Query         gi|254780236|ref|YP_003064649.1| 50S ribosomal protein L17 [Candidatus Liberibacter asiaticus str. psy62]
Match_columns 136
No_of_seqs    117 out of 1412
Neff          4.8 
Searched_HMMs 39220
Date          Tue May 24 00:06:32 2011
Command       /home/congqian_1/programs/hhpred/hhsearch -i 254780236.hhm -d /home/congqian_1/database/cdd/Cdd.hhm 

 No Hit                             Prob E-value P-value  Score    SS Cols Query HMM  Template HMM
  1 PRK05591 rplQ 50S ribosomal pr 100.0       0       0  331.0  15.7  117    1-117     1-117 (117)
  2 COG0203 RplQ Ribosomal protein 100.0       0       0  329.2  13.8  116    1-116     1-116 (116)
  3 TIGR00059 L17 ribosomal protei 100.0       0       0  326.3   8.8  111    7-117     2-125 (125)
  4 PTZ00076 60S ribosomal protein 100.0       0       0  293.4   9.5  125    4-128    16-142 (257)
  5 pfam01196 Ribosomal_L17 Riboso 100.0 1.1E-42       0  271.9  12.0   97   20-116     1-97  (97)
  6 KOG3280 consensus              100.0 1.2E-42       0  271.7   9.3  128    1-128     8-138 (171)
  7 PRK11823 DNA repair protein Ra  55.3      14 0.00035   18.1   3.1   83   42-127   190-279 (454)
  8 TIGR02885 spore_sigF RNA polym  35.7      30 0.00077   16.1   2.4   45   51-101     1-45  (231)
  9 PRK11536 hypothetical protein;  34.2      39 0.00098   15.4   2.8   41   68-119   125-166 (223)
 10 TIGR01173 glmU UDP-N-acetylglu  28.1      46  0.0012   15.0   2.3   73   47-123    64-169 (461)
 11 cd01452 VWA_26S_proteasome_sub  25.9      54  0.0014   14.6   2.6   47   88-134    78-132 (187)
 12 TIGR03060 PS_II_psb29 photosys  25.8      47  0.0012   14.9   2.0   80   12-103    68-148 (214)
 13 cd05399 NT_Rel-Spo_like Nucleo  25.0     5.8 0.00015   20.3  -2.8   79   19-97      5-99  (129)
 14 PRK13266 Thf1-like protein; Re  24.4      58  0.0015   14.4   2.4   80   12-103    68-149 (224)
 15 COG4463 CtsR Transcriptional r  24.3      44  0.0011   15.1   1.6   13   91-103    64-76  (153)
 16 KOG2188 consensus               23.1      61  0.0016   14.3   3.7   40   50-89    373-413 (650)
 17 COG5095 TAF6 Transcription ini  23.1      61  0.0016   14.3   3.8   31   42-72    193-224 (450)
 18 cd06541 ASCH ASC-1 homology or  22.6      63  0.0016   14.2   3.5   36   89-130    31-66  (105)
 19 cd01121 Sms Sms (bacterial rad  20.9      68  0.0017   14.0   3.4   82   43-127   184-272 (372)
 20 TIGR02817 adh_fam_1 zinc-bindi  20.0      71  0.0018   13.9   2.5   23   18-40    285-307 (338)

No 1  
>PRK05591 rplQ 50S ribosomal protein L17; Validated
Probab=100.00  E-value=0  Score=331.05  Aligned_cols=117  Identities=64%  Similarity=0.955  Sum_probs=116.6

Q ss_pred             CCCCCCCCCCCCCHHHHHHHHHHHHHHHHHCCEEEECHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHCCHHHHHHHH
Q ss_conf             99888899999788999999999999998689378759999998864216762311387677889998725668899999
Q gi|254780236|r    1 MRHAISGRKLNRTSSHRKAMFSNMAASIIWHEQIVTTLPKAKELRPIVEKLVTLGKKGGLHSLRLAISKIGDVDVVNKLF   80 (136)
Q Consensus         1 MrH~~~~rklgr~~~hR~allrnl~~~Li~herI~TT~~KAKelr~~aEklIt~AK~~~~~~rr~~~~~l~~~~~v~kLf   80 (136)
                      |||++++++|||+++||++|||||+++||+||+|+||++||||+|+|+|+|||+||+|++|++|++.+||.|+++++|||
T Consensus         1 MrH~~~~~klgr~~~hR~allrnl~~~Li~h~rI~TT~~KAKelr~~~EklIT~AK~~~~~~rR~~~~~l~~~~~v~kLf   80 (117)
T PRK05591          1 MRHRKSGRKLGRTSSHRKAMLRNLATSLIEHERIKTTLPKAKELRRVVEKLITLAKKGDLAARRQAFARLRDKEAVHKLF   80 (117)
T ss_pred             CCCCCCCCCCCCCHHHHHHHHHHHHHHHHHCCEEEECHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHCCCHHHHHHHH
T ss_conf             99888889899886999999999999999669687239999999999999998871785888999998548889999999


Q ss_pred             HHHHHHHCCCCCCEEEEEECCCCCCCCCCEEEEEEEC
Q ss_conf             9999885058775599875378999887579999526
Q gi|254780236|r   81 GIIAKRYSDRSGGYLRIMKRGFRYGDSAPMAVIEFVD  117 (136)
Q Consensus        81 ~~l~prf~~R~GGYTRi~kl~~R~gD~A~ma~iElVd  117 (136)
                      ++|+|||++||||||||+|+|+|.||+|+||+|||||
T Consensus        81 ~~iapry~~R~GGYTRI~kl~~R~gD~A~ma~iElVd  117 (117)
T PRK05591         81 DELAPRYADRNGGYTRILKLGFRRGDNAPMAIIELVD  117 (117)
T ss_pred             HHHHHHHCCCCCCEEEEEECCCCCCCCCCEEEEEEEC
T ss_conf             9998996779987588986389999988777998309


No 2  
>COG0203 RplQ Ribosomal protein L17 [Translation, ribosomal structure and biogenesis]
Probab=100.00  E-value=0  Score=329.24  Aligned_cols=116  Identities=65%  Similarity=0.961  Sum_probs=115.6

Q ss_pred             CCCCCCCCCCCCCHHHHHHHHHHHHHHHHHCCEEEECHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHCCHHHHHHHH
Q ss_conf             99888899999788999999999999998689378759999998864216762311387677889998725668899999
Q gi|254780236|r    1 MRHAISGRKLNRTSSHRKAMFSNMAASIIWHEQIVTTLPKAKELRPIVEKLVTLGKKGGLHSLRLAISKIGDVDVVNKLF   80 (136)
Q Consensus         1 MrH~~~~rklgr~~~hR~allrnl~~~Li~herI~TT~~KAKelr~~aEklIt~AK~~~~~~rr~~~~~l~~~~~v~kLf   80 (136)
                      |||++++++|||++|||+||++||++|||.||+|+||++||||+|+++|+|||+||+|++|++|+++++|.|++++.|||
T Consensus         1 Mrh~~~~rkl~rtsshR~amlrnla~sLi~he~I~TT~~KAKelr~~vEkLITlaK~~~l~~RR~a~~~l~d~~~v~kLF   80 (116)
T COG0203           1 MRHRKKGRKLGRTSSHRKAMLRNLATSLIEHERIETTLPKAKELRRVVEKLITLAKKGDLANRRLAFARLRDKDAVKKLF   80 (116)
T ss_pred             CCCCCCCCCCCCCHHHHHHHHHHHHHHHHHCCCEEECHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHCCHHHHHHHH
T ss_conf             99765678789877999999999999998738656337889999999999988850344888999998712189999999


Q ss_pred             HHHHHHHCCCCCCEEEEEECCCCCCCCCCEEEEEEE
Q ss_conf             999988505877559987537899988757999952
Q gi|254780236|r   81 GIIAKRYSDRSGGYLRIMKRGFRYGDSAPMAVIEFV  116 (136)
Q Consensus        81 ~~l~prf~~R~GGYTRi~kl~~R~gD~A~ma~iElV  116 (136)
                      ++|+|||.+||||||||+|+|+|.|||||||+||||
T Consensus        81 ~~iapry~~R~GGYtRIlK~g~R~GD~A~maiiElV  116 (116)
T COG0203          81 DEIAPRYAERNGGYTRILKLGFRRGDNAPMAIIELV  116 (116)
T ss_pred             HHHCHHHCCCCCCEEEEEECCCCCCCCCCEEEEEEC
T ss_conf             985723336899726777537888888753777729


No 3  
>TIGR00059 L17 ribosomal protein L17; InterPro: IPR000456   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 L17 is one of the proteins from the large ribosomal subunit. Bacterial L17 is a protein of 120 to 130 amino-acid residues while yeast YmL8 is twice as large (238 residues). The N-terminal half of YmL8 is colinear with the sequence of L17 from Escherichia coli.; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome.
Probab=100.00  E-value=0  Score=326.30  Aligned_cols=111  Identities=55%  Similarity=0.783  Sum_probs=109.0

Q ss_pred             C-CCCCCCHHHHHHHHHHHHHHHHHCCEEEECHHHHHHHHHHHHHHHHHHC----CCCHHHHHHHHHHHCCHHH------
Q ss_conf             9-9999788999999999999998689378759999998864216762311----3876778899987256688------
Q gi|254780236|r    7 G-RKLNRTSSHRKAMFSNMAASIIWHEQIVTTLPKAKELRPIVEKLVTLGK----KGGLHSLRLAISKIGDVDV------   75 (136)
Q Consensus         7 ~-rklgr~~~hR~allrnl~~~Li~herI~TT~~KAKelr~~aEklIt~AK----~~~~~~rr~~~~~l~~~~~------   75 (136)
                      + |||||+++||+||||||+++||.||+|+||.+||||+|+++|||||+||    .|++|++|.+.+||.|+++      
T Consensus         2 ~~rkLgr~s~hR~Allrnl~~~L~~he~I~TT~~KAKe~r~~~EklIT~AKrait~d~~~aRR~~~~~~~n~~~~~~dN~   81 (125)
T TIGR00059         2 YIRKLGRTSAHRKALLRNLASALIRHEKIETTLAKAKELRRVVEKLITLAKRAITVDNVNARREAKAYIRNKEALDVDNR   81 (125)
T ss_pred             CCCCCCCCHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHCCHHHHHHHH
T ss_conf             88888887588999999999999862886203578888888885776676453046888999999998731024456579


Q ss_pred             --HHHHHHHHHHHHCCCCCCEEEEEECCCCCCCCCCEEEEEEEC
Q ss_conf             --999999999885058775599875378999887579999526
Q gi|254780236|r   76 --VNKLFGIIAKRYSDRSGGYLRIMKRGFRYGDSAPMAVIEFVD  117 (136)
Q Consensus        76 --v~kLf~~l~prf~~R~GGYTRi~kl~~R~gD~A~ma~iElVd  117 (136)
                        ++|||.+|||||++|+||||||+|+|+|.||+||||+|||||
T Consensus        82 ~l~~kLF~~iaPry~~R~GGYTRilklg~RrGD~A~mA~iELVD  125 (125)
T TIGR00059        82 QLLNKLFSEIAPRYAQRNGGYTRILKLGPRRGDAAEMAIIELVD  125 (125)
T ss_pred             HHHHHHHHHHCCCCCCCCCCCEEEECCCCCCCCCCCHHHHHHCC
T ss_conf             99998765305532348778313000567788863014553069


No 4  
>PTZ00076 60S ribosomal protein L17; Provisional
Probab=100.00  E-value=0  Score=293.41  Aligned_cols=125  Identities=29%  Similarity=0.346  Sum_probs=117.9

Q ss_pred             CCCCCCCCCCHHHHHHHHHHHHHHHHHCCEEEECHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHCCHHHHHHHHHHH
Q ss_conf             88899999788999999999999998689378759999998864216762311387677889998725668899999999
Q gi|254780236|r    4 AISGRKLNRTSSHRKAMFSNMAASIIWHEQIVTTLPKAKELRPIVEKLVTLGKKGGLHSLRLAISKIGDVDVVNKLFGII   83 (136)
Q Consensus         4 ~~~~rklgr~~~hR~allrnl~~~Li~herI~TT~~KAKelr~~aEklIt~AK~~~~~~rr~~~~~l~~~~~v~kLf~~l   83 (136)
                      +..+|||||+++|||+|||||+++||+||||+||++||||+|+|||+|||+||+|+++|+|+|.+++.+.+++.|||+++
T Consensus        16 ~R~FRKl~r~s~HR~amlRnmv~~LI~heRIeTTl~KAKElrr~AE~lItlAK~~t~~arr~a~s~lRt~e~~~KLF~el   95 (257)
T PTZ00076         16 RRLFRRAHKQPHHKWDSIKNQLNELLKYGRIETTLTKAKELQGYAEELIYLAKKDNAENNLKVESMLRTAQGRRKLYEFY   95 (257)
T ss_pred             HHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHCCHHHHHHHHHHH
T ss_conf             77888707994155999999999998751121120768999999999999860488888999998854699999999986


Q ss_pred             HHHHCCCCCCEEEEEE-CCCCCCCCCCEEEEEEECCCCCCCC-CCCH
Q ss_conf             9885058775599875-3789998875799995268866222-5402
Q gi|254780236|r   84 AKRYSDRSGGYLRIMK-RGFRYGDSAPMAVIEFVDRDLSAKG-TPVS  128 (136)
Q Consensus        84 ~prf~~R~GGYTRi~k-l~~R~gD~A~ma~iElVd~~~~~~~-~~~~  128 (136)
                      +|||++||||||||++ .++|.||+||||+|||||+|.+... .|+.
T Consensus        96 ~PRYkdRpggyTRILn~~~~R~gDaAPMAyIEfVDRpGElRpAKPvg  142 (257)
T PTZ00076         96 VPLYRHRPFFFTRIINQWKLRLRDAAPLAFIEFIDRPGELRPAKPVG  142 (257)
T ss_pred             HHHHCCCCCCEEHHHHHHCCCCCCCCCEEEEEECCCCCCCCCCCCCC
T ss_conf             43540588761102443055555667604556506877636688744


No 5  
>pfam01196 Ribosomal_L17 Ribosomal protein L17.
Probab=100.00  E-value=1.1e-42  Score=271.86  Aligned_cols=97  Identities=59%  Similarity=0.882  Sum_probs=96.1

Q ss_pred             HHHHHHHHHHHCCEEEECHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHCCHHHHHHHHHHHHHHHCCCCCCEEEEEE
Q ss_conf             99999999986893787599999988642167623113876778899987256688999999999885058775599875
Q gi|254780236|r   20 MFSNMAASIIWHEQIVTTLPKAKELRPIVEKLVTLGKKGGLHSLRLAISKIGDVDVVNKLFGIIAKRYSDRSGGYLRIMK   99 (136)
Q Consensus        20 llrnl~~~Li~herI~TT~~KAKelr~~aEklIt~AK~~~~~~rr~~~~~l~~~~~v~kLf~~l~prf~~R~GGYTRi~k   99 (136)
                      |||||+++||+||+|+||++||||+|+|+|+|||+||+|++|++|++.++|.|+++++|||++++|||++||||||||+|
T Consensus         1 llrnl~~~Li~herI~TT~~KAKelr~~~ErlIt~AK~~~~~~rr~~~~~l~~~~~v~kLf~~iapry~~R~GGYTRi~k   80 (97)
T pfam01196         1 LLRNLATSLIRHERIETTLAKAKELRPYAEKLITLAKKGDLHARRQALSFLRDKEAVKKLFDELAPRYADRNGGYTRIIK   80 (97)
T ss_pred             CHHHHHHHHHHCCEEEECHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHCCCHHHHHHHHHHHHHHHCCCCCCEEEEEE
T ss_conf             96899999984796885789899999999999999972878889999962187468999999998986679988488886


Q ss_pred             CCCCCCCCCCEEEEEEE
Q ss_conf             37899988757999952
Q gi|254780236|r  100 RGFRYGDSAPMAVIEFV  116 (136)
Q Consensus       100 l~~R~gD~A~ma~iElV  116 (136)
                      +|+|.||+|+||+||||
T Consensus        81 l~~R~gD~A~ma~iElV   97 (97)
T pfam01196        81 LGPRRGDNAPMAIIELV   97 (97)
T ss_pred             CCCCCCCCCCEEEEEEC
T ss_conf             48999999885899749


No 6  
>KOG3280 consensus
Probab=100.00  E-value=1.2e-42  Score=271.66  Aligned_cols=128  Identities=42%  Similarity=0.664  Sum_probs=121.8

Q ss_pred             CCCCCCCCCCCCCHHHHHHHHHHHHHHHHHCCEEEECHHHHHHHHHHHHHHHHHH-CCCCHHHH--HHHHHHHCCHHHHH
Q ss_conf             9988889999978899999999999999868937875999999886421676231-13876778--89998725668899
Q gi|254780236|r    1 MRHAISGRKLNRTSSHRKAMFSNMAASIIWHEQIVTTLPKAKELRPIVEKLVTLG-KKGGLHSL--RLAISKIGDVDVVN   77 (136)
Q Consensus         1 MrH~~~~rklgr~~~hR~allrnl~~~Li~herI~TT~~KAKelr~~aEklIt~A-K~~~~~~r--r~~~~~l~~~~~v~   77 (136)
                      |+|+....|+|+++.||.+|||||+|+||+||||+||++||||+|+|||+|||+| |.|+++++  +++..||..+++++
T Consensus         8 mt~~~~~~Klgr~~~~R~~lLR~lvt~LvkHErIe~t~ara~Ear~~aEklIt~~~k~g~~~~~~~~~a~~~l~ekdli~   87 (171)
T KOG3280           8 MTHGRRKLKLGRPPAHRLALLRNLVTQLVKHERIETTWARAKEARRYAEKLITLGKKAGSLHERTARMADGWLREKDLLH   87 (171)
T ss_pred             ECCCCHHHHCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHCCCCCCHHHH
T ss_conf             41440013137990889999999999997755666689889999999999999988508674899998734224005899


Q ss_pred             HHHHHHHHHHCCCCCCEEEEEECCCCCCCCCCEEEEEEECCCCCCCCCCCH
Q ss_conf             999999988505877559987537899988757999952688662225402
Q gi|254780236|r   78 KLFGIIAKRYSDRSGGYLRIMKRGFRYGDSAPMAVIEFVDRDLSAKGTPVS  128 (136)
Q Consensus        78 kLf~~l~prf~~R~GGYTRi~kl~~R~gD~A~ma~iElVd~~~~~~~~~~~  128 (136)
                      |||++|+|||.||+|||||++++.+|.||+|+||+|||++++.+.-..+..
T Consensus        88 KlF~vl~pRY~dr~ggYTRllrlppr~~d~apmavlE~~Gn~~p~~~a~~p  138 (171)
T KOG3280          88 KLFTVLAPRYKDRNGGYTRLLRLPPRRGDRAPMAVLELVGNPLPQQAADRP  138 (171)
T ss_pred             HHHHHHCHHHCCCCCCCEEHHCCCCCCCCCCCCEEEEECCCCCCCCCCCCC
T ss_conf             999986515326888700000267533455672344432776643357984


No 7  
>PRK11823 DNA repair protein RadA; Provisional
Probab=55.32  E-value=14  Score=18.09  Aligned_cols=83  Identities=18%  Similarity=0.390  Sum_probs=54.7

Q ss_pred             HHHHHHHHHHHHHHCCCCHHHHHHH------HHHHCCHHHHHHHHHHHHHHHCCCCCCEEEEEEC-CCCCCCCCCEEEEE
Q ss_conf             9988642167623113876778899------9872566889999999998850587755998753-78999887579999
Q gi|254780236|r   42 KELRPIVEKLVTLGKKGGLHSLRLA------ISKIGDVDVVNKLFGIIAKRYSDRSGGYLRIMKR-GFRYGDSAPMAVIE  114 (136)
Q Consensus        42 Kelr~~aEklIt~AK~~~~~~rr~~------~~~l~~~~~v~kLf~~l~prf~~R~GGYTRi~kl-~~R~gD~A~ma~iE  114 (136)
                      -++|--+..|+.+||..+...  .+      ...|--+.++.++.|.+. -|+.-.+..-||++. .+|.|..-++++.|
T Consensus       190 sQVre~a~~L~~~AK~~~i~~--~lVGHVTKdG~iAGPkvLEHmVDtVl-~fEGd~~~~~RiLR~~KNRFG~t~EiGvFe  266 (454)
T PRK11823        190 SQVRECAAELTRLAKQSGIAV--FLVGHVTKEGAIAGPRVLEHMVDTVL-YFEGDRHSRFRILRAVKNRFGATNEIGVFE  266 (454)
T ss_pred             HHHHHHHHHHHHHHHHCCCCE--EEEEEECCCCCCCCCHHHHHHHCEEE-EECCCCCCCCEEEEEECCCCCCCCEEEEEE
T ss_conf             999999999999997449828--99997726776466145222010468-751576655024563124677666058998


Q ss_pred             EECCCCCCCCCCC
Q ss_conf             5268866222540
Q gi|254780236|r  115 FVDRDLSAKGTPV  127 (136)
Q Consensus       115 lVd~~~~~~~~~~  127 (136)
                      ..+.-+..-.+|-
T Consensus       267 M~~~GL~~v~nPS  279 (454)
T PRK11823        267 MTEKGLREVSNPS  279 (454)
T ss_pred             ECCCCCEECCCHH
T ss_conf             6168845668877


No 8  
>TIGR02885 spore_sigF RNA polymerase sigma-F factor; InterPro: IPR014236   The bacterial core RNA polymerase complex, which consists of five subunits, is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme . RNA polymerase recruits alternative sigma factors as a means of switching on specific regulons. Most bacteria express a multiplicity of sigma factors. Two of these factors, sigma-70 (gene rpoD), generally known as the major or primary sigma factor, and sigma-54 (gene rpoN or ntrA) direct the transcription of a wide variety of genes. The other sigma factors, known as alternative sigma factors, are required for the transcription of specific subsets of genes.   With regard to sequence similarity, sigma factors can be grouped into two classes, the sigma-54 and sigma-70 families. Sequence alignments of the sigma70 family members reveal four conserved regions that can be further divided into subregions eg. sub-region 2.2, which may be involved in the binding of the sigma factor to the core RNA polymerase; and sub-region 4.2, which seems to harbor a DNA-binding 'helix-turn-helix' motif involved in binding the conserved -35 region of promoters recognized by the major sigma factors , .    Members of this entry represent RNA polymerase sigma factor F. Within the Firmicutes, Sigma-F is specifically, and universally, a component of the endospore formation program, and is expressed in the forespore to turn on the expression of dozens of genes. It is closely related to sigma-G, which is also expressed in the forespore.; GO: 0003677 DNA binding, 0003700 transcription factor activity, 0016987 sigma factor activity, 0006352 transcription initiation, 0006355 regulation of transcription DNA-dependent.
Probab=35.68  E-value=30  Score=16.08  Aligned_cols=45  Identities=27%  Similarity=0.381  Sum_probs=28.5

Q ss_pred             HHHHHCCCCHHHHHHHHHHHCCHHHHHHHHHHHHHHHCCCCCCEEEEEECC
Q ss_conf             762311387677889998725668899999999988505877559987537
Q gi|254780236|r   51 LVTLGKKGGLHSLRLAISKIGDVDVVNKLFGIIAKRYSDRSGGYLRIMKRG  101 (136)
Q Consensus        51 lIt~AK~~~~~~rr~~~~~l~~~~~v~kLf~~l~prf~~R~GGYTRi~kl~  101 (136)
                      ||.+||.||..|+-.+..      .--+|..-++.||.+|=.-|==+...|
T Consensus         1 Li~~a~~GDk~A~dkLi~------~N~~LV~siv~rF~nRGYe~eDlFQIG   45 (231)
T TIGR02885         1 LIKLAKEGDKEARDKLIE------ENLRLVSSIVKRFLNRGYEYEDLFQIG   45 (231)
T ss_pred             CCHHHHHHHHHHHHHHHH------HCCHHHHHHHHHHHCCCCCCCHHHHHH
T ss_conf             904567404899999987------233468999998520688700002221


No 9  
>PRK11536 hypothetical protein; Provisional
Probab=34.24  E-value=39  Score=15.44  Aligned_cols=41  Identities=17%  Similarity=0.273  Sum_probs=26.9

Q ss_pred             HHHCCHHHHHHHHHHHHHHHCCCCCCEEEEEECC-CCCCCCCCEEEEEEECCC
Q ss_conf             8725668899999999988505877559987537-899988757999952688
Q gi|254780236|r   68 SKIGDVDVVNKLFGIIAKRYSDRSGGYLRIMKRG-FRYGDSAPMAVIEFVDRD  119 (136)
Q Consensus        68 ~~l~~~~~v~kLf~~l~prf~~R~GGYTRi~kl~-~R~gD~A~ma~iElVd~~  119 (136)
                      .....++++..+.+      ..|.|-|.||++-| ...||     -||||+++
T Consensus       125 ~r~~~~~~~~~~~~------tgrtGwY~RVL~~G~v~agD-----~i~l~~R~  166 (223)
T PRK11536        125 YHFDISDIAQLMQN------TGKVGWLYRVIAPGKVSADA-----PLELVSRV  166 (223)
T ss_pred             HHHCCCCHHHHHHH------HCCCEEEEEEECCCEECCCC-----EEEEEECC
T ss_conf             88488129999998------48856999980263766999-----78997349


No 10 
>TIGR01173 glmU UDP-N-acetylglucosamine pyrophosphorylase; InterPro: IPR005882    N-Acetylglucosamine-1-PO(4) uridyltransferase (GlmU, 2.7.7.23 from EC) is a trimeric bifunctional enzyme that catalyzes the last two sequential reactions in the de novo biosynthetic pathway for UDP-GlcNAc.    The X-ray crystal structure of Escherichia coli GlmU in complex with UDP-GlcNAc and CoA has been determined to 2.1 A resolution and reveals a two-domain architecture that is responsible for these two reactions . The C-terminal domain is responsible for the CoA-dependent acetylation of Glc-1-PO(4) to GlcNAc-1-PO(4) and displays the longest left-handed parallel beta-helix observed to date. The acetyltransferase active site defined by the binding site for CoA makes use of residues from all three subunits and is positioned beneath an open cavity large enough to accommodate the Glc-1-PO(4) acetyl acceptor. The N-terminal domain catalyzes uridyl transfer from UTP to GlcNAc-1-PO(4) to form the final products UDP-GlcNAc and pyrophosphate. This domain is composed of a central seven-stranded beta-sheet surrounded by six alpha-helices in a Rossmann fold-like topology. ; GO: 0003977 UDP-N-acetylglucosamine diphosphorylase activity, 0009103 lipopolysaccharide biosynthetic process.
Probab=28.05  E-value=46  Score=14.97  Aligned_cols=73  Identities=22%  Similarity=0.246  Sum_probs=53.0

Q ss_pred             HHHHHHHHHC----CC-CHHHHHHHHHHHC-----------------CHHHHH-HHHHHHHH-HH---------CCCCCC
Q ss_conf             4216762311----38-7677889998725-----------------668899-99999998-85---------058775
Q gi|254780236|r   47 IVEKLVTLGK----KG-GLHSLRLAISKIG-----------------DVDVVN-KLFGIIAK-RY---------SDRSGG   93 (136)
Q Consensus        47 ~aEklIt~AK----~~-~~~~rr~~~~~l~-----------------~~~~v~-kLf~~l~p-rf---------~~R~GG   93 (136)
                      ..|+.|.|+-    .| |=||..++.++|.                 +.+... .|.+.-.+ .=         .+=|-|
T Consensus        64 ~~d~t~~~v~Q~~qlGGTGHAv~~a~~~l~~~~~~~vLvLyGDvPLi~~eTL~m~Ll~~~~~~~~~~~tlLt~~l~DP~G  143 (461)
T TIGR01173        64 ENDKTVNWVLQAEQLGGTGHAVLQALPFLSEDDDGRVLVLYGDVPLISAETLEMRLLESHRQLNGAKVTLLTAKLEDPTG  143 (461)
T ss_pred             CCCCEEEEEEECCCCCCHHHHHHHHCCCCCCCCCCEEEEEECCCCCCCHHHHHHHHHHHHHCCCCCCEEEEEEEECCCCC
T ss_conf             79967999996889787289998711678886686089995887877567787798886300010451799987188895


Q ss_pred             EEEEEECCCCCCCCCCEEEEEEECCCCCCC
Q ss_conf             599875378999887579999526886622
Q gi|254780236|r   94 YLRIMKRGFRYGDSAPMAVIEFVDRDLSAK  123 (136)
Q Consensus        94 YTRi~kl~~R~gD~A~ma~iElVd~~~~~~  123 (136)
                      |=||++    ..|++=++|||.-|-+.+-+
T Consensus       144 YGRI~r----~~~g~V~~IVE~KDA~~eqk  169 (461)
T TIGR01173       144 YGRIIR----ENDGAVQAIVEEKDANEEQK  169 (461)
T ss_pred             CCEEEE----CCCCCEEEEECCCCCCHHHH
T ss_conf             435898----48995899973359886980


No 11 
>cd01452 VWA_26S_proteasome_subunit 26S proteasome plays a major role in eukaryotic protein breakdown, especially for ubiquitin-tagged proteins. It is an ATP-dependent protease responsible for the bulk of non-lysosomal proteolysis in eukaryotes, often using covalent modification of proteins by ubiquitylation. It consists of a 20S proteolytic core particle (CP) and a 19S regulatory particle (RP). The CP is an ATP independent peptidase consisting of hydrolyzing activities. One or both ends of CP carry the RP that confers both ubiquitin and ATP dependence to the 26S proteosome. The RP's  proposed functions include recognition of substrates and translocation of these to CP for proteolysis. The RP can dissociate into a stable lid and base subcomplexes. The base is composed of three non-ATPase subunits (Rpn 1, 2 and 10). A single residue in the vWA domain of Rpn10 has been implicated to be responsible for stabilizing the lid-base association.
Probab=25.85  E-value=54  Score=14.58  Aligned_cols=47  Identities=9%  Similarity=0.212  Sum_probs=31.2

Q ss_pred             CCCCCCEEEEE--------ECCCCCCCCCCEEEEEEECCCCCCCCCCCHHHHHHH
Q ss_conf             05877559987--------537899988757999952688662225402567764
Q gi|254780236|r   88 SDRSGGYLRIM--------KRGFRYGDSAPMAVIEFVDRDLSAKGTPVSRKSHKV  134 (136)
Q Consensus        88 ~~R~GGYTRi~--------kl~~R~gD~A~ma~iElVd~~~~~~~~~~~~~~~~~  134 (136)
                      .-.+||=..+.        -|..|.+.+..|-+|=||++|.+.......+-.++.
T Consensus        78 ~i~~~G~~~~~~~IqiA~LALKHRqnk~~~qRIv~FVgSPi~~~ek~l~~laKkl  132 (187)
T cd01452          78 DVQPKGKANFITGIQIAQLALKHRQNKNQKQRIVAFVGSPIEEDEKDLVKLAKRL  132 (187)
T ss_pred             CCCCCCEECHHHHHHHHHHHHHCCCCCCCCEEEEEEECCCCCCCHHHHHHHHHHH
T ss_conf             6771876518879999999972346777544799997898755789999999987


No 12 
>TIGR03060 PS_II_psb29 photosystem II biogenesis protein Psp29. Psp29, originally designated sll1414 in Synechocystis 6803, is found universally in Cyanobacteria and in Arabidopsis. It was isolated and partially sequenced from purified photosystem II (PS II) in Synechocystis. While its function is unknown, mutant studies show an impairment in photosystem II biogenesis and/or stability, rather than in PS II core function.
Probab=25.75  E-value=47  Score=14.94  Aligned_cols=80  Identities=20%  Similarity=0.242  Sum_probs=52.9

Q ss_pred             CCHHHHHHHHHHHHHHHHHCCEEEECHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHCCHHHHHHHHHHHHHHHCCCC
Q ss_conf             78899999999999999868937875999999886421676231138767788999872566889999999998850587
Q gi|254780236|r   12 RTSSHRKAMFSNMAASIIWHEQIVTTLPKAKELRPIVEKLVTLGKKGGLHSLRLAISKIGDVDVVNKLFGIIAKRYSDRS   91 (136)
Q Consensus        12 r~~~hR~allrnl~~~Li~herI~TT~~KAKelr~~aEklIt~AK~~~~~~rr~~~~~l~~~~~v~kLf~~l~prf~~R~   91 (136)
                      ++..|+-.++.-||.++=         --+.+++..++++..+|+.-+...   +.+|+............+...=.+..
T Consensus        68 ~Pee~~~~IF~Alc~s~~---------~dp~~~r~dA~~l~~~a~~~s~~~---i~~~l~~~~~~~~~~~~l~~~a~n~k  135 (214)
T TIGR03060        68 RPEEHLDALFDALCNSNG---------FDPEQLREDAKQLLEQAKGKGLDE---ILSWLTQANLSNGGGDTLQGIAGRHK  135 (214)
T ss_pred             CCHHHHHHHHHHHHHHCC---------CCHHHHHHHHHHHHHHHHCCCHHH---HHHHHHCCCCCCCHHHHHHHHHCCCC
T ss_conf             982569999999987348---------999999999999999997489999---99998504755411679998741787


Q ss_pred             CCEEEEEECC-CC
Q ss_conf             7559987537-89
Q gi|254780236|r   92 GGYLRIMKRG-FR  103 (136)
Q Consensus        92 GGYTRi~kl~-~R  103 (136)
                      .-|.|+.-+| ++
T Consensus       136 f~YSRl~AIGL~~  148 (214)
T TIGR03060       136 FKYSRLFAIGLYS  148 (214)
T ss_pred             CCHHHHHHHHHHH
T ss_conf             4089999999999


No 13 
>cd05399 NT_Rel-Spo_like Nucleotidyltransferase (NT) domain of RelA- and SpoT-like ppGpp synthetases and hydrolases. This family includes the catalytic domains of Escherichia coli ppGpp synthetase (RelA), ppGpp synthetase/hydrolase (SpoT), and related proteins. RelA synthesizes (p)ppGpp in response to amino-acid starvation and in association with ribosomes. (p)ppGpp triggers the bacterial stringent response. SpoT catalyzes (p)ppGpp synthesis under carbon limitation in a ribosome-independent manner. It also catalyzes (p)ppGpp degradation. Gram-negative bacteria have two enzymes involved in (p)ppGpp metabolism while most Gram-positive organisms have a single Rel-Spo enzyme (Rel), which both synthesizes and degrades (p)ppGpp. The Arabidopsis thaliana Rel-Spo proteins, At-RSH1,-2, and-3 appear to regulate a rapid (p)ppGpp-mediated response to pathogens and other stresses. This catalytic domain is found in association with an N-terminal HD domain and a C-terminal metal dependent phosphohydro
Probab=25.03  E-value=5.8  Score=20.29  Aligned_cols=79  Identities=22%  Similarity=0.320  Sum_probs=44.4

Q ss_pred             HHHHHHHHHHHHCCEEEECHHHHHHHHHHHHHHHHHHCCC-------CHHHHHHHHHHHCCHH----HHHHHHHHHHHHH
Q ss_conf             9999999999868937875999999886421676231138-------7677889998725668----8999999999885
Q gi|254780236|r   19 AMFSNMAASIIWHEQIVTTLPKAKELRPIVEKLVTLGKKG-------GLHSLRLAISKIGDVD----VVNKLFGIIAKRY   87 (136)
Q Consensus        19 allrnl~~~Li~herI~TT~~KAKelr~~aEklIt~AK~~-------~~~~rr~~~~~l~~~~----~v~kLf~~l~prf   87 (136)
                      ..+.+++.++..++.+.....+.|..-...+||....+..       |+...|.+..+..|-.    ++...|+....++
T Consensus         5 ~~i~~~L~~~~~~~~~~~i~~RvK~~~S~~~Kl~rk~~~~~~~~~i~Dl~g~Rii~~~~~d~~~v~~~l~~~f~~~~~~~   84 (129)
T cd05399           5 EEIADLLRDAGIIGRVASVSGRVKSPYSIYEKLRRKGKDLPILDEITDLVGVRVVLLFVDDCYRVLDLLHSLFKVIPGRV   84 (129)
T ss_pred             HHHHHHHHHCCCCCCCEEEECCCCCHHHHHHHHHHHCCCCCCHHHHCCHHEEEEEEECCHHHHHHHHHHHCCCCCCCCCC
T ss_conf             99999999879988820896716997999999985488867687712014699999431679999999971798624411


Q ss_pred             CC-----CCCCEEEE
Q ss_conf             05-----87755998
Q gi|254780236|r   88 SD-----RSGGYLRI   97 (136)
Q Consensus        88 ~~-----R~GGYTRi   97 (136)
                      .|     .++||--+
T Consensus        85 ~D~i~~pk~~GYrs~   99 (129)
T cd05399          85 KDYIAEPKENGYQSL   99 (129)
T ss_pred             CCCCCCCCCCCCCEE
T ss_conf             466678888897878


No 14 
>PRK13266 Thf1-like protein; Reviewed
Probab=24.36  E-value=58  Score=14.41  Aligned_cols=80  Identities=21%  Similarity=0.344  Sum_probs=56.7

Q ss_pred             CCHHHHHHHHHHHHHHHHHCCEEEECHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHCCH-HHHHHHHHHHHHHHCCC
Q ss_conf             78899999999999999868937875999999886421676231138767788999872566-88999999999885058
Q gi|254780236|r   12 RTSSHRKAMFSNMAASIIWHEQIVTTLPKAKELRPIVEKLVTLGKKGGLHSLRLAISKIGDV-DVVNKLFGIIAKRYSDR   90 (136)
Q Consensus        12 r~~~hR~allrnl~~~Li~herI~TT~~KAKelr~~aEklIt~AK~~~~~~rr~~~~~l~~~-~~v~kLf~~l~prf~~R   90 (136)
                      ++..|+-+++..||.++=         --+.++|..++++..+|+..+...   +.+||..+ +....|...+.-.-.+-
T Consensus        68 ~Pee~~~~IF~Alc~s~~---------~dp~~~r~dA~~l~~~a~~~s~~~---i~~~l~~~~~~~~~l~~~~~~~~~~~  135 (224)
T PRK13266         68 RPEEHKDALFEALCQAVG---------FDPEQLREDAEQLLELAKGKSLDE---ILSWLTQKGGGANELLATLQAIANNS  135 (224)
T ss_pred             CCHHHHHHHHHHHHHHCC---------CCHHHHHHHHHHHHHHHHCCCHHH---HHHHHHHCCCCCCHHHHHHHHHHCCC
T ss_conf             982569999999998448---------999999999999999987589999---99999735455506889999874278


Q ss_pred             CCCEEEEEECC-CC
Q ss_conf             77559987537-89
Q gi|254780236|r   91 SGGYLRIMKRG-FR  103 (136)
Q Consensus        91 ~GGYTRi~kl~-~R  103 (136)
                      +.-|.|+.-+| ++
T Consensus       136 ~f~YSRl~AIGL~~  149 (224)
T PRK13266        136 KFKYSRLFAIGLYT  149 (224)
T ss_pred             CCHHHHHHHHHHHH
T ss_conf             73289999999999


No 15 
>COG4463 CtsR Transcriptional repressor of class III stress genes [Transcription]
Probab=24.34  E-value=44  Score=15.12  Aligned_cols=13  Identities=46%  Similarity=1.043  Sum_probs=9.6

Q ss_pred             CCCEEEEEECCCC
Q ss_conf             7755998753789
Q gi|254780236|r   91 SGGYLRIMKRGFR  103 (136)
Q Consensus        91 ~GGYTRi~kl~~R  103 (136)
                      -|||-||+|..++
T Consensus        64 GGGYIRI~Kv~~~   76 (153)
T COG4463          64 GGGYIRIIKVEYS   76 (153)
T ss_pred             CCCEEEEEEECCC
T ss_conf             8756999985125


No 16 
>KOG2188 consensus
Probab=23.14  E-value=61  Score=14.27  Aligned_cols=40  Identities=18%  Similarity=0.218  Sum_probs=27.8

Q ss_pred             HHHHHHCCCCHH-HHHHHHHHHCCHHHHHHHHHHHHHHHCC
Q ss_conf             676231138767-7889998725668899999999988505
Q gi|254780236|r   50 KLVTLGKKGGLH-SLRLAISKIGDVDVVNKLFGIIAKRYSD   89 (136)
Q Consensus        50 klIt~AK~~~~~-~rr~~~~~l~~~~~v~kLf~~l~prf~~   89 (136)
                      ++.++|+....+ ..+.++..+.+.+.+.-+|++++|++.+
T Consensus       373 rl~~La~~p~aNF~lQrli~h~~~~e~v~~v~eeL~P~~~~  413 (650)
T KOG2188         373 RLDELAVHPIANFPLQRLINHLTSLEDVGSVIEELAPKLSS  413 (650)
T ss_pred             HHHHHHHCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
T ss_conf             89998727543425999998656788899999997277999


No 17 
>COG5095 TAF6 Transcription initiation factor TFIID, subunit TAF6 (also component of histone acetyltransferase SAGA) [Transcription]
Probab=23.08  E-value=61  Score=14.26  Aligned_cols=31  Identities=19%  Similarity=0.314  Sum_probs=12.6

Q ss_pred             HHHHHHHHHHHH-HHCCCCHHHHHHHHHHHCC
Q ss_conf             998864216762-3113876778899987256
Q gi|254780236|r   42 KELRPIVEKLVT-LGKKGGLHSLRLAISKIGD   72 (136)
Q Consensus        42 Kelr~~aEklIt-~AK~~~~~~rr~~~~~l~~   72 (136)
                      ||+|-|.||+|. ++-..+.+.+.-+.+-|++
T Consensus       193 KELq~YF~kvisal~dEs~~~~r~aAl~sLr~  224 (450)
T COG5095         193 KELQMYFDKVISALLDESDEQTRDAALESLRN  224 (450)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCC
T ss_conf             99999999999999877789999999987516


No 18 
>cd06541 ASCH ASC-1 homology or ASCH domain, a small beta-barrel domain found in all three kingdoms of life. ASCH resembles the RNA-binding PUA domain and may also interact with RNA. ASCH has been proposed to function as an RNA-binding domain during coactivation, RNA-processing and the regulation of prokaryotic translation. The domain has been named after the ASC-1 protein, the activating signal cointegrator 1 or thyroid hormone receptor interactor protein 4 (TRIP4). ASC-1 is conserved in many eukaryotes and has been suggested to participate in a protein complex that interacts with RNA. It has been shown that ASC-1 mediates the interaction between various transciption factors and the basal transcriptional machinery.
Probab=22.55  E-value=63  Score=14.20  Aligned_cols=36  Identities=28%  Similarity=0.554  Sum_probs=23.8

Q ss_pred             CCCCCEEEEEECCCCCCCCCCEEEEEEECCCCCCCCCCCHHH
Q ss_conf             587755998753789998875799995268866222540256
Q gi|254780236|r   89 DRSGGYLRIMKRGFRYGDSAPMAVIEFVDRDLSAKGTPVSRK  130 (136)
Q Consensus        89 ~R~GGYTRi~kl~~R~gD~A~ma~iElVd~~~~~~~~~~~~~  130 (136)
                      -+.|+|-.|+.     || -|.|+||+|.-+..+.-+.+.+.
T Consensus        31 ~K~G~y~iild-----g~-~pl~~ievv~v~~~~~~~ev~ee   66 (105)
T cd06541          31 PKAGDYLIILD-----GQ-QPLAIAEVVKVEIMPMVNELSEE   66 (105)
T ss_pred             CCCCCEEEEEC-----CC-CCEEEEEEEEEEEEECCCCCCHH
T ss_conf             66675789974-----99-96589999889998602413489


No 19 
>cd01121 Sms Sms (bacterial radA) DNA repair protein. This protein is not related to archael radA any more than is to other RecA-like NTPases. Sms has a role in recombination and recombinational repair and is responsible for the stabilization or processing of branched DNA molecules.
Probab=20.94  E-value=68  Score=14.00  Aligned_cols=82  Identities=16%  Similarity=0.363  Sum_probs=50.6

Q ss_pred             HHHHHHHHHHHHHCCCCHHHHHHHH------HHHCCHHHHHHHHHHHHHHHCCCCCCEEEEEEC-CCCCCCCCCEEEEEE
Q ss_conf             9886421676231138767788999------872566889999999998850587755998753-789998875799995
Q gi|254780236|r   43 ELRPIVEKLVTLGKKGGLHSLRLAI------SKIGDVDVVNKLFGIIAKRYSDRSGGYLRIMKR-GFRYGDSAPMAVIEF  115 (136)
Q Consensus        43 elr~~aEklIt~AK~~~~~~rr~~~------~~l~~~~~v~kLf~~l~prf~~R~GGYTRi~kl-~~R~gD~A~ma~iEl  115 (136)
                      ++|--+..|+.+||..+..-  ++.      ..+--+.+..++.+.+. -|+.-.+..-||++. .+|.|..-++++.|.
T Consensus       184 QVReca~~L~~~AK~~~i~~--~lVGHVTK~G~iAGPkvLEHmVDtVl-~fEgd~~~~~R~LR~~KNRFG~t~EiGvFeM  260 (372)
T cd01121         184 QVRECTAELMRFAKERNIPI--FIVGHVTKEGSIAGPKVLEHMVDTVL-YFEGDRHSEYRILRSVKNRFGSTNELGVFEM  260 (372)
T ss_pred             HHHHHHHHHHHHHHHCCCEE--EEEEEECCCCCCCCCHHHEEEEEEEE-EECCCCCCCEEEEEEECCCCCCCCEEEEEEE
T ss_conf             99999999999998619739--99987626886377403100213688-7515776550356741156777540588873


Q ss_pred             ECCCCCCCCCCC
Q ss_conf             268866222540
Q gi|254780236|r  116 VDRDLSAKGTPV  127 (136)
Q Consensus       116 Vd~~~~~~~~~~  127 (136)
                      .+.-+..-.+|-
T Consensus       261 ~~~GL~~V~nPS  272 (372)
T cd01121         261 RENGLREVSNPS  272 (372)
T ss_pred             CCCCCEECCCHH
T ss_conf             168705636856


No 20 
>TIGR02817 adh_fam_1 zinc-binding alcohol dehydrogenase family protein; InterPro: IPR014182   Members of this entry form a distinct subset of the larger family of oxidoreductases that includes zinc-binding alcohol dehydrogenases and NADPH:quinone reductases. Some current members of this entry carry designations as putative alginate lyase, however none have been characterised as such..
Probab=20.04  E-value=71  Score=13.89  Aligned_cols=23  Identities=26%  Similarity=0.235  Sum_probs=19.4

Q ss_pred             HHHHHHHHHHHHHCCEEEECHHH
Q ss_conf             99999999999868937875999
Q gi|254780236|r   18 KAMFSNMAASIIWHEQIVTTLPK   40 (136)
Q Consensus        18 ~allrnl~~~Li~herI~TT~~K   40 (136)
                      .+-|=|=|..||-.|+|.||++.
T Consensus       285 QH~LLn~VA~LvD~G~irTTl~e  307 (338)
T TIGR02817       285 QHELLNRVARLVDAGKIRTTLAE  307 (338)
T ss_pred             HHHHHHHHHHHHCCCEEEEEECC
T ss_conf             99999999888649846531103


Done!