999999999999510211233575333689999999999999980798756
Q gi|254780509|r   41 ACDKSKSVPEMTQKLQGIMFQYFIKSILPEETVKSLGGGFNGDFWQEILAENISDVIVKQQRITLD  106 (112)
Q Consensus        41 ~~~~~~~l~~~a~~fEa~fl~~~lksmr~~~~~~~lggg~a~d~~~sMl~ee~a~~iAk~ggiGL~  106 (112)
                      .++..++||+||+|||++|+||||||||++.++++++.+. .++|++|+|||+|..|++.|||||-
T Consensus        14 ~kndpaaLr~VAqQFEslFvqMMLKSMRdAt~~d~l~ss~-sk~Y~~M~DQQLA~~LS~~gGiGLA   78 (392)
T PRK12711         14 TKADPAKIDKVSRQLEGQFAQMLVKSMRDASSGDPMFPGE-NQMFREMYDQQMAKALTDGKGLGLS   78 (392)
T ss_pred             CCCCHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCHH-HHHHHHHHHHHHHHHHHCCCCCCHH
T ss_conf             3299899999999999999999999997178889998624-4788889999999998658997199


No 8  
>PRK12790 chemotactic signal-response protein CheL; Provisional
Probab=99.83  E-value=1e-20  Score=133.46  Aligned_cols=68  Identities=9%  Similarity=0.243  Sum_probs=62.1

Q ss_pred             HCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCC-CCCCCHHHHHHHHHHHHHHHHHHHCCCCCCC
Q ss_conf             7022855479999999999999999999951021123-3575333689999999999999980798756
Q gi|254780509|r   39 QEACDKSKSVPEMTQKLQGIMFQYFIKSILPEETVKS-LGGGFNGDFWQEILAENISDVIVKQQRITLD  106 (112)
Q Consensus        39 ~~~~~~~~~l~~~a~~fEa~fl~~~lksmr~~~~~~~-lggg~a~d~~~sMl~ee~a~~iAk~ggiGL~  106 (112)
                      +..+++.+.+|++|++|||+||++||++||.+...++ ||+|.++++|||||++|||+.|||+|||||-
T Consensus        31 kv~p~~~ak~k~tAqdFEA~FLn~Ml~~M~~gl~~dGpfG~g~ge~iwRSML~eeyak~iAkaGGIGIA   99 (115)
T PRK12790         31 KVSPQAQAKAKATATDFEAMFLNSMFSQMTSGLKGEGPFGDTVGTGVWRSMLTEQYSKSFAKAGGVGIS   99 (115)
T ss_pred             HCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHCCCCCHH
T ss_conf             279367899999999999999999999998237778887898426689999999999999873886479


No 9  
>COG3951 Rod binding protein [Cell envelope biogenesis, outer membrane / Cell motility and secretion / Posttranslational modification, protein turnover, chaperones]
Probab=99.82  E-value=2.4e-20  Score=131.49  Aligned_cols=81  Identities=15%  Similarity=0.272  Sum_probs=73.6

Q ss_pred             HHHHHCCHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCC--CCCCCHHHHHHHHHHHHHHHHHHHCCC
Q ss_conf             323120789999987022855479999999999999999999951021123--357533368999999999999998079
Q gi|254780509|r   25 DDSSFQSFLQLKDVQEACDKSKSVPEMTQKLQGIMFQYFIKSILPEETVKS--LGGGFNGDFWQEILAENISDVIVKQQR  102 (112)
Q Consensus        25 ~~~s~q~~~~Lk~~~~~~~~~~~l~~~a~~fEa~fl~~~lksmr~~~~~~~--lggg~a~d~~~sMl~ee~a~~iAk~gg  102 (112)
                      .....+.++.|+. .+..++.++|+.||+|||++|+++||||||++.++.+  ++.+..+++|++||||++|.++++++|
T Consensus         9 ~~~daq~l~~lk~-~a~~d~~~~l~~~ArqfE~vFv~mMLKSMR~Al~~~~~dl~~S~q~rlY~dmyDqqlaqqlss~~g   87 (166)
T COG3951           9 SAWDAQSLNELKQ-GARRDPAANLRQVARQFEGVFVQMMLKSMREALPKDGADLFNSQQTRLYTDMYDQQLAQQLSSQKG   87 (166)
T ss_pred             HHHHHHHHHHHHH-HHCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCHHCCCHHHHHHHHHHHHHHHHHHHHCCC
T ss_conf             7999987788764-110181778999999999999999999999872530300104226889999999999999972588


Q ss_pred             CCCC
Q ss_conf             8756
Q gi|254780509|r  103 ITLD  106 (112)
Q Consensus       103 iGL~  106 (112)
                      |||-
T Consensus        88 ~GLA   91 (166)
T COG3951          88 LGLA   91 (166)
T ss_pred             CCHH
T ss_conf             5489


No 10 
>PRK12708 flgJ peptidoglycan hydrolase; Reviewed
Probab=99.77  E-value=5.8e-19  Score=123.90  Aligned_cols=82  Identities=11%  Similarity=0.161  Sum_probs=70.6

Q ss_pred             HHHHHCCHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHCC----CCCCCCCCCHHHHHHHHHHHHHHHHHHHC
Q ss_conf             32312078999998702285547999999999999999999995102----11233575333689999999999999980
Q gi|254780509|r   25 DDSSFQSFLQLKDVQEACDKSKSVPEMTQKLQGIMFQYFIKSILPEE----TVKSLGGGFNGDFWQEILAENISDVIVKQ  100 (112)
Q Consensus        25 ~~~s~q~~~~Lk~~~~~~~~~~~l~~~a~~fEa~fl~~~lksmr~~~----~~~~lggg~a~d~~~sMl~ee~a~~iAk~  100 (112)
                      +.+.|.......++........+|++||+|||++|+|+|||+||.+.    .++..+.+...++||+|+|+|+|..||++
T Consensus         5 ~~~~yl~~~~~~~l~k~n~e~~al~~va~QFE~~F~q~mlksMR~A~dal~~eD~p~nS~~~~~YrdM~DqQLA~~LS~~   84 (134)
T PRK12708          5 NSSPYLPGLNAGDLIPQNLEQGALKLAAQQFEAQFLQTVLKQMRSASDVMADEDDPFNSKNQGMYRDFYDAELASRLSSQ   84 (134)
T ss_pred             CCCCHHCCCCHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCHHHHHHHHHHHHHHHHHHHHC
T ss_conf             77520102777778660453779999999999999999999999865430456885430578899999999999999866


Q ss_pred             CCCCCC
Q ss_conf             798756
Q gi|254780509|r  101 QRITLD  106 (112)
Q Consensus       101 ggiGL~  106 (112)
                      ||+||-
T Consensus        85 gg~GLA   90 (134)
T PRK12708         85 RSMGLA   90 (134)
T ss_pred             CCCCHH
T ss_conf             896499


No 11 
>pfam10135 Rod-binding Rod binding protein. Members of this family are involved in the assembly of the prokaryotic flagellar rod.
Probab=99.00  E-value=2.2e-10  Score=77.04  Aligned_cols=42  Identities=24%  Similarity=0.394  Sum_probs=37.1

Q ss_pred             HHHHHCCCCCCCC-CCCHHHHHHHHHHHHHHHHHHHCCCCCCC
Q ss_conf             9995102112335-75333689999999999999980798756
Q gi|254780509|r   65 KSILPEETVKSLG-GGFNGDFWQEILAENISDVIVKQQRITLD  106 (112)
Q Consensus        65 ksmr~~~~~~~lg-gg~a~d~~~sMl~ee~a~~iAk~ggiGL~  106 (112)
                      |+||++.++++++ +++++++|++|||+|+|+.||++|||||-
T Consensus         1 ksMr~t~~~~~~~~~~~~~~~~~~m~d~q~a~~~a~~ggiGLA   43 (49)
T pfam10135         1 KSMRKAVPKDGLFGSGFAEDMFRSMLDQQLAKQLAKRGGIGLA   43 (49)
T ss_pred             CCHHHCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHCCCCCHH
T ss_conf             9455358776887885399999999999999999876998699


No 12 
>TIGR01371 met_syn_B12ind 5-methyltetrahydropteroyltriglutamate--homocysteine S-methyltransferase; InterPro: IPR006276   This group represents cobalamin-independent methionine synthase. A family of uncharacterised archaeal proteins having substantial homology to the C-terminal region of this family, are not included in this group, though they are contained in a larger family of vitamin-B12 independent methionine synthase.; GO: 0003871 5-methyltetrahydropteroyltriglutamate-homocysteine S-methyltransferase activity, 0009086 methionine biosynthetic process.
Probab=51.01  E-value=18  Score=17.44  Aligned_cols=30  Identities=27%  Similarity=0.510  Sum_probs=27.6

Q ss_pred             CCCHHHHHHHHHHHHHHHHHHHCCCCCCCC
Q ss_conf             753336899999999999999807987564
Q gi|254780509|r   78 GGFNGDFWQEILAENISDVIVKQQRITLDL  107 (112)
Q Consensus        78 gg~a~d~~~sMl~ee~a~~iAk~ggiGL~~  107 (112)
                      |.-.++-|+..+-+|+.+.|..|.-||||.
T Consensus       473 g~iS~e~Ye~~~k~eI~~~I~~QEelGLDV  502 (778)
T TIGR01371       473 GEISEEEYEKFIKEEIKKVIKIQEELGLDV  502 (778)
T ss_pred             CCCCHHHHHHHHHHHHHHHHHHHHHCCCCE
T ss_conf             587789999999988999998742327860


No 13 
>PRK05222 5-methyltetrahydropteroyltriglutamate--homocysteine S-methyltransferase; Provisional
Probab=43.55  E-value=24  Score=16.83  Aligned_cols=31  Identities=23%  Similarity=0.444  Sum_probs=27.4

Q ss_pred             CCCHHHHHHHHHHHHHHHHHHHCCCCCCCCH
Q ss_conf             7533368999999999999998079875640
Q gi|254780509|r   78 GGFNGDFWQEILAENISDVIVKQQRITLDLP  108 (112)
Q Consensus        78 gg~a~d~~~sMl~ee~a~~iAk~ggiGL~~~  108 (112)
                      |-...+-|+.++.++++..|..|..||||.-
T Consensus       450 G~is~~~Y~~~i~~~I~~~I~~QE~igLDVL  480 (756)
T PRK05222        450 GELSAEEYEAFIKEEIARAIRLQEELGLDVL  480 (756)
T ss_pred             CCCCHHHHHHHHHHHHHHHHHHHHHCCCCEE
T ss_conf             9989999999999999999999997299777


No 14 
>TIGR02506 NrdE_NrdA ribonucleoside-diphosphate reductase, alpha subunit; InterPro: IPR013346    This entry represents the alpha (large) chain of the class I ribonucleotide reductase (RNR). RNR's are responsible for the conversion of the ribose sugar of RNA into the deoxyribose sugar of DNA. This is the rate-limiting step of DNA biosynthesis. Class I RNR's generate the required radical (on tyrosine) via a "non-heme" iron cofactor which resides in the beta (small) subunit. The alpha subunit contains the catalytic and allosteric regulatory sites. The mechanism of this enzyme requires molecular oxygen . E. coli contains two versions of this enzyme which are regulated independently (NrdAB and NrdEF, where NrdA and NrdE are the large chains , ). Most organisms contain only one, but the application of the gene symbols NrdA and NrdE are somewhat arbitrary. This model identifies RNR's in diverse clades of bacteria, eukaryotes as well as numerous DNA viruses and phage.; GO: 0005971 ribonucleoside-diphosphate reductase complex.
Probab=32.47  E-value=25  Score=16.64  Aligned_cols=20  Identities=15%  Similarity=0.391  Sum_probs=10.1

Q ss_pred             HHHHHHHHHCCCCCCCCHHH
Q ss_conf             99999999807987564010
Q gi|254780509|r   91 ENISDVIVKQQRITLDLPEI  110 (112)
Q Consensus        91 ee~a~~iAk~ggiGL~~~~~  110 (112)
                      .+.++.++.+||||+++-++
T Consensus       100 ~~~~~l~~~~GGiG~~~~~~  119 (685)
T TIGR02506       100 DDVAQLSKHGGGIGLNLSKL  119 (685)
T ss_pred             HHHHHHHHCCCCEEEECCCC
T ss_conf             99999986179768642340


No 15 
>COG0307 RibC Riboflavin synthase alpha chain [Coenzyme metabolism]
Probab=23.01  E-value=5.6  Score=20.24  Aligned_cols=29  Identities=28%  Similarity=0.461  Sum_probs=24.8

Q ss_pred             CCHHHHHHHHHHHHHHHHHHHCCCCCCCC
Q ss_conf             53336899999999999999807987564
Q gi|254780509|r   79 GFNGDFWQEILAENISDVIVKQQRITLDL  107 (112)
Q Consensus        79 g~a~d~~~sMl~ee~a~~iAk~ggiGL~~  107 (112)
                      +.+-++|..+..+++++-|+.+|+|++|=
T Consensus       113 ~na~~~~~~~~~~~l~kyiv~KGsIavDG  141 (204)
T COG0307         113 GNAVRFWFKAPPEELAKYIVEKGSIAVDG  141 (204)
T ss_pred             CCEEEEEEECCCHHHHHHHCCCCEEEEEE
T ss_conf             87099999759989985520464499831


No 16 
>PRK00448 polC DNA polymerase III PolC; Validated
Probab=20.17  E-value=34  Score=15.97  Aligned_cols=37  Identities=11%  Similarity=0.230  Sum_probs=27.4

Q ss_pred             HHHHHHHHHHHHHHHHHCCCCCCC---CCCCHHHHHHHHH
Q ss_conf             999999999999999510211233---5753336899999
Q gi|254780509|r   53 QKLQGIMFQYFIKSILPEETVKSL---GGGFNGDFWQEIL   89 (112)
Q Consensus        53 ~~fEa~fl~~~lksmr~~~~~~~l---ggg~a~d~~~sMl   89 (112)
                      -+|+.-|+++||+.++|+...+..   |=++++|+|..+-
T Consensus      1147 pEFgT~fvR~mL~~~kP~~F~DLi~IsgLsHGtdVwl~Na 1186 (1436)
T PRK00448       1147 PEFGTKFVRQMLEETKPKTFAELVQISGLSHGTDVWLGNA 1186 (1436)
T ss_pred             CCCCCHHHHHHHHHCCCCCHHHHHHHHHCCCCCCCCCCCH
T ss_conf             4346588999999769997999999970457864443357


Done!