Query         gi|254780194|ref|YP_003064607.1| 50S ribosomal protein L31 [Candidatus Liberibacter asiaticus str. psy62]
Match_columns 74
No_of_seqs    107 out of 844
Neff          5.1 
Searched_HMMs 39220
Date          Mon May 23 10:39:34 2011
Command       /home/congqian_1/programs/hhpred/hhsearch -i 254780194.hhm -d /home/congqian_1/database/cdd/Cdd.hhm 

 No Hit                             Prob E-value P-value  Score    SS Cols Query HMM  Template HMM
  1 PRK00528 rpmE 50S ribosomal pr 100.0 2.2E-31 5.7E-36  207.1   9.4   71    1-71      1-71  (71)
  2 PRK01678 rpmE2 50S ribosomal p 100.0 1.3E-30 3.2E-35  202.7   7.9   73    1-74      1-83  (86)
  3 PRK00019 rpmE 50S ribosomal pr 100.0 2.7E-29   7E-34  194.8   8.5   70    1-74      1-70  (71)
  4 COG0254 RpmE Ribosomal protein  99.9 7.1E-28 1.8E-32  186.4   8.5   70    1-73      1-72  (75)
  5 pfam01197 Ribosomal_L31 Riboso  99.9 1.2E-27 2.9E-32  185.2   8.7   67    1-70      1-68  (69)
  6 TIGR00105 L31 ribosomal protei  99.9   5E-27 1.3E-31  181.4   5.9   67    1-70      2-69  (77)
  7 PRK01397 50S ribosomal protein  99.9 2.8E-26   7E-31  177.0   8.1   71    1-74      1-72  (78)
  8 CHL00136 rpl31 ribosomal prote  99.9 3.3E-26 8.5E-31  176.5   7.3   67    1-72      2-69  (72)
  9 PRK03564 formate dehydrogenase  67.1     3.2 8.2E-05   22.9   1.6   52    8-62    221-274 (307)
 10 pfam04216 FdhE Protein involve  59.1     5.4 0.00014   21.5   1.6   38    8-45    200-239 (283)
 11 TIGR03442 conserved hypothetic  58.8       5 0.00013   21.8   1.4   25   40-66    100-124 (251)
 12 TIGR01393 lepA GTP-binding pro  54.6     4.5 0.00011   22.0   0.6   47    1-55    518-568 (598)
 13 TIGR01562 FdhE formate dehydro  51.0      13 0.00033   19.3   2.5   47    8-55    223-280 (312)
 14 cd01908 YafJ Glutamine amidotr  33.9      23 0.00058   17.9   1.5   25   40-66     97-121 (257)
 15 COG0121 Predicted glutamine am  31.5      17 0.00043   18.6   0.5   25   41-66     88-115 (252)
 16 KOG4584 consensus               27.0      25 0.00063   17.7   0.7   37   35-71     29-69  (348)
 17 COG2139 RPL21A Ribosomal prote  25.5      64  0.0016   15.2   3.4   31   30-61     34-70  (98)
 18 TIGR01246 dapE_proteo succinyl  24.4      28 0.00071   17.3   0.6   43   30-73    284-330 (383)
 19 pfam00845 Gemini_BL1 Geminivir  22.8      23 0.00058   17.9  -0.1   35   17-53    192-226 (276)

No 1  
>PRK00528 rpmE 50S ribosomal protein L31; Reviewed
Probab=99.97  E-value=2.2e-31  Score=207.14  Aligned_cols=71  Identities=63%  Similarity=1.091  Sum_probs=68.0

Q ss_pred             CCCCCCCCCEEEEEEECCCCEEEEEEEECCCCCEEEEEECCCCCCCEECCCEEEEECCCHHHHHHHHHHCC
Q ss_conf             98878898407999987999799887654768869998548778971168178972136489999776026
Q gi|254780194|r    1 MKKNIHPETHLITVVMTDGTQYQTRSTWKEEGAVMKLDIDPLSHFAWIGGRQKITDRGGQVSRFKKRFAGL   71 (74)
Q Consensus         1 MKk~IHP~y~~v~v~~t~g~~~~t~sT~g~~~~~~~vdi~s~~HP~fytgkq~~~dt~GrveKF~kkfg~~   71 (74)
                      |||||||+|++++++|+||++|+|+||+|+++|+|+|||||+|||||++|+|+++|++|||||||+|||+|
T Consensus         1 MKk~IHP~y~~~~v~~~~G~~~~t~st~G~~~~~i~vdi~s~~HPfyTgG~q~~~dt~GRV~kF~kryg~l   71 (71)
T PRK00528          1 MKKDIHPDYHPIKVVMTDGTEYETRSTWGKEGPELRLDIDSGNHPAWTGGTQKILDTGGRVAKFKKKFGGL   71 (71)
T ss_pred             CCCCCCCCCEEEEEEECCCCEEEEEEECCCCCCEEEEEECCCCCCCEECCCEEEECCCCCHHHHHHHHCCC
T ss_conf             98987999887899994999999867678778859998679888768589248971665699998770699


No 2  
>PRK01678 rpmE2 50S ribosomal protein L31 type B; Reviewed
Probab=99.97  E-value=1.3e-30  Score=202.70  Aligned_cols=73  Identities=33%  Similarity=0.549  Sum_probs=68.9

Q ss_pred             CCCCCCCCCEEEEEE-ECCCCEEEEEEEE---------CCCCCEEEEEECCCCCCCEECCCEEEEECCCHHHHHHHHHHC
Q ss_conf             988788984079999-8799979988765---------476886999854877897116817897213648999977602
Q gi|254780194|r    1 MKKNIHPETHLITVV-MTDGTQYQTRSTW---------KEEGAVMKLDIDPLSHFAWIGGRQKITDRGGQVSRFKKRFAG   70 (74)
Q Consensus         1 MKk~IHP~y~~v~v~-~t~g~~~~t~sT~---------g~~~~~~~vdi~s~~HP~fytgkq~~~dt~GrveKF~kkfg~   70 (74)
                      ||+||||+|++|+|. |+||++|.++||+         |++||++.|||||+||| ||||+|+++|++|||||||+|||+
T Consensus         1 MKk~IHP~Y~~v~f~d~s~g~~f~~~ST~~~~~t~~~eG~~yP~~~vdi~S~~HP-FyTG~qk~vdt~GRVekF~kRy~~   79 (86)
T PRK01678          1 MKKGIHPEYRPVVFHDTSTGFKFLTGSTITTDETIEWEGKTYPLVKVEVSSASHP-FYTGKQKFVDTEGRVEKFNKRFGR   79 (86)
T ss_pred             CCCCCCCCCEEEEEEECCCCCEEEECCCCCCCCEEEECCEECCEEEEEECCCCCC-CEECCEEEEECCHHHHHHHHHHHH
T ss_conf             9898799980688898879999982754367840667786777698610688885-481876786143129999988731


Q ss_pred             CCCC
Q ss_conf             6789
Q gi|254780194|r   71 LSIE   74 (74)
Q Consensus        71 ~~~k   74 (74)
                      +..+
T Consensus        80 ~~~~   83 (86)
T PRK01678         80 FASK   83 (86)
T ss_pred             HCCC
T ss_conf             0223


No 3  
>PRK00019 rpmE 50S ribosomal protein L31; Reviewed
Probab=99.96  E-value=2.7e-29  Score=194.78  Aligned_cols=70  Identities=40%  Similarity=0.656  Sum_probs=66.1

Q ss_pred             CCCCCCCCCEEEEEEECCCCEEEEEEEECCCCCEEEEEECCCCCCCEECCCEEEEECCCHHHHHHHHHHCCCCC
Q ss_conf             98878898407999987999799887654768869998548778971168178972136489999776026789
Q gi|254780194|r    1 MKKNIHPETHLITVVMTDGTQYQTRSTWKEEGAVMKLDIDPLSHFAWIGGRQKITDRGGQVSRFKKRFAGLSIE   74 (74)
Q Consensus         1 MKk~IHP~y~~v~v~~t~g~~~~t~sT~g~~~~~~~vdi~s~~HP~fytgkq~~~dt~GrveKF~kkfg~~~~k   74 (74)
                      ||++|||+|++++|.|+||++|.++||++.+   +.|||||+||| ||||+|+++|++|||||||+|||.++.+
T Consensus         1 MKk~IHP~y~~v~~~cscg~~f~~~ST~~~~---~~vdi~s~~HP-FyTG~q~~~dt~GRVekF~kry~~~~~~   70 (71)
T PRK00019          1 MKKDIHPKYEEVTVTCSCGNVFKTRSTKGKD---INIDVCSKCHP-FYTGKQKIVDTGGRVERFNKRFGKPGAK   70 (71)
T ss_pred             CCCCCCCCCEEEEEEECCCCEEEECCCCCCC---EEEEECCCCCC-CEECCEEEEECCCCHHHHHHHHCCCCCC
T ss_conf             9887799988899998889989851324753---88887689876-1848777871467699999877023468


No 4  
>COG0254 RpmE Ribosomal protein L31 [Translation, ribosomal structure and biogenesis]
Probab=99.95  E-value=7.1e-28  Score=186.41  Aligned_cols=70  Identities=40%  Similarity=0.645  Sum_probs=65.3

Q ss_pred             CCCCCCCCC-EEEEEEEC-CCCEEEEEEEECCCCCEEEEEECCCCCCCEECCCEEEEECCCHHHHHHHHHHCCCC
Q ss_conf             988788984-07999987-99979988765476886999854877897116817897213648999977602678
Q gi|254780194|r    1 MKKNIHPET-HLITVVMT-DGTQYQTRSTWKEEGAVMKLDIDPLSHFAWIGGRQKITDRGGQVSRFKKRFAGLSI   73 (74)
Q Consensus         1 MKk~IHP~y-~~v~v~~t-~g~~~~t~sT~g~~~~~~~vdi~s~~HP~fytgkq~~~dt~GrveKF~kkfg~~~~   73 (74)
                      ||+||||+| ++++|.|+ ||+.|.|+||++.+  +|.|||||+||| ||||+|+++|++|||||||+|||.+..
T Consensus         1 MKk~IHP~y~~~v~~~~~s~g~~f~~~ST~~~~--~i~vdV~s~~HP-FyTG~qk~~d~~GRv~kF~kRf~~~~~   72 (75)
T COG0254           1 MKKDIHPEYYRPVVFVCSSCGNEFTTRSTKGTD--EINLDVCSKCHP-FYTGKQKIVDTEGRVEKFNKRFGGFKG   72 (75)
T ss_pred             CCCCCCCCCCCEEEEEECCCCCEEEEEECCCCC--EEEEEECCCCCC-CCCCCEEEECCCCCHHHHHHHHCCCCC
T ss_conf             988769876324899967899789977516886--089986799877-693854576065539999877634344


No 5  
>pfam01197 Ribosomal_L31 Ribosomal protein L31.
Probab=99.95  E-value=1.2e-27  Score=185.18  Aligned_cols=67  Identities=40%  Similarity=0.625  Sum_probs=63.3

Q ss_pred             CCCCCCCCCEEEEEEEC-CCCEEEEEEEECCCCCEEEEEECCCCCCCEECCCEEEEECCCHHHHHHHHHHC
Q ss_conf             98878898407999987-99979988765476886999854877897116817897213648999977602
Q gi|254780194|r    1 MKKNIHPETHLITVVMT-DGTQYQTRSTWKEEGAVMKLDIDPLSHFAWIGGRQKITDRGGQVSRFKKRFAG   70 (74)
Q Consensus         1 MKk~IHP~y~~v~v~~t-~g~~~~t~sT~g~~~~~~~vdi~s~~HP~fytgkq~~~dt~GrveKF~kkfg~   70 (74)
                      ||+||||+|++++|.|+ ||++|.|+||.  ++|++.|||||+||| ||||+|+++|++|||||||+||+.
T Consensus         1 MKk~IHP~y~~v~~~c~~cg~~f~t~ST~--~~~~i~vdi~s~cHP-fyTG~~~~~dt~GRVeKF~kkf~~   68 (69)
T pfam01197         1 MKKGIHPEYREVVFTCSSCGNVFVTRSTK--EYPVIKIDVCSACHP-FYTGKQKLVDTAGRVEKFNKRFGK   68 (69)
T ss_pred             CCCCCCCCCEEEEEEECCCCCEEEEEECC--CCCCEEEEECCCCCC-EECCCEEEECCCHHHHHHHHHHCC
T ss_conf             98877998735689999999799973703--586099986489888-481987885142359999888746


No 6  
>TIGR00105 L31 ribosomal protein L31; InterPro: IPR002150   Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites , . About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits.    Many of ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome , .   Ribosomal protein L31 is one of the proteins from the large ribosomal subunit. L31 is a protein of 66 to 97 amino-acid residues which has only been found so far in bacteria and in some plant and algal chloroplasts.; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome.
Probab=99.94  E-value=5e-27  Score=181.42  Aligned_cols=67  Identities=37%  Similarity=0.561  Sum_probs=63.2

Q ss_pred             CCCCCCCCCEEEEEEEC-CCCEEEEEEEECCCCCEEEEEECCCCCCCEECCCEEEEECCCHHHHHHHHHHC
Q ss_conf             98878898407999987-99979988765476886999854877897116817897213648999977602
Q gi|254780194|r    1 MKKNIHPETHLITVVMT-DGTQYQTRSTWKEEGAVMKLDIDPLSHFAWIGGRQKITDRGGQVSRFKKRFAG   70 (74)
Q Consensus         1 MKk~IHP~y~~v~v~~t-~g~~~~t~sT~g~~~~~~~vdi~s~~HP~fytgkq~~~dt~GrveKF~kkfg~   70 (74)
                      ||+||||+|.++...|+ |++.+.++||.++  ++|.|||||.||| ||||+|+++|++||||||++||+-
T Consensus         2 MK~~IHP~y~~~~~~~~~C~~~~~~~s~~~k--~e~~~dics~CHP-FYtG~~~~~~t~GRVerf~~kf~~   69 (77)
T TIGR00105         2 MKKGIHPEYQEIPAACVSCNNGFEIESTSTK--KEINIDICSKCHP-FYTGKQKIVDTGGRVERFNKKFNL   69 (77)
T ss_pred             CCCCCCCCCCCEECEEEEECCCEEEEECCCC--CEEEEEECCCCCC-CEECCEEEEECCCCHHHHHHHCCC
T ss_conf             8887898953010106662597787552777--3146886489889-420440367426641311213288


No 7  
>PRK01397 50S ribosomal protein L31; Provisional
Probab=99.93  E-value=2.8e-26  Score=177.01  Aligned_cols=71  Identities=32%  Similarity=0.519  Sum_probs=67.0

Q ss_pred             CCCCCCCCCEEEEEEECCCCEEEEEEEECCCCCEEEEEECCCCCCCEECCCEEEEECCCH-HHHHHHHHHCCCCC
Q ss_conf             988788984079999879997998876547688699985487789711681789721364-89999776026789
Q gi|254780194|r    1 MKKNIHPETHLITVVMTDGTQYQTRSTWKEEGAVMKLDIDPLSHFAWIGGRQKITDRGGQ-VSRFKKRFAGLSIE   74 (74)
Q Consensus         1 MKk~IHP~y~~v~v~~t~g~~~~t~sT~g~~~~~~~vdi~s~~HP~fytgkq~~~dt~Gr-veKF~kkfg~~~~k   74 (74)
                      ||++|||+|+.|+|.|+ |++|+|+||+  +++++.||||+.|||||++|.++++|+.|| |+||||||+||++.
T Consensus         1 MKkdIHPdYh~I~V~~~-G~~f~trST~--~gd~l~LDIDp~~HPAWTGg~~~lld~ggrqVskFnKrf~gL~f~   72 (78)
T PRK01397          1 MKSGIHPEYKKFLIKVG-SDVFETMSTH--PTGEILMDVDFRKHPAWNKDSGNVVNQSNKSVSDFNKRFSGLSFG   72 (78)
T ss_pred             CCCCCCCCCEEEEEEEC-CCEEEEEECC--CCCEEEEECCCCCCCCEECCCCEEEECCCCCHHHHHHHCCCCCCC
T ss_conf             98776888748999968-9778876024--797689823898887446786267806896547754013566657


No 8  
>CHL00136 rpl31 ribosomal protein L31; Validated
Probab=99.93  E-value=3.3e-26  Score=176.54  Aligned_cols=67  Identities=33%  Similarity=0.356  Sum_probs=57.7

Q ss_pred             CCCCCCCCCEE-EEEEECCCCEEEEEEEECCCCCEEEEEECCCCCCCEECCCEEEEECCCHHHHHHHHHHCCC
Q ss_conf             98878898407-9999879997998876547688699985487789711681789721364899997760267
Q gi|254780194|r    1 MKKNIHPETHL-ITVVMTDGTQYQTRSTWKEEGAVMKLDIDPLSHFAWIGGRQKITDRGGQVSRFKKRFAGLS   72 (74)
Q Consensus         1 MKk~IHP~y~~-v~v~~t~g~~~~t~sT~g~~~~~~~vdi~s~~HP~fytgkq~~~dt~GrveKF~kkfg~~~   72 (74)
                      ||+||||+|++ +.+.|+||+.+.+.||    +++++|||||+||| ||||+|+++|++||||||++|||--+
T Consensus         2 ~Kk~IHP~y~~~~~v~c~g~~~~~~~st----~~~~~vdIcS~cHP-FyTG~Qr~vdt~GRVekF~kryg~~~   69 (72)
T CHL00136          2 PKKNIHPTWYPDAKVYCDGQLVMTIGST----KPELHVDIWSGNHP-FYTGSQKIIDTEGRVERFMRKYGLNS   69 (72)
T ss_pred             CCCCCCCCCEEEEEEECCCCCEEEECCC----CCCEEEEECCCCCC-CCCCCEEEEECCCCHHHHHHHHCCCC
T ss_conf             8887898763148999389858986655----77589888689988-58487678714756999977547876


No 9  
>PRK03564 formate dehydrogenase accessory protein FdhE; Provisional
Probab=67.07  E-value=3.2  Score=22.87  Aligned_cols=52  Identities=13%  Similarity=0.056  Sum_probs=29.5

Q ss_pred             CCEEEEEEEC-CCCEEEEE-EEECCCCCEEEEEECCCCCCCEECCCEEEEECCCHHH
Q ss_conf             8407999987-99979988-7654768869998548778971168178972136489
Q gi|254780194|r    8 ETHLITVVMT-DGTQYQTR-STWKEEGAVMKLDIDPLSHFAWIGGRQKITDRGGQVS   62 (74)
Q Consensus         8 ~y~~v~v~~t-~g~~~~t~-sT~g~~~~~~~vdi~s~~HP~fytgkq~~~dt~Grve   62 (74)
                      +|+-+-+.|+ ||++-.+. .++..+.+-+++|+|..||- | . |.-....++.++
T Consensus       221 eW~~~R~~C~~C~~~~~l~y~~~~~~~~~vrae~C~~C~~-Y-l-K~l~~~kd~~~~  274 (307)
T PRK03564        221 EWHVVRVKCSNCEQSGKLHYWSLDSEQAAVKAESCGDCGT-Y-L-KILYQEKDPKVE  274 (307)
T ss_pred             CCCCCCCCCCCCCCCCCEEEEEECCCCCCEEEEECCCHHH-H-H-HHHHHHCCCCCC
T ss_conf             4021353468888988820366637876467764640665-7-8-787450088888


No 10 
>pfam04216 FdhE Protein involved in formate dehydrogenase formation. The function of these proteins is unknown. They may possibly be involved in the formation of formate dehydrogenase.
Probab=59.11  E-value=5.4  Score=21.55  Aligned_cols=38  Identities=18%  Similarity=0.135  Sum_probs=23.3

Q ss_pred             CCEEEEEEEC-CCCEEEEE-EEECCCCCEEEEEECCCCCC
Q ss_conf             8407999987-99979988-76547688699985487789
Q gi|254780194|r    8 ETHLITVVMT-DGTQYQTR-STWKEEGAVMKLDIDPLSHF   45 (74)
Q Consensus         8 ~y~~v~v~~t-~g~~~~t~-sT~g~~~~~~~vdi~s~~HP   45 (74)
                      +|+-+-+.|+ ||++=... ...-.+.+-+++|+|..||-
T Consensus       200 eW~~~R~~C~~Cg~~~~~~~~~~~~~~~~~r~e~C~~C~~  239 (283)
T pfam04216       200 EWHFVRVKCTNCGSTKGLAYWSLEEGEPGVRAETCDTCHS  239 (283)
T ss_pred             CCCCCCCCCCCCCCCCCCCEEEECCCCCCEEEEECCCCCC
T ss_conf             3242265479999999643033316887666640563110


No 11 
>TIGR03442 conserved hypothetical protein TIGR03442. Members of this strictly bacterial protein family show similarity to class II glutamine amidotransferases (see pfam00310). They are distinguished by appearing in a genome context with, and usually adjacent to or between, members of families TIGR03438 (an uncharacterized methyltransferase) and TIGR03440 (an uncharacterized protein).
Probab=58.79  E-value=5  Score=21.75  Aligned_cols=25  Identities=20%  Similarity=0.380  Sum_probs=18.0

Q ss_pred             CCCCCCCEECCCEEEEECCCHHHHHHH
Q ss_conf             487789711681789721364899997
Q gi|254780194|r   40 DPLSHFAWIGGRQKITDRGGQVSRFKK   66 (74)
Q Consensus        40 ~s~~HP~fytgkq~~~dt~GrveKF~k   66 (74)
                      -++||| |.-|+--++-. |.|+.|.+
T Consensus       100 ~~NcHP-F~~g~~lF~HN-G~I~~f~~  124 (251)
T TIGR03442       100 ESACAP-FSDGRWLFSHN-GFVDNFRQ  124 (251)
T ss_pred             CCCCCC-CEECCEEEEEC-CCCCCHHH
T ss_conf             234788-33577899947-72377458


No 12 
>TIGR01393 lepA GTP-binding protein LepA; InterPro: IPR006297   LepA (GUF1 in Saccaromyces) is a GTP-binding membrane protein related to EF-G and EF-Tu. Two types of phylogenetic tree, rooted by other GTP-binding proteins, suggest that eukaryotic homologs (including GUF1 of yeast) originated within the bacterial LepA family. The function of the proteins in this family are unknown. ; GO: 0005525 GTP binding.
Probab=54.58  E-value=4.5  Score=22.04  Aligned_cols=47  Identities=23%  Similarity=0.367  Sum_probs=40.2

Q ss_pred             CCCCCCCCCEEEEEEECCCCEEEEEEEECCCCCEEEEEECCCCCCCEECC----CEEEE
Q ss_conf             98878898407999987999799887654768869998548778971168----17897
Q gi|254780194|r    1 MKKNIHPETHLITVVMTDGTQYQTRSTWKEEGAVMKLDIDPLSHFAWIGG----RQKIT   55 (74)
Q Consensus         1 MKk~IHP~y~~v~v~~t~g~~~~t~sT~g~~~~~~~vdi~s~~HP~fytg----kq~~~   55 (74)
                      ||.=|+++..+|.+.-+=|+...-|+|+..    ++=||.++|    |||    |++++
T Consensus       518 LKE~IPRQqF~ipIQA~IG~KIIARETiKa----~RKdVtAKC----YGGDiTRKrKLL  568 (598)
T TIGR01393       518 LKELIPRQQFEIPIQAAIGGKIIARETIKA----LRKDVTAKC----YGGDITRKRKLL  568 (598)
T ss_pred             HHHCCCCCCCCCCHHEECCCEEEEECCCCC----CCCCEEEEE----CCCCCCHHHHHH
T ss_conf             662286346664110221880687503541----225502352----087704324545


No 13 
>TIGR01562 FdhE formate dehydrogenase accessory protein FdhE; InterPro: IPR006452   This family of sequences describe an accessory protein required for the assembly of formate dehydrogenase of certain proteobacteria although not present in the final complex . The exact nature of the function of FdhE in the assembly of the complex is unknown, but considering the presence of selenocysteine, molybdopterin, iron-sulphur clusters and cytochrome b556, it is likely to be involved in the insertion of cofactors. .
Probab=50.96  E-value=13  Score=19.27  Aligned_cols=47  Identities=17%  Similarity=0.136  Sum_probs=31.4

Q ss_pred             CCEEEEEEEC-CCCE----EEEEEEEC--CCCCEEEEEECCCCCCCE----ECCCEEEE
Q ss_conf             8407999987-9997----99887654--768869998548778971----16817897
Q gi|254780194|r    8 ETHLITVVMT-DGTQ----YQTRSTWK--EEGAVMKLDIDPLSHFAW----IGGRQKIT   55 (74)
Q Consensus         8 ~y~~v~v~~t-~g~~----~~t~sT~g--~~~~~~~vdi~s~~HP~f----ytgkq~~~   55 (74)
                      ++|.|-|.|+ ||++    |....+.+  .|...|+-|+|..|.- |    |-.+.+.+
T Consensus       223 ~Wh~VRvKCs~Ce~sk~l~Y~sle~~~qPaE~A~~kAE~Cd~C~~-ylKilY~ekdp~~  280 (312)
T TIGR01562       223 EWHVVRVKCSACEESKKLAYLSLEDDDQPAEKAVVKAEVCDDCDS-YLKILYQEKDPKL  280 (312)
T ss_pred             CCCEEEEEECCCCCCCCEEEEEECCCCCCHHHHEEECCCCCCCCH-HHHHHHHCCCCCC
T ss_conf             767066665277876760256632787743462330256887115-8888744148852


No 14 
>cd01908 YafJ Glutamine amidotransferases class-II (Gn-AT)_YafJ-type.  YafJ is a glutamine amidotransferase-like protein of unknown function found in prokaryotes, eukaryotes and archaea.  YafJ has a conserved structural fold similar to those of other class II glutamine amidotransferases including lucosamine-fructose 6-phosphate synthase (GLMS or GFAT), glutamine phosphoribosylpyrophosphate (Prpp) amidotransferase (GPATase),  asparagine synthetase B (AsnB), beta lactam synthetase (beta-LS) and glutamate synthase (GltS).  The YafJ fold is also somwhat similar to the Ntn (N-terminal nucleophile) hydrolase fold of the proteasomal alpha and beta subunits.
Probab=33.90  E-value=23  Score=17.85  Aligned_cols=25  Identities=24%  Similarity=0.333  Sum_probs=16.9

Q ss_pred             CCCCCCCEECCCEEEEECCCHHHHHHH
Q ss_conf             487789711681789721364899997
Q gi|254780194|r   40 DPLSHFAWIGGRQKITDRGGQVSRFKK   66 (74)
Q Consensus        40 ~s~~HP~fytgkq~~~dt~GrveKF~k   66 (74)
                      -.+||| |.-|.= +.--.|.|++|..
T Consensus        97 ~~N~HP-F~~~~~-~F~HNG~i~~~~~  121 (257)
T cd01908          97 LENCHP-FTRGRW-LFAHNGQLDGFRL  121 (257)
T ss_pred             CCCCCC-EEECCE-EEEECCCCCCHHH
T ss_conf             356787-266579-9996773478788


No 15 
>COG0121 Predicted glutamine amidotransferase [General function prediction only]
Probab=31.53  E-value=17  Score=18.61  Aligned_cols=25  Identities=20%  Similarity=0.236  Sum_probs=16.2

Q ss_pred             CCCCCCEECCCE---EEEECCCHHHHHHH
Q ss_conf             877897116817---89721364899997
Q gi|254780194|r   41 PLSHFAWIGGRQ---KITDRGGQVSRFKK   66 (74)
Q Consensus        41 s~~HP~fytgkq---~~~dt~GrveKF~k   66 (74)
                      ++||| |+-+.-   -+.--.|.|++|..
T Consensus        88 ~ntHP-F~~~~~~~~~~FaHNG~l~~~~~  115 (252)
T COG0121          88 SNTHP-FTRELWGYIWLFAHNGQLDKFKL  115 (252)
T ss_pred             CCCCC-CCCCCCCCCEEEEECCCCCCCCC
T ss_conf             57898-04157774079985680266541


No 16 
>KOG4584 consensus
Probab=26.99  E-value=25  Score=17.65  Aligned_cols=37  Identities=19%  Similarity=0.358  Sum_probs=20.9

Q ss_pred             EEEEECCCCCCCEEC---CCEE-EEECCCHHHHHHHHHHCC
Q ss_conf             999854877897116---8178-972136489999776026
Q gi|254780194|r   35 MKLDIDPLSHFAWIG---GRQK-ITDRGGQVSRFKKRFAGL   71 (74)
Q Consensus        35 ~~vdi~s~~HP~fyt---gkq~-~~dt~GrveKF~kkfg~~   71 (74)
                      +-+++-+++-|-|.-   ..|. ..|+.-|.|+|.+||.++
T Consensus        29 ~Wi~~f~~~ip~f~krA~asq~~~~DA~~RAe~F~~~y~~~   69 (348)
T KOG4584          29 YWINVFSNSIPSFKKRAEASQENVPDAPARAEKFAQRYAGI   69 (348)
T ss_pred             HHHHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHHHH
T ss_conf             79999987767888888615788985567899999999999


No 17 
>COG2139 RPL21A Ribosomal protein L21E [Translation, ribosomal structure and biogenesis]
Probab=25.47  E-value=64  Score=15.21  Aligned_cols=31  Identities=26%  Similarity=0.487  Sum_probs=20.9

Q ss_pred             CCCCEEEEEECCCC-----CCCEECCC-EEEEECCCHH
Q ss_conf             76886999854877-----89711681-7897213648
Q gi|254780194|r   30 EEGAVMKLDIDPLS-----HFAWIGGR-QKITDRGGQV   61 (74)
Q Consensus        30 ~~~~~~~vdi~s~~-----HP~fytgk-q~~~dt~Grv   61 (74)
                      ++++.+.|+|++.-     ||. |-|+ -.++...||.
T Consensus        34 ~~Gd~V~I~IdpSv~kGmPh~r-f~G~TG~Vvg~~g~a   70 (98)
T COG2139          34 KVGDKVHIDIDPSVHKGMPHPR-FQGKTGTVVGVRGRA   70 (98)
T ss_pred             CCCCEEEEEECCCCCCCCCCCC-CCCCCEEEEECCCCE
T ss_conf             7998799984762026987753-047630798414877


No 18 
>TIGR01246 dapE_proteo succinyl-diaminopimelate desuccinylase; InterPro: IPR005941   The lysine/diaminopimelic acid branch of the aspartate pathway produces the essential amino acid lysine via the intermediate meso-diaminopimelic acid (meso-DAP), which is also a vital cell wall component in Gram-negative bacteria . The production of dihydropicolinate from aspartate-semialdehyde controls flux into the lysine/diaminopimelic acid pathway. Three variants of this pathway exist, differing in how tetrahydropicolinate (formed by reduction of dihydropicolinate) is metabolised to meso-DAP. One variant, the most commonly found one in archaea and bacteria, uses primarily succinyl intermediates, while a second variant, found only in Bacillus, utilises primarily acetyl intermediates. In the third variant, found in some Gram-positive bacteria, a dehydrogenase converts tetrahydropicolinate directly to meso-DAP. In all variants meso-DAP is subsequently converted to lysine by a decarboxylase, or, in Gram-negative bacteria, assimilated into the cell wall. Evidence exists that a fourth, currently unknown, variant of this pathway may function in plants .    Succinyl-diaminopimelate desuccinylase (3.5.1.18 from EC) hydrolyses N-succinyl-L,L-diaminopimelic acid which is required for the bacterial synthesis of lysine and meso-diaminopimelic acid.    This group of bacterial sequences belong to the MEROPS peptidase family M20 (clan MH), subfamily M20A (non-peptidase homologs).  ; GO: 0009014 succinyl-diaminopimelate desuccinylase activity, 0009089 lysine biosynthetic process via diaminopimelate.
Probab=24.45  E-value=28  Score=17.32  Aligned_cols=43  Identities=14%  Similarity=0.131  Sum_probs=32.5

Q ss_pred             CCCCE-EEEEECCCCCCCEECC--CEEEEECCCH-HHHHHHHHHCCCC
Q ss_conf             76886-9998548778971168--1789721364-8999977602678
Q gi|254780194|r   30 EEGAV-MKLDIDPLSHFAWIGG--RQKITDRGGQ-VSRFKKRFAGLSI   73 (74)
Q Consensus        30 ~~~~~-~~vdi~s~~HP~fytg--kq~~~dt~Gr-veKF~kkfg~~~~   73 (74)
                      +||.+ |.|+.....-| |+|.  .-+++++.-. |++|.+.=..++.
T Consensus       284 keY~l~Y~lew~~Sg~p-FlT~P~~g~l~~~~~~~i~~~~~~~P~lsT  330 (383)
T TIGR01246       284 KEYGLDYDLEWSLSGEP-FLTNPIDGKLIDKVREAIEETNGIKPELST  330 (383)
T ss_pred             CCCCCCEEEEECCCCCC-CCCCCCCCHHHHHHHHHHHHHCCCCCCCCC
T ss_conf             00388416987215855-278888763899999999997086755347


No 19 
>pfam00845 Gemini_BL1 Geminivirus BL1 movement protein. Geminiviruses encode two movement proteins that are essential for systemic infection of their host but dispensable for replication and encapsidation.
Probab=22.79  E-value=23  Score=17.87  Aligned_cols=35  Identities=17%  Similarity=0.210  Sum_probs=25.5

Q ss_pred             CCCCEEEEEEEECCCCCEEEEEECCCCCCCEECCCEE
Q ss_conf             7999799887654768869998548778971168178
Q gi|254780194|r   17 TDGTQYQTRSTWKEEGAVMKLDIDPLSHFAWIGGRQK   53 (74)
Q Consensus        17 t~g~~~~t~sT~g~~~~~~~vdi~s~~HP~fytgkq~   53 (74)
                      .-|.++.++||+|.....-.-++....||  |-+-.+
T Consensus       192 ~PGEsWAsrS~IG~~~s~~~~~~~~~~~P--Yr~L~r  226 (276)
T pfam00845       192 QPGETWATRSTIGPSQSETDSEVENAEHP--YRHLHR  226 (276)
T ss_pred             CCCCCCCCCCCCCCCCCCCCCCCCCCCCC--HHHHCC
T ss_conf             89974302212377766566543212363--567535


Done!