Query         gi|254780275|ref|YP_003064688.1| SsrA-binding protein [Candidatus Liberibacter asiaticus str. psy62]
Match_columns 159
No_of_seqs    124 out of 1655
Neff          4.4 
Searched_HMMs 39220
Date          Tue May 24 16:16:04 2011
Command       /home/congqian_1/programs/hhpred/hhsearch -i 254780275.hhm -d /home/congqian_1/database/cdd/Cdd.hhm 

 No Hit                             Prob E-value P-value  Score    SS Cols Query HMM  Template HMM
  1 TIGR00086 smpB SsrA-binding pr 100.0       0       0  473.2  11.4  144   13-156     1-145 (145)
  2 COG0691 SmpB tmRNA-binding pro 100.0       0       0  430.1  11.8  150    9-159     3-152 (153)
  3 PRK05422 smpB SsrA-binding pro 100.0       0       0  420.8  14.9  149   10-159     2-150 (150)
  4 pfam01668 SmpB SmpB protein.   100.0 1.3E-29 3.3E-34  196.8   6.2   67   12-78      1-67  (68)
  5 pfam03293 Pox_RNA_pol Poxvirus  52.4     9.1 0.00023   19.4   1.8   28   45-72    111-139 (160)
  6 TIGR02298 HpaD_Fe 3,4-dihydrox  43.5       9 0.00023   19.5   0.7   17  109-126   186-202 (343)
  7 pfam04661 Pox_I3 Poxvirus I3 s  30.7      46  0.0012   15.2   5.1   67   57-131   135-204 (263)
  8 KOG2963 consensus               28.6      50  0.0013   15.0   3.6   46  109-157   286-336 (405)
  9 COG1710 Uncharacterized protei  28.5      50  0.0013   15.0   5.1   42   94-147    64-105 (139)
 10 pfam03712 Cu2_monoox_C Copper   27.0      46  0.0012   15.2   2.1   39   29-67      1-41  (157)
 11 KOG3995 consensus               25.8      30 0.00075   16.4   0.9   67   17-87     41-110 (279)
 12 KOG3545 consensus               24.8      32 0.00081   16.2   1.0   49   40-89    184-232 (249)
 13 pfam11169 DUF2956 Protein of u  23.3      26 0.00067   16.7   0.3   56   94-158     6-61  (103)

No 1  
>TIGR00086 smpB SsrA-binding protein; InterPro: IPR000037 In bacteria, SsrA RNA recognises ribosomes stalled on defective messages and acts as a tRNA and mRNA to mediate the addition of a short peptide tag to the C-terminus of the partially synthesized nascent polypeptide chain. The SsrA-tagged protein is then degraded by C-terminal-specific proteases.   SmpB, a unique RNA-binding protein that is conserved throughout the bacterial kingdom is an essential component of the SsrA quality-control system. Deletion of the smpB gene in Escherichia coli results in the same phenotypes observed in ssrA-defective cells, including a variety of phage development defects and the failure to tag proteins translated from defective mRNAs. Purified SmpB binds specifically and with high affinity to SsrA RNA and is required for stable association of SsrA with ribosomes in vivo. Formation of an SmpB-SsrA complex appears to be critical in mediating SsrA activity after aminoacylation with alanine but prior to the transpeptidation reaction that couples this alanine to the nascent chain. SsrA RNA is present at wild-type levels in the smpB mutant arguing against a model of SsrA action that involves direct competition for transcription factors .; GO: 0003723 RNA binding, 0006412 translation.
Probab=100.00  E-value=0  Score=473.25  Aligned_cols=144  Identities=50%  Similarity=0.835  Sum_probs=141.7

Q ss_pred             EEEEECCEEEEEEEEEEEECCEEEEEHHHHHHHHCCCEEEEEEEEEECCEEEEEECCCC-CHHCCCCCCCCCHHHHHHHC
Q ss_conf             89841233310257665622417750436667629820011158865660777403037-20002332110001345530
Q gi|254780275|r   13 VVSDNRKARYNYHIVRSFEAGIVLTGTEVKSLRVSKVNISDSYATFENDEIWLTNSYIP-EYLQANRFNHYPRRNRKLLL   91 (159)
Q Consensus        13 ii~~NkkA~~~Y~i~e~~eAGIvL~G~EVKSiR~g~v~l~~sy~~~~~~E~~L~n~~I~-~y~~~~~~~~~p~R~RKLLL   91 (159)
                      +|+.||||+|||||+|+|||||||+||||||||+|+|||+||||.|++||+||.||||+ +|.+|+++||||+|+|||||
T Consensus         1 ~i~~NKKA~fdY~i~~~~EAGivL~G~EVKS~R~g~~sL~dsy~~~~~gE~wL~N~~I~~~y~~g~~~nhdp~R~RKLLL   80 (145)
T TIGR00086         1 LIASNKKAFFDYEILDTIEAGIVLKGSEVKSIRAGKVSLKDSYVIIKKGEVWLKNMHIAPPYKFGNIFNHDPRRTRKLLL   80 (145)
T ss_pred             CCCCCCCEEECEEEEEEEEECEEECCCEEEEEECCCCCCCCCEEEEECCEEEEECCCCCCHHHCCCCCCCCCCCCCHHHC
T ss_conf             95538730115167601320505647045744407888210478983684899636224101148620489887631231


Q ss_pred             CHHHHHHHHHHHHCCCCEEEEEEEEEECCCEEEEEEEEECCCCCCCCHHHHHHHHHHHHHHHHHH
Q ss_conf             38999999986303893399996378079819999987224321100798987278888998876
Q gi|254780275|r   92 SKREIHRLYAAVRRDGMTLVPMKIYFNAKGLAKIDLALAQGKKNYDKRETEKKRDWDRQKHRILR  156 (159)
Q Consensus        92 ~k~EI~kl~~~~~~kG~TiVPlkly~~~~g~~Kv~IalaKGKK~~DKR~~iK~rd~~re~~R~~K  156 (159)
                      ||+||.+|++.+.++|||||||++||+++|+|||+||||||||+|||||+||+|||+||++|+||
T Consensus        81 HK~EI~kL~~~~~~~GlTlVPl~~Yf~~~~~~KveiaLaKGKK~~DKRe~iK~rd~~re~~r~~k  145 (145)
T TIGR00086        81 HKKEIAKLQGKIKEKGLTLVPLKLYFKNKGKVKVEIALAKGKKLHDKRESIKKRDAKRELKRALK  145 (145)
T ss_pred             CHHHHHHHHHHHCCCCCEEEEEEEEEECCCEEEEEEEEECCCCCCCHHHHHHHHHHHHHHHHHCC
T ss_conf             67889999987512684464444556068838999972079866440689999888999999619


No 2  
>COG0691 SmpB tmRNA-binding protein [Posttranslational modification, protein turnover, chaperones]
Probab=100.00  E-value=0  Score=430.06  Aligned_cols=150  Identities=54%  Similarity=0.886  Sum_probs=145.9

Q ss_pred             CCCEEEEEECCEEEEEEEEEEEECCEEEEEHHHHHHHHCCCEEEEEEEEEECCEEEEEECCCCCHHCCCCCCCCCHHHHH
Q ss_conf             98428984123331025766562241775043666762982001115886566077740303720002332110001345
Q gi|254780275|r    9 PPKKVVSDNRKARYNYHIVRSFEAGIVLTGTEVKSLRVSKVNISDSYATFENDEIWLTNSYIPEYLQANRFNHYPRRNRK   88 (159)
Q Consensus         9 ~~~~ii~~NkkA~~~Y~i~e~~eAGIvL~G~EVKSiR~g~v~l~~sy~~~~~~E~~L~n~~I~~y~~~~~~~~~p~R~RK   88 (159)
                      +..++|++||||+|||||+|+|||||||+||||||||+|+|||.||||.+++||+||.||||+||.+++.+||||.|+||
T Consensus         3 ~~~~~ia~NkkA~~dY~I~e~~EAGivL~GtEVKSlRag~~nl~dsy~~i~~gE~~L~n~hI~py~~~~~~nhdp~R~RK   82 (153)
T COG0691           3 MGSKTIAQNKKARHDYFIEETFEAGIVLQGTEVKSLRAGKANLKDSYARIKKGEAWLINAHISPYEAGNRFNHDPRRTRK   82 (153)
T ss_pred             CCCCEECCCCHHHCCEEEEEEEECCEEEEEEEEEEHHCCCCCCCCCEEEEECCEEEEEECCCCHHHHCCCCCCCCCHHHH
T ss_conf             65531000621421200103103206881017624131675711126998688099972624346617845688421666


Q ss_pred             HHCCHHHHHHHHHHHHCCCCEEEEEEEEEECCCEEEEEEEEECCCCCCCCHHHHHHHHHHHHHHHHHHHCC
Q ss_conf             53038999999986303893399996378079819999987224321100798987278888998876449
Q gi|254780275|r   89 LLLSKREIHRLYAAVRRDGMTLVPMKIYFNAKGLAKIDLALAQGKKNYDKRETEKKRDWDRQKHRILREHN  159 (159)
Q Consensus        89 LLL~k~EI~kl~~~~~~kG~TiVPlkly~~~~g~~Kv~IalaKGKK~~DKR~~iK~rd~~re~~R~~K~~n  159 (159)
                      ||||++||.+|.+.++++|||||||++||+ +|||||+||||||||.|||||++|+|||+||++|+||+.+
T Consensus        83 LLLhk~EI~kL~~kv~~~G~TlVpL~lY~k-~g~vKvei~lakGKK~~DKRe~iK~r~~~Re~~r~mk~~~  152 (153)
T COG0691          83 LLLHKREIDKLIGKVEQEGYTLVPLKLYFK-KGKVKVEIGLAKGKKLHDKRETIKERDWKREKARLMKNRR  152 (153)
T ss_pred             HHCCHHHHHHHHHHHHCCCEEEEEEHHHCC-CCEEEEEEEEECCCCHHHHHHHHHHHHHHHHHHHHHHHHC
T ss_conf             610799999999887518748985066410-8757899987047600136788988888899999876413


No 3  
>PRK05422 smpB SsrA-binding protein; Validated
Probab=100.00  E-value=0  Score=420.83  Aligned_cols=149  Identities=54%  Similarity=0.879  Sum_probs=145.4

Q ss_pred             CCEEEEEECCEEEEEEEEEEEECCEEEEEHHHHHHHHCCCEEEEEEEEEECCEEEEEECCCCCHHCCCCCCCCCHHHHHH
Q ss_conf             84289841233310257665622417750436667629820011158865660777403037200023321100013455
Q gi|254780275|r   10 PKKVVSDNRKARYNYHIVRSFEAGIVLTGTEVKSLRVSKVNISDSYATFENDEIWLTNSYIPEYLQANRFNHYPRRNRKL   89 (159)
Q Consensus        10 ~~~ii~~NkkA~~~Y~i~e~~eAGIvL~G~EVKSiR~g~v~l~~sy~~~~~~E~~L~n~~I~~y~~~~~~~~~p~R~RKL   89 (159)
                      +.++|++||+|+|||+|+|+|||||||+||||||||+|+|||+||||.+.+||+||+||||+||.++++++|||+|+|||
T Consensus         2 ~~~~i~~NrkA~~~Y~i~e~~eaGIvL~G~EVKSiR~g~vsl~~sy~~~~~~E~~l~n~~I~~y~~~~~~~~~p~R~RKL   81 (150)
T PRK05422          2 GMKTIAQNKKARHDYFIEETFEAGIVLTGTEVKSLRAGKANLKDSYVLIKNGEAWLINAHISPYEQGNHFNHDPRRTRKL   81 (150)
T ss_pred             CCCEEEECCCCCCCEEEEEEEEEEEEEECCCHHHHHCCCCCCCCCEEEEECCEEEEEEEEEEECCCCCCCCCCCCCCCHH
T ss_conf             97442145743310367377998789811432758729987351379999998999954885022344124786721003


Q ss_pred             HCCHHHHHHHHHHHHCCCCEEEEEEEEEECCCEEEEEEEEECCCCCCCCHHHHHHHHHHHHHHHHHHHCC
Q ss_conf             3038999999986303893399996378079819999987224321100798987278888998876449
Q gi|254780275|r   90 LLSKREIHRLYAAVRRDGMTLVPMKIYFNAKGLAKIDLALAQGKKNYDKRETEKKRDWDRQKHRILREHN  159 (159)
Q Consensus        90 LL~k~EI~kl~~~~~~kG~TiVPlkly~~~~g~~Kv~IalaKGKK~~DKR~~iK~rd~~re~~R~~K~~n  159 (159)
                      ||||+||.+|.+.+.++|+|||||++||+ +|||||+||||+|||+|||||+||+|||+||++|++|+++
T Consensus        82 LL~k~Ei~kl~~~~~~kG~TiVPl~ly~~-~g~iKv~IalakGKK~~DKR~~iK~rd~~re~~R~lk~~~  150 (150)
T PRK05422         82 LLHKKEIDKLIGKVERKGYTLVPLKLYFK-NGRVKVEIGLAKGKKLHDKRETIKERDWKREKARAMKRRG  150 (150)
T ss_pred             HCCHHHHHHHHHHHHCCCEEEEEEEEEEE-CCEEEEEEEEEECCCHHHHHHHHHHHHHHHHHHHHHHHCC
T ss_conf             15899999996066449816652467881-9999999999608821214778988888999999875568


No 4  
>pfam01668 SmpB SmpB protein.
Probab=99.96  E-value=1.3e-29  Score=196.81  Aligned_cols=67  Identities=58%  Similarity=0.907  Sum_probs=64.9

Q ss_pred             EEEEEECCEEEEEEEEEEEECCEEEEEHHHHHHHHCCCEEEEEEEEEECCEEEEEECCCCCHHCCCC
Q ss_conf             2898412333102576656224177504366676298200111588656607774030372000233
Q gi|254780275|r   12 KVVSDNRKARYNYHIVRSFEAGIVLTGTEVKSLRVSKVNISDSYATFENDEIWLTNSYIPEYLQANR   78 (159)
Q Consensus        12 ~ii~~NkkA~~~Y~i~e~~eAGIvL~G~EVKSiR~g~v~l~~sy~~~~~~E~~L~n~~I~~y~~~~~   78 (159)
                      ++|++||||+|||+|+|+|||||||+||||||||+|++||.||||.+++||+||.||||+||.+++.
T Consensus         1 kii~~NrkA~~~Y~i~e~~eAGivL~G~EVKSiR~g~~~l~~sy~~~~~~E~~L~n~~I~~y~~a~~   67 (68)
T pfam01668         1 KIIAQNKKARHDYFIEETYEAGIVLTGTEVKSLRAGKVNLKDSYVRIKNGEAWLINAHISPYKQANR   67 (68)
T ss_pred             CCCEECCCCCEEEEEEEEEEEEEEEEEHHHHHHHHCCCCCCCCEEEEECCEEEEECCCCCCCCCCCC
T ss_conf             9423577342015883789987899205315277099371314899999989998262566402487


No 5  
>pfam03293 Pox_RNA_pol Poxvirus DNA-directed RNA polymerase, 18 kD subunit.
Probab=52.39  E-value=9.1  Score=19.42  Aligned_cols=28  Identities=21%  Similarity=0.369  Sum_probs=24.1

Q ss_pred             HHCCCEEEEE-EEEEECCEEEEEECCCCC
Q ss_conf             6298200111-588656607774030372
Q gi|254780275|r   45 RVSKVNISDS-YATFENDEIWLTNSYIPE   72 (159)
Q Consensus        45 R~g~v~l~~s-y~~~~~~E~~L~n~~I~~   72 (159)
                      -+|.|+.+|| ||.+++|-+|-.+..++.
T Consensus       111 dsGtVSf~dsKYCfirng~vY~ngs~Vsv  139 (160)
T pfam03293       111 DSGTVSFNDSKYCFIRNGKVYDNGSTVSV  139 (160)
T ss_pred             CCCEEEECCCEEEEEECCEEECCCCEEEE
T ss_conf             68617865860799978899628988999


No 6  
>TIGR02298 HpaD_Fe 3,4-dihydroxyphenylacetate 2,3-dioxygenase; InterPro: IPR011984    This enzyme catalyses the ring-opening step in the degradation of 4-hydroxyphenylacetate ..
Probab=43.52  E-value=9  Score=19.46  Aligned_cols=17  Identities=47%  Similarity=0.712  Sum_probs=14.9

Q ss_pred             EEEEEEEEEECCCEEEEE
Q ss_conf             399996378079819999
Q gi|254780275|r  109 TLVPMKIYFNAKGLAKID  126 (159)
Q Consensus       109 TiVPlkly~~~~g~~Kv~  126 (159)
                      ||||+. |.|..++.||-
T Consensus       186 TlVPMr-YmN~D~hfkvV  202 (343)
T TIGR02298       186 TLVPMR-YMNEDKHFKVV  202 (343)
T ss_pred             CCCCCH-HHCCCCEEEEE
T ss_conf             404423-10789805799


No 7  
>pfam04661 Pox_I3 Poxvirus I3 ssDNA-binding protein.
Probab=30.67  E-value=46  Score=15.24  Aligned_cols=67  Identities=21%  Similarity=0.215  Sum_probs=41.8

Q ss_pred             EEECCEEEEEECCC--CCHHCCCCCCCCCHHHHHHHCCHHHHHHHHHHHHCCC-CEEEEEEEEEECCCEEEEEEEEEC
Q ss_conf             86566077740303--7200023321100013455303899999998630389-339999637807981999998722
Q gi|254780275|r   57 TFENDEIWLTNSYI--PEYLQANRFNHYPRRNRKLLLSKREIHRLYAAVRRDG-MTLVPMKIYFNAKGLAKIDLALAQ  131 (159)
Q Consensus        57 ~~~~~E~~L~n~~I--~~y~~~~~~~~~p~R~RKLLL~k~EI~kl~~~~~~kG-~TiVPlkly~~~~g~~Kv~IalaK  131 (159)
                      +|++|-+|+.-+.=  -+|...+    .+-+.   .---+||..|...-.|-- .-+||.-+|= +.+-+||.+||-|
T Consensus       135 Tfk~gclyINkm~gaivEyt~~g----~~s~v---~si~~ElE~L~kRD~Qmak~IlvpiVfyr-ng~~~KvTFALKK  204 (263)
T pfam04661       135 TFKKGCLYINKLNGAIVEYTVNG----GVSIV---QSISRELENLAKRDPQMAKAILVPIVFYR-NGNECKVTFALKK  204 (263)
T ss_pred             HHHCCEEEEECCCCEEEEEECCC----CCCEE---EEHHHHHHHHHHHCHHHHEEEEEEEEEEE-CCCEEEEEEEHHH
T ss_conf             43067089850353278994279----85504---40789998886407555316876799995-5973899987022


No 8  
>KOG2963 consensus
Probab=28.63  E-value=50  Score=15.03  Aligned_cols=46  Identities=28%  Similarity=0.372  Sum_probs=30.7

Q ss_pred             EEEEEEEEEECCCEEEEEEEEECCCCCCCCH-----HHHHHHHHHHHHHHHHHH
Q ss_conf             3999963780798199999872243211007-----989872788889988764
Q gi|254780275|r  109 TLVPMKIYFNAKGLAKIDLALAQGKKNYDKR-----ETEKKRDWDRQKHRILRE  157 (159)
Q Consensus       109 TiVPlkly~~~~g~~Kv~IalaKGKK~~DKR-----~~iK~rd~~re~~R~~K~  157 (159)
                      |=|--.|-+   -+|||+=|+|-|+=.|-.-     +.++.-+.-.|..|.+|.
T Consensus       286 ~EIGPRlTl---qLvKIeEGi~~GkVlyH~hv~Kt~eEi~~l~~~~ekk~~lKe  336 (405)
T KOG2963         286 TEIGPRLTL---QLVKIEEGICEGKVLYHEHVQKTEEEIKALRKRHEKKRRLKE  336 (405)
T ss_pred             EEECCCCEE---EEEEEECCCCCCEEEEEEHHCCCHHHHHHHHHHHHHHHHHHH
T ss_conf             764563067---787754065565057760102798999999999999998999


No 9  
>COG1710 Uncharacterized protein conserved in archaea [Function unknown]
Probab=28.50  E-value=50  Score=15.02  Aligned_cols=42  Identities=19%  Similarity=0.522  Sum_probs=27.2

Q ss_pred             HHHHHHHHHHHCCCCEEEEEEEEEECCCEEEEEEEEECCCCCCCCHHHHHHHHH
Q ss_conf             999999986303893399996378079819999987224321100798987278
Q gi|254780275|r   94 REIHRLYAAVRRDGMTLVPMKIYFNAKGLAKIDLALAQGKKNYDKRETEKKRDW  147 (159)
Q Consensus        94 ~EI~kl~~~~~~kG~TiVPlkly~~~~g~~Kv~IalaKGKK~~DKR~~iK~rd~  147 (159)
                      +--.++....+|-|.++||+++  +++|.          ..+||++--+.-++.
T Consensus        64 k~skkvlkaleq~gI~vIPvk~--KgrGr----------prkyd~~t~~~i~em  105 (139)
T COG1710          64 KVSKKVLKALEQMGIKVIPVKL--KGRGR----------PRKYDRNTLLRIREM  105 (139)
T ss_pred             HHHHHHHHHHHHCCCEEEEEEE--CCCCC----------CCCCCHHHHHHHHHH
T ss_conf             7899999889868956865530--47899----------754345489999999


No 10 
>pfam03712 Cu2_monoox_C Copper type II ascorbate-dependent monooxygenase, C-terminal domain. The N and C-terminal domains of members of this family adopt the same PNGase F-like fold.
Probab=26.99  E-value=46  Score=15.21  Aligned_cols=39  Identities=15%  Similarity=0.283  Sum_probs=29.4

Q ss_pred             EEECCEEEEEHHHHHHHHCCCE-EEEEEEEEECC-EEEEEE
Q ss_conf             5622417750436667629820-01115886566-077740
Q gi|254780275|r   29 SFEAGIVLTGTEVKSLRVSKVN-ISDSYATFEND-EIWLTN   67 (159)
Q Consensus        29 ~~eAGIvL~G~EVKSiR~g~v~-l~~sy~~~~~~-E~~L~n   67 (159)
                      +|.|||-++|++.=.|--|+-+ ..+++|...-. .++++.
T Consensus         1 ~ydaGil~lG~~~~~IPP~~~~~~~~~~C~~~c~~~i~~fa   41 (157)
T pfam03712         1 KYDAGIMLLGSGYFAIPPGQTAYPVEGSCEIECTKTMFPFA   41 (157)
T ss_pred             CCEEEEEEECCCCCEECCCCCEEEEEEEECCCCCCEEEEEE
T ss_conf             93178877156463019699527767786787882178889


No 11 
>KOG3995 consensus
Probab=25.76  E-value=30  Score=16.38  Aligned_cols=67  Identities=27%  Similarity=0.270  Sum_probs=43.0

Q ss_pred             ECCEEEEEEEEEEEECCEEEEEHHH-HHHHHCCCEEEEEEEEEECCEEEEEECCC--CCHHCCCCCCCCCHHHH
Q ss_conf             1233310257665622417750436-66762982001115886566077740303--72000233211000134
Q gi|254780275|r   17 NRKARYNYHIVRSFEAGIVLTGTEV-KSLRVSKVNISDSYATFENDEIWLTNSYI--PEYLQANRFNHYPRRNR   87 (159)
Q Consensus        17 NkkA~~~Y~i~e~~eAGIvL~G~EV-KSiR~g~v~l~~sy~~~~~~E~~L~n~~I--~~y~~~~~~~~~p~R~R   87 (159)
                      -.--+-+|+|++.=|-=-.+.|.-| |-|-.|++-    -+.|+-||+||.-+.+  +|-.+++...-...|.|
T Consensus        41 GPN~RkdyHieegeE~FyQ~KGdMvLKVie~g~~r----DivI~qGe~flLParVpHSPqRFantvGlVVEr~R  110 (279)
T KOG3995          41 GPNTRKDYHIEEGEEVFYQLKGDMVLKVLEQGKHR----DVVIRQGEIFLLPARVPHSPQRFANTVGLVVERRR  110 (279)
T ss_pred             CCCCCCCCCCCCCCHHHEECCCCEEEEEECCCCCE----EEEEECCCEEEECCCCCCCCHHHCCCEEEEEEECC
T ss_conf             89866763457770322000674578773147501----36772474787126789971552143237998416


No 12 
>KOG3545 consensus
Probab=24.83  E-value=32  Score=16.19  Aligned_cols=49  Identities=24%  Similarity=0.337  Sum_probs=36.4

Q ss_pred             HHHHHHHCCCEEEEEEEEEECCEEEEEECCCCCHHCCCCCCCCCHHHHHH
Q ss_conf             36667629820011158865660777403037200023321100013455
Q gi|254780275|r   40 EVKSLRVSKVNISDSYATFENDEIWLTNSYIPEYLQANRFNHYPRRNRKL   89 (159)
Q Consensus        40 EVKSiR~g~v~l~~sy~~~~~~E~~L~n~~I~~y~~~~~~~~~p~R~RKL   89 (159)
                      -|.|...++.+|.-||-.-.+.+..+-=-..-+|++.+..++.| |+|+|
T Consensus       184 ~v~S~~~~~~~i~yaydt~~~~~~~~~ipf~N~y~~~~~idYNP-~D~~L  232 (249)
T KOG3545         184 VVHSYNCTHTQISYAYDTTTGTQERIDLPFPNPYSYATMIDYNP-RDRRL  232 (249)
T ss_pred             EEECCCCCCCEEEEEEECCCCCEECCCCCCCCHHHHHHCCCCCC-CCCEE
T ss_conf             87213468725999997577825114655564110211267885-63515


No 13 
>pfam11169 DUF2956 Protein of unknown function (DUF2956). This family of proteins with unknown function appears to be restricted to Gammaproteobacteria.
Probab=23.27  E-value=26  Score=16.68  Aligned_cols=56  Identities=21%  Similarity=0.401  Sum_probs=37.8

Q ss_pred             HHHHHHHHHHHCCCCEEEEEEEEEECCCEEEEEEEEECCCCCCCCHHHHHHHHHHHHHHHHHHHC
Q ss_conf             99999998630389339999637807981999998722432110079898727888899887644
Q gi|254780275|r   94 REIHRLYAAVRRDGMTLVPMKIYFNAKGLAKIDLALAQGKKNYDKRETEKKRDWDRQKHRILREH  158 (159)
Q Consensus        94 ~EI~kl~~~~~~kG~TiVPlkly~~~~g~~Kv~IalaKGKK~~DKR~~iK~rd~~re~~R~~K~~  158 (159)
                      .|--++...++.+|-|==-+++-         --|+-||=-.|-|+|..|.||.++...+..|..
T Consensus         6 qEAmkiAKatQKPGQTKEQTKLI---------AqGIeKGIa~YKKqqK~KaRe~DK~rKk~~k~k   61 (103)
T pfam11169         6 QEAMKIAKATQKPGQTKEQTKLI---------AQGIEKGIAEYKKQQKAKAREADKARKQQLKAK   61 (103)
T ss_pred             HHHHHHHHHHCCCCCCHHHHHHH---------HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             99999998515898888999999---------999998999999998999898889999999988


Done!