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!