Query         gi|254780712|ref|YP_003065125.1| 30S ribosomal protein S16 [Candidatus Liberibacter asiaticus str. psy62]
Match_columns 116
No_of_seqs    112 out of 1084
Neff          5.9 
Searched_HMMs 39220
Date          Sun May 29 19:49:50 2011
Command       /home/congqian_1/programs/hhpred/hhsearch -i 254780712.hhm -d /home/congqian_1/database/cdd/Cdd.hhm 

 No Hit                             Prob E-value P-value  Score    SS Cols Query HMM  Template HMM
  1 KOG3419 consensus              100.0 5.9E-39 1.5E-43  258.9   8.0  104    1-104     1-104 (112)
  2 CHL00005 rps16 ribosomal prote 100.0 6.5E-36 1.7E-40  240.3   7.2   80    2-86      1-80  (82)
  3 COG0228 RpsP Ribosomal protein 100.0 8.1E-36 2.1E-40  239.7   7.1   78    2-81      1-78  (87)
  4 PRK00040 rpsP 30S ribosomal pr 100.0 3.7E-35 9.5E-40  235.7   7.5   75    2-79      1-75  (75)
  5 TIGR00002 S16 ribosomal protei 100.0 1.5E-32 3.9E-37  219.8   7.2   81    3-83      1-81  (81)
  6 pfam00886 Ribosomal_S16 Riboso  99.9 2.6E-26 6.6E-31  181.9   6.7   58    9-70      1-58  (58)
  7 KOG0135 consensus               67.9     6.5 0.00016   21.1   3.3   36   28-68    168-206 (661)
  8 pfam08755 YccV-like Hemimethyl  52.2      10 0.00026   19.9   2.1   16   12-27     45-60  (100)
  9 TIGR02097 yccV hemimethylated   39.5      20 0.00052   18.1   2.0   15   13-27     47-61  (103)
 10 pfam11875 DUF3395 Domain of un  38.4      18 0.00046   18.4   1.6   20   32-53    102-121 (144)
 11 TIGR01132 pgm phosphoglucomuta  36.1      23  0.0006   17.7   1.9   43   17-67    142-189 (553)
 12 KOG2321 consensus               29.0      16 0.00041   18.7   0.0   33   27-59     59-91  (703)
 13 pfam09086 DUF1924 Domain of un  27.6      50  0.0013   15.7   2.4   34   28-68     46-79  (98)
 14 TIGR00625 tfb2 Transcription f  26.3      47  0.0012   15.8   2.1   28   67-94    154-182 (507)
 15 TIGR01249 pro_imino_pep_1 prol  25.1      39   0.001   16.3   1.5   43   16-65     52-94  (310)
 16 KOG3471 consensus               23.9      67  0.0017   14.9   2.9   64   10-87    120-186 (465)
 17 KOG3423 consensus               22.9      64  0.0016   15.0   2.2   39   32-80     75-115 (176)
 18 TIGR00845 caca sodium/calcium   21.5      20 0.00052   18.1  -0.6   13   10-22    399-411 (1067)
 19 cd06364 PBP1_CaSR Ligand-bindi  21.1      76  0.0019   14.6   3.8   41   16-59    467-508 (510)
 20 COG3785 Uncharacterized conser  20.8      58  0.0015   15.3   1.6   17   12-28     56-72  (116)
 21 KOG2806 consensus               20.7      78   0.002   14.5   3.6   61   15-77    234-295 (432)
 22 COG5162 Transcription initiati  20.5      78   0.002   14.5   2.4   40   32-81     77-118 (197)

No 1  
>KOG3419 consensus
Probab=100.00  E-value=5.9e-39  Score=258.86  Aligned_cols=104  Identities=43%  Similarity=0.674  Sum_probs=97.3

Q ss_pred             CCCHHHHHHCCCCCCCEEEEEEEECCCCCCCCCEEEEEEECCCCCCCCCCEEEECHHHHHHHHHCCCCCCHHHHHHHHHC
Q ss_conf             93014123066878882799992067877684102221215678788864479739999999841983568999999972
Q gi|254780712|r    1 MTLKIRLACGGSKSRHHYRIVVANSRSPRDGKFIEKLGTWNPTLPKENPLRFTMNFERIQHWMSKGAQPTDRILFFLDKA   80 (116)
Q Consensus         1 M~vkIRL~r~G~k~rp~yrIVvadsr~~Rdgk~iE~lG~YnP~~~k~~~~~i~l~~eRi~yWL~~GAqpS~~V~~LL~~~   80 (116)
                      |+|+|||+|+||||||||||||||+|++|||++||+||||||++++++.+.|.||+|||+|||++|||||++|..||+++
T Consensus         1 ~~vkIRLar~GcknRPfY~Ivva~~r~~rdgk~iE~lG~ydPlp~~~~~~~v~Ln~dRikyWl~~GAqpS~tv~~Ll~~a   80 (112)
T KOG3419           1 MVVKIRLARFGCKNRPFYRIVVADSRKRRDGKPIEQLGTYDPLPNQDNEKLVALNFDRIKYWLGVGAQPSDTVEELLGKA   80 (112)
T ss_pred             CEEEEEEHHCCCCCCCEEEEEEEECCCCCCCCCHHHEECCCCCCCCCCCCCEEECHHHHHHHHHCCCCCCHHHHHHHHHC
T ss_conf             91788623118667872699983044566688653223345788878873146318999999854884686899998754


Q ss_pred             CCCCCCCCCCCHHHHHHHHHHHHH
Q ss_conf             986668000511225428898899
Q gi|254780712|r   81 GLIKRSPQNNPKKSQPKKKALERL  104 (116)
Q Consensus        81 Gl~~~~~~~~~~~~~~~kk~~e~~  104 (116)
                      |+++.+|..+......++...+..
T Consensus        81 Gl~p~~p~~~~~a~~~rr~~a~~~  104 (112)
T KOG3419          81 GLFPIHPMTFMNAKRNRRLTAEQV  104 (112)
T ss_pred             CCCCCCHHHHHCCCCCHHHHHHHC
T ss_conf             788886366512312235565530


No 2  
>CHL00005 rps16 ribosomal protein S16
Probab=100.00  E-value=6.5e-36  Score=240.34  Aligned_cols=80  Identities=35%  Similarity=0.530  Sum_probs=75.5

Q ss_pred             CCHHHHHHCCCCCCCEEEEEEEECCCCCCCCCEEEEEEECCCCCCCCCCEEEECHHHHHHHHHCCCCCCHHHHHHHHHCC
Q ss_conf             30141230668788827999920678776841022212156787888644797399999998419835689999999729
Q gi|254780712|r    2 TLKIRLACGGSKSRHHYRIVVANSRSPRDGKFIEKLGTWNPTLPKENPLRFTMNFERIQHWMSKGAQPTDRILFFLDKAG   81 (116)
Q Consensus         2 ~vkIRL~r~G~k~rp~yrIVvadsr~~Rdgk~iE~lG~YnP~~~k~~~~~i~l~~eRi~yWL~~GAqpS~~V~~LL~~~G   81 (116)
                      ||+|||+|+|+||+|||||||+|||+||||+|||+||||||+.     +.+.||.||++|||++||||||||.+||+++|
T Consensus         1 MVkIRL~R~G~kk~P~YrIVv~dsr~~RdGk~iE~lG~YnP~~-----~~~~l~~eri~~Wl~~GAqpT~tV~~Llk~~g   75 (82)
T CHL00005          1 MVKLRLKRCGRKQQAVYRIVAIDVRSRREGRDLRKVGFYDPIK-----NQTYLNVPAILYFLEKGAQPTGTVYDILKKAE   75 (82)
T ss_pred             CEEEECCCCCCCCCCEEEEEEEECCCCCCCCCEEEEEEECCCC-----CCCCCCHHHHHHHHHCCCCCCHHHHHHHHHCC
T ss_conf             9178301289888982689987357778998536777757999-----86533899999999976988899999999837


Q ss_pred             CCCCC
Q ss_conf             86668
Q gi|254780712|r   82 LIKRS   86 (116)
Q Consensus        82 l~~~~   86 (116)
                      +++..
T Consensus        76 i~~~~   80 (82)
T CHL00005         76 VFKEL   80 (82)
T ss_pred             CHHHH
T ss_conf             37765


No 3  
>COG0228 RpsP Ribosomal protein S16 [Translation, ribosomal structure and biogenesis]
Probab=100.00  E-value=8.1e-36  Score=239.73  Aligned_cols=78  Identities=60%  Similarity=0.961  Sum_probs=75.6

Q ss_pred             CCHHHHHHCCCCCCCEEEEEEEECCCCCCCCCEEEEEEECCCCCCCCCCEEEECHHHHHHHHHCCCCCCHHHHHHHHHCC
Q ss_conf             30141230668788827999920678776841022212156787888644797399999998419835689999999729
Q gi|254780712|r    2 TLKIRLACGGSKSRHHYRIVVANSRSPRDGKFIEKLGTWNPTLPKENPLRFTMNFERIQHWMSKGAQPTDRILFFLDKAG   81 (116)
Q Consensus         2 ~vkIRL~r~G~k~rp~yrIVvadsr~~Rdgk~iE~lG~YnP~~~k~~~~~i~l~~eRi~yWL~~GAqpS~~V~~LL~~~G   81 (116)
                      ||+|||+|+|+||+|||||||||||+||||+|||.||||||++  +.++.|.||.||+.|||++||||||||.+||+++|
T Consensus         1 ~vkIRL~R~G~kk~P~YrIVVaDsrs~RDGr~IE~lG~ynP~~--~~~~~v~l~~eri~~Wl~~GAqpSdtV~~ll~~~g   78 (87)
T COG0228           1 MVKIRLARGGSKKRPFYRIVVADSRSPRDGRFIERLGTYNPLL--GKEERVKLDEERILYWLSQGAQPSDTVRRLLKKAG   78 (87)
T ss_pred             CEEEEHHHCCCCCCCEEEEEEECCCCCCCCCCHHHHCCCCCCC--CCCCEEEECHHHHHHHHHCCCCCCHHHHHHHHHHH
T ss_conf             9078530178766984799984168888986445400237887--87634788699999999859974489999999852


No 4  
>PRK00040 rpsP 30S ribosomal protein S16; Reviewed
Probab=100.00  E-value=3.7e-35  Score=235.71  Aligned_cols=75  Identities=53%  Similarity=0.925  Sum_probs=71.8

Q ss_pred             CCHHHHHHCCCCCCCEEEEEEEECCCCCCCCCEEEEEEECCCCCCCCCCEEEECHHHHHHHHHCCCCCCHHHHHHHHH
Q ss_conf             301412306687888279999206787768410222121567878886447973999999984198356899999997
Q gi|254780712|r    2 TLKIRLACGGSKSRHHYRIVVANSRSPRDGKFIEKLGTWNPTLPKENPLRFTMNFERIQHWMSKGAQPTDRILFFLDK   79 (116)
Q Consensus         2 ~vkIRL~r~G~k~rp~yrIVvadsr~~Rdgk~iE~lG~YnP~~~k~~~~~i~l~~eRi~yWL~~GAqpS~~V~~LL~~   79 (116)
                      ||+|||+|+||||+|||||||+|+|+||||+|||+||||||+.   +++.+.||.|||+|||++|||||++|.+||++
T Consensus         1 mvkIRL~R~G~k~~P~YrIVv~d~r~~RdGk~iE~lG~ydP~~---~~~~~~l~~eri~~Wl~~GAqpS~~V~~Llkk   75 (75)
T PRK00040          1 MVKIRLARGGAKKRPFYRIVVADSRSPRDGRFIERVGFYNPLA---KPAEVKLDEERVLYWLGQGAQPTDTVARLLKK   75 (75)
T ss_pred             CEEEEHHCCCCCCCCEEEEEEEECCCCCCCCCHHEEEEECCCC---CCCEEEECHHHHHHHHHCCCCCCHHHHHHHCC
T ss_conf             9388120089989985899996266678886100004777989---98669984999999998789868999998639


No 5  
>TIGR00002 S16 ribosomal protein S16; InterPro: IPR000307   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 S16 is one of the proteins from the small ribosomal subunit. It belongs to a family of ribosomal proteins which, on the basis of sequence similarities , groups:  Eubacterial S16. Algal and plant chloroplast S16. Cyanelle S16. Neurospora crassa mitochondrial S24 (cyt-21). S16 proteins have about 100 amino-acid residues. ; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome.
Probab=99.97  E-value=1.5e-32  Score=219.80  Aligned_cols=81  Identities=56%  Similarity=0.948  Sum_probs=78.3

Q ss_pred             CHHHHHHCCCCCCCEEEEEEEECCCCCCCCCEEEEEEECCCCCCCCCCEEEECHHHHHHHHHCCCCCCHHHHHHHHHCCC
Q ss_conf             01412306687888279999206787768410222121567878886447973999999984198356899999997298
Q gi|254780712|r    3 LKIRLACGGSKSRHHYRIVVANSRSPRDGKFIEKLGTWNPTLPKENPLRFTMNFERIQHWMSKGAQPTDRILFFLDKAGL   82 (116)
Q Consensus         3 vkIRL~r~G~k~rp~yrIVvadsr~~Rdgk~iE~lG~YnP~~~k~~~~~i~l~~eRi~yWL~~GAqpS~~V~~LL~~~Gl   82 (116)
                      |+|||+|+|||++|||||||+|++++|||+|||+||+|||++..++.+++.||.|||.|||++||||||||.+||.++|+
T Consensus         1 vkiRL~r~G~k~~p~Yrivv~d~~~~RdG~~ie~lG~y~P~~~~~~~~~~~l~~~~~~~wl~~Ga~pt~tv~~ll~~~g~   80 (81)
T TIGR00002         1 VKIRLKRGGRKKRPFYRIVVADSRSPRDGRYIEELGFYNPLLKEDDEERVKLDVERIKYWLSKGAQPTDTVRNLLKKAGV   80 (81)
T ss_pred             CEEECCCCCCCCCCEEEEEEECCCCCCCCCHHHHCCCCCCCCCCCCCCEEEECHHHHHHHHHCCCCCCHHHHHHHHHHCC
T ss_conf             91110237765686157886247897454123331544788889875246636799999986699857788999886147


Q ss_pred             C
Q ss_conf             6
Q gi|254780712|r   83 I   83 (116)
Q Consensus        83 ~   83 (116)
                      +
T Consensus        81 ~   81 (81)
T TIGR00002        81 F   81 (81)
T ss_pred             C
T ss_conf             9


No 6  
>pfam00886 Ribosomal_S16 Ribosomal protein S16.
Probab=99.93  E-value=2.6e-26  Score=181.86  Aligned_cols=58  Identities=60%  Similarity=1.021  Sum_probs=55.3

Q ss_pred             HCCCCCCCEEEEEEEECCCCCCCCCEEEEEEECCCCCCCCCCEEEECHHHHHHHHHCCCCCC
Q ss_conf             06687888279999206787768410222121567878886447973999999984198356
Q gi|254780712|r    9 CGGSKSRHHYRIVVANSRSPRDGKFIEKLGTWNPTLPKENPLRFTMNFERIQHWMSKGAQPT   70 (116)
Q Consensus         9 r~G~k~rp~yrIVvadsr~~Rdgk~iE~lG~YnP~~~k~~~~~i~l~~eRi~yWL~~GAqpS   70 (116)
                      |+||||+|||||||+|||++|||+|||+||+|||+++    +.+.||.|||+|||++|||||
T Consensus         1 R~G~k~~P~YrIVv~d~r~~RdGk~iE~lG~YdP~~~----~~~~l~~eri~~Wl~~GAqPs   58 (58)
T pfam00886         1 RGGRKKRPFYRIVVADSRSPRDGRFIEELGTYNPIAN----GEVKLDVERIKYWLGKGAQPT   58 (58)
T ss_pred             CCCCCCCCEEEEEEEECCCCCCCCCHHEEEEECCCCC----CEEEEEHHHHHHHHHCCCCCC
T ss_conf             9887789868999974777889976103545659998----558982899999998749993


No 7  
>KOG0135 consensus
Probab=67.88  E-value=6.5  Score=21.11  Aligned_cols=36  Identities=28%  Similarity=0.577  Sum_probs=26.9

Q ss_pred             CCCCCCEEEEEEECCCCCCCCCCEEEE---CHHHHHHHHHCCCC
Q ss_conf             776841022212156787888644797---39999999841983
Q gi|254780712|r   28 PRDGKFIEKLGTWNPTLPKENPLRFTM---NFERIQHWMSKGAQ   68 (116)
Q Consensus        28 ~Rdgk~iE~lG~YnP~~~k~~~~~i~l---~~eRi~yWL~~GAq   68 (116)
                      --+-+-|+-.-||||.+     ++..|   |++.+++|+|+-|.
T Consensus       168 GSNt~~I~TtatyDP~t-----~EfVinTP~~~A~K~WiGn~a~  206 (661)
T KOG0135         168 GSNTKGIQTTATYDPTT-----EEFVINTPDFSAIKCWIGNAAK  206 (661)
T ss_pred             CCCCCCEEEEEEECCCC-----CEEEECCCCHHHHHHHHCCCCC
T ss_conf             76645314554126987-----7267548968888887503223


No 8  
>pfam08755 YccV-like Hemimethylated DNA-binding protein YccV like. YccV is a hemimethylated DNA binding protein which has been shown to regulate dnaA gene expression. The structure of one of the hypothetical proteins in this family has been solved and it forms a beta sheet structure with a terminating alpha helix.
Probab=52.25  E-value=10  Score=19.91  Aligned_cols=16  Identities=19%  Similarity=0.540  Sum_probs=13.0

Q ss_pred             CCCCCEEEEEEEECCC
Q ss_conf             8788827999920678
Q gi|254780712|r   12 SKSRHHYRIVVANSRS   27 (116)
Q Consensus        12 ~k~rp~yrIVvadsr~   27 (116)
                      .|+.|||||.|-|..+
T Consensus        45 ~k~QPfYhvLv~~~~~   60 (100)
T pfam08755        45 ARDQPFYHVLVEDDDS   60 (100)
T ss_pred             CCCCCCEEEEEECCCC
T ss_conf             5679836999966986


No 9  
>TIGR02097 yccV hemimethylated DNA binding domain; InterPro: IPR011722   This entry describes the small protein from E. coli YccV and its homologs in other Proteobacteria. YccV is now described as a hemimethylated DNA binding protein . The model entry describes a domain in longer eukaryotic proteins..
Probab=39.53  E-value=20  Score=18.08  Aligned_cols=15  Identities=20%  Similarity=0.538  Sum_probs=11.6

Q ss_pred             CCCCEEEEEEEECCC
Q ss_conf             788827999920678
Q gi|254780712|r   13 KSRHHYRIVVANSRS   27 (116)
Q Consensus        13 k~rp~yrIVvadsr~   27 (116)
                      ++.|||+|+|=|...
T Consensus        47 ~~qPfY~vl~e~~~~   61 (103)
T TIGR02097        47 KDQPFYHVLVEDDEG   61 (103)
T ss_pred             CCCCCEEEEEECCCC
T ss_conf             578972688864899


No 10 
>pfam11875 DUF3395 Domain of unknown function (DUF3395). This domain is functionally uncharacterized. This domain is found in eukaryotes. This presumed domain is typically between 147 to 176 amino acids in length. This domain is found associated with pfam00226.
Probab=38.39  E-value=18  Score=18.38  Aligned_cols=20  Identities=20%  Similarity=0.272  Sum_probs=13.0

Q ss_pred             CCEEEEEEECCCCCCCCCCEEE
Q ss_conf             4102221215678788864479
Q gi|254780712|r   32 KFIEKLGTWNPTLPKENPLRFT   53 (116)
Q Consensus        32 k~iE~lG~YnP~~~k~~~~~i~   53 (116)
                      ..-..+|||||.+.  .++.+.
T Consensus       102 ~Ks~L~GF~DPcpg--~~K~L~  121 (144)
T pfam11875       102 SKSNLLGFYDPCPG--EPKVLY  121 (144)
T ss_pred             CHHCCCCCCCCCCC--CCCEEE
T ss_conf             35217765699989--986799


No 11 
>TIGR01132 pgm phosphoglucomutase, alpha-D-glucose phosphate-specific; InterPro: IPR005852    Phosphoglucomutase, alpha-D-glucose phosphate-specific () links the anaerobic or aerobic glycolysis of glucose-6-phosphate and glucose-1-phosphate produced by various glycan phosphorylases by catalysing the transfer of a phosphate group between C-1 and C-6 of glucose .     Alpha-D-glucose 1-phosphate = alpha-D-glucose 6-phosphate.; GO: 0004614 phosphoglucomutase activity, 0005975 carbohydrate metabolic process.
Probab=36.11  E-value=23  Score=17.70  Aligned_cols=43  Identities=30%  Similarity=0.539  Sum_probs=26.2

Q ss_pred             EEEEEEEECCC-CCCCCCEEEEEE-ECCCCCCCCCCE---EEECHHHHHHHHHCCC
Q ss_conf             27999920678-776841022212-156787888644---7973999999984198
Q gi|254780712|r   17 HYRIVVANSRS-PRDGKFIEKLGT-WNPTLPKENPLR---FTMNFERIQHWMSKGA   67 (116)
Q Consensus        17 ~yrIVvadsr~-~Rdgk~iE~lG~-YnP~~~k~~~~~---i~l~~eRi~yWL~~GA   67 (116)
                      -==||++-|.. |.||      |. |||  |..+|.+   .+.=.+|+...|..|-
T Consensus       142 ADGIviTPSHNPP~DG------GiKYNP--P~GGPA~~~~T~~i~~RAN~~l~~~~  189 (553)
T TIGR01132       142 ADGIVITPSHNPPEDG------GIKYNP--PNGGPADTEATQAIEDRANELLKAGL  189 (553)
T ss_pred             CCEEEECCCCCCCCCC------CEECCC--CCCCCCCHHHHHHHHHHHHHHHHHHC
T ss_conf             5614775877747886------764077--44588866888999999999997223


No 12 
>KOG2321 consensus
Probab=29.03  E-value=16  Score=18.71  Aligned_cols=33  Identities=24%  Similarity=0.539  Sum_probs=16.9

Q ss_pred             CCCCCCCEEEEEEECCCCCCCCCCEEEECHHHH
Q ss_conf             877684102221215678788864479739999
Q gi|254780712|r   27 SPRDGKFIEKLGTWNPTLPKENPLRFTMNFERI   59 (116)
Q Consensus        27 ~~Rdgk~iE~lG~YnP~~~k~~~~~i~l~~eRi   59 (116)
                      ..+||+||=-.|+|-|...=-+-..+.|++||-
T Consensus        59 ~s~DGqY~lAtG~YKP~ikvydlanLSLKFERh   91 (703)
T KOG2321          59 VSPDGQYLLATGTYKPQIKVYDLANLSLKFERH   91 (703)
T ss_pred             ECCCCCEEEEECCCCCCEEEEECCCCEEEEEEC
T ss_conf             668886798743668724898701142432331


No 13 
>pfam09086 DUF1924 Domain of unknown function (DUF1924). This domain is found in a set of bacterial proteins, including Cytochrome c-type protein. It is functionally uncharacterized.
Probab=27.63  E-value=50  Score=15.72  Aligned_cols=34  Identities=35%  Similarity=0.770  Sum_probs=26.3

Q ss_pred             CCCCCCEEEEEEECCCCCCCCCCEEEECHHHHHHHHHCCCC
Q ss_conf             77684102221215678788864479739999999841983
Q gi|254780712|r   28 PRDGKFIEKLGTWNPTLPKENPLRFTMNFERIQHWMSKGAQ   68 (116)
Q Consensus        28 ~Rdgk~iE~lG~YnP~~~k~~~~~i~l~~eRi~yWL~~GAq   68 (116)
                      .+.||.||      ||.|.-||+++. |..+|..|+...+.
T Consensus        46 ~~TgK~I~------PmAps~Np~Rft-D~akvEKwF~RNC~   79 (98)
T pfam09086        46 VKTGKPIE------PMAPSVNPERFT-DAAKVEKWFTRNCN   79 (98)
T ss_pred             CCCCCCCC------CCCCCCCHHHHC-CHHHHHHHHHCCCH
T ss_conf             65788646------768766856406-98999999971055


No 14 
>TIGR00625 tfb2 Transcription factor tfb2; InterPro: IPR004598 Members of this family are part of the TFIIH complex which is involved in the initiation of transcription and nucleotide excision repair. The core-TFIIH basal transcription factor complex has six subunits, this is the p52 subunit.; GO: 0003702 RNA polymerase II transcription factor activity, 0006281 DNA repair, 0006355 regulation of transcription DNA-dependent, 0005634 nucleus.
Probab=26.28  E-value=47  Score=15.84  Aligned_cols=28  Identities=29%  Similarity=0.539  Sum_probs=20.5

Q ss_pred             CCCCHHHHHHHHHCCCCCCC-CCCCCHHH
Q ss_conf             83568999999972986668-00051122
Q gi|254780712|r   67 AQPTDRILFFLDKAGLIKRS-PQNNPKKS   94 (116)
Q Consensus        67 AqpS~~V~~LL~~~Gl~~~~-~~~~~~~~   94 (116)
                      +-||+.|..||+++||+... +.+..+.+
T Consensus       154 k~p~e~vl~LLk~~gLM~~~~~~~~~~IT  182 (507)
T TIGR00625       154 KVPSEDVLSLLKRAGLMKEVESKEELKIT  182 (507)
T ss_pred             CCCHHHHHHHHHHCCCCCCCCCCCCCEEC
T ss_conf             47857999997404777888888884136


No 15 
>TIGR01249 pro_imino_pep_1 proline iminopeptidase; InterPro: IPR005944   Proteolytic enzymes that exploit serine in their catalytic activity are ubiquitous, being found in viruses, bacteria and eukaryotes . They include a wide range of peptidase activity, including exopeptidase, endopeptidase, oligopeptidase and omega-peptidase activity. Over 20 families (denoted S1 - S66) of serine protease have been identified, these being grouped into clans on the basis of structural similarity and other functional evidence . Structures are known for members of the clans and the structures indicate that some appear to be totally unrelated, suggesting different evolutionary origins for the serine peptidases .   Not withstanding their different evolutionary origins, there are similarities in the reaction mechanisms of several peptidases. Chymotrypsin, subtilisin and carboxypeptidase C have a catalytic triad of serine, aspartate and histidine in common: serine acts as a nucleophile, aspartate as an electrophile, and histidine as a base . The geometric orientations of the catalytic residues are similar between families, despite different protein folds . The linear arrangements of the catalytic residues commonly reflect clan relationships. For example the catalytic triad in the chymotrypsin clan (PA) is ordered HDS, but is ordered DHS in the subtilisin clan (SB) and SDH in the carboxypeptidase clan (SC) , .   Peptidases are grouped into clans and families. Clans are groups of families for which there is evidence of common ancestry. Each clan is identified with two letters, the first representing the catalytic type of the families included in the clan (with the letter 'P' being used for a clan containing families of more than one of the catalytic types serine, threonine and cysteine). Some families cannot yet be assigned to clans, and when a formal assignment is required, such a family is described as belonging to clan A-, C-, M-, S-, T- or U-, according to the catalytic type. Some clans are divided into subclans because there is evidence of a very ancient divergence within the clan, for example MA(E), the gluzincins, and MA(M), the metzincins.   Families are grouped by their catalytic type, the first character representing the catalytic type: A, aspartic; C, cysteine; G, glutamic acid; M, metallo; S, serine; T, threonine; and U, unknown. The serine, threonine and cysteine peptidases utilise the amino acid as a nucleophile and form an acyl intermediate - these peptidases can also readily act as transferases. In the case of aspartic, glutamic and metallopeptidases, the nucleophile is an activated water molecule.    This group of serine peptidase belong to MEROPS peptidase family S33 (clan SC). They are proline iminopeptidase (Prolyl aminopeptidase, 3.4.11.5 from EC), which catalyzes the removal of the N-terminal proline from peptides. This family represents one of two related families of proline iminopeptidase containing the alpha/beta fold. The fine specificities of the various members, including both the range of short peptides from which proline can be removed and whether other amino acids such as alanine can be also removed, may vary among members.  ; GO: 0016804 prolyl aminopeptidase activity, 0005737 cytoplasm.
Probab=25.11  E-value=39  Score=16.34  Aligned_cols=43  Identities=14%  Similarity=0.203  Sum_probs=23.6

Q ss_pred             CEEEEEEEECCCCCCCCCEEEEEEECCCCCCCCCCEEEECHHHHHHHHHC
Q ss_conf             82799992067877684102221215678788864479739999999841
Q gi|254780712|r   16 HHYRIVVANSRSPRDGKFIEKLGTWNPTLPKENPLRFTMNFERIQHWMSK   65 (116)
Q Consensus        16 p~yrIVvadsr~~Rdgk~iE~lG~YnP~~~k~~~~~i~l~~eRi~yWL~~   65 (116)
                      =+||||..|+|-.=..+.      |+=..+ .+.--+.=|+|.++.=|+-
T Consensus        52 e~~rIvL~DQRGcGkS~p------~a~~~e-NtTWdLV~DiEkLR~~L~I   94 (310)
T TIGR01249        52 ETYRIVLLDQRGCGKSTP------HACLEE-NTTWDLVADIEKLREKLGI   94 (310)
T ss_pred             CCEEEEEEEECCCCCCCC------CCCCCC-CCCHHHHHHHHHHHHHCCC
T ss_conf             635899983078889862------433224-7705667439999986289


No 16 
>KOG3471 consensus
Probab=23.91  E-value=67  Score=14.93  Aligned_cols=64  Identities=28%  Similarity=0.527  Sum_probs=39.3

Q ss_pred             CCCCCCCEEEEEEEECCCCCCCCCEEEEEEECCCCCCCCCCEEEECHHHHHHHHHC---CCCCCHHHHHHHHHCCCCCCC
Q ss_conf             66878882799992067877684102221215678788864479739999999841---983568999999972986668
Q gi|254780712|r   10 GGSKSRHHYRIVVANSRSPRDGKFIEKLGTWNPTLPKENPLRFTMNFERIQHWMSK---GAQPTDRILFFLDKAGLIKRS   86 (116)
Q Consensus        10 ~G~k~rp~yrIVvadsr~~Rdgk~iE~lG~YnP~~~k~~~~~i~l~~eRi~yWL~~---GAqpS~~V~~LL~~~Gl~~~~   86 (116)
                      +|.+.++|=-.|+-+...+||+.++|.   |.-           =.-|-|.|.+--   -.-||+.|.+||+++|++...
T Consensus       120 gg~~~~s~~s~~l~~~~~~r~v~~ld~---ya~-----------~rwe~ILh~mvgt~~a~~~se~v~~ll~~a~lm~~~  185 (465)
T KOG3471         120 GGGKQNSFGSLVLGEDKHNRDVDFLDK---YAS-----------ERWECILHFMVGTPEAKAVSEGVLNLLKHAGLMSRD  185 (465)
T ss_pred             CCCCCCCCCCCCCCCCCCCCCCHHHHH---HHH-----------HHHHHHHHHHHCCCCCCCCCHHHHHHHHHCCCCCCC
T ss_conf             577766677754287757666315678---888-----------889999988717863135574299999854755789


Q ss_pred             C
Q ss_conf             0
Q gi|254780712|r   87 P   87 (116)
Q Consensus        87 ~   87 (116)
                      .
T Consensus       186 ~  186 (465)
T KOG3471         186 E  186 (465)
T ss_pred             C
T ss_conf             8


No 17 
>KOG3423 consensus
Probab=22.88  E-value=64  Score=15.04  Aligned_cols=39  Identities=31%  Similarity=0.617  Sum_probs=26.8

Q ss_pred             CCEEEEEEECCCCCCCCCCEEEECHHHHHHHHHC-CCCCCH-HHHHHHHHC
Q ss_conf             4102221215678788864479739999999841-983568-999999972
Q gi|254780712|r   32 KFIEKLGTWNPTLPKENPLRFTMNFERIQHWMSK-GAQPTD-RILFFLDKA   80 (116)
Q Consensus        32 k~iE~lG~YnP~~~k~~~~~i~l~~eRi~yWL~~-GAqpS~-~V~~LL~~~   80 (116)
                      -||++|-.|-|+.|          ..=+.|+|.. |-|-+| +|.+|++.+
T Consensus        75 efl~qLddYtP~IP----------Davt~~yL~~aGf~~~D~rv~RLvsLa  115 (176)
T KOG3423          75 EFLAQLDDYTPTIP----------DAVTDHYLKKAGFQTSDPRVKRLVSLA  115 (176)
T ss_pred             HHHHHHHCCCCCCC----------HHHHHHHHHHCCCCCCCHHHHHHHHHH
T ss_conf             99998730799883----------899999998558776768799999999


No 18 
>TIGR00845 caca sodium/calcium exchanger 1; InterPro: IPR004836   Na^+/Ca^2+ exchange proteins are involved in maintaining Ca^2+ homeostasis in a wide variety of cell types. They are found in both the plasma membrane and intracellular organellar membranes, where they exchange Na^+ for Ca^2+ in an electrogenic manner. When located in the plasma membrane, they generally utilise the transmembrane (TM) Na^+ concentration gradient in order to extrude Ca^2+ from cells. Three mammalian isoforms have been cloned to date (NCX1-3), which consist of 920-970 amino acid residues that are predicted to possess 11 or 12 TM domains. Interestingly, they possess a short motif (~30 residues) that is similar to the Na^+/K^+-ATPase, although its function is unknown , .   NCX1 has been found to be predominantly expressed in the heart, where it plays an important role in excitation-contraction coupling, but it is also abundant in a variety of other tissues . NCX2 and NCX3 transcripts have been detected in the brain and skeletal muscle , . Homologous Na^+/Ca^2+ exchange proteins have also been found in Caenorhabditis elegans, Drosophila melanogaster and Loligo opalescens (California market squid). ; GO: 0005432 calcium:sodium antiporter activity, 0006816 calcium ion transport, 0016020 membrane.
Probab=21.53  E-value=20  Score=18.09  Aligned_cols=13  Identities=46%  Similarity=0.577  Sum_probs=7.0

Q ss_pred             CCCCCCCEEEEEE
Q ss_conf             6687888279999
Q gi|254780712|r   10 GGSKSRHHYRIVV   22 (116)
Q Consensus        10 ~G~k~rp~yrIVv   22 (116)
                      .|.|-|+||||.|
T Consensus       399 r~~KSRAFYRIQA  411 (1067)
T TIGR00845       399 RQQKSRAFYRIQA  411 (1067)
T ss_pred             CCCCCCHHHHHHH
T ss_conf             4898400135345


No 19 
>cd06364 PBP1_CaSR Ligand-binding domain of the CaSR calcium-sensing receptor, which is a member of the family C receptors within the G-protein coupled receptor superfamily. Ligand-binding domain of the CaSR calcium-sensing receptor, which is a member of the family C receptors within the G-protein coupled receptor superfamily. CaSR provides feedback control of extracellular calcium homeostasis by responding sensitively to acute fluctuations in extracellular ionized Ca2+ concentration. This ligand-binding domain has homology to the bacterial leucine-isoleucine-valine binding protein (LIVBP) and a leucine binding protein (LBP). CaSR is widely expressed in mammalian tissues and is active in tissues that are not directly involved in extracellular calcium homeostasis. Moreover, CaSR responds to aromatic, aliphatic, and polar amino acids, but not to positively charged or branched chain amino acids, which suggests that changes in plasma amino acid levels are likely to modulate whole body calci
Probab=21.14  E-value=76  Score=14.59  Aligned_cols=41  Identities=27%  Similarity=0.412  Sum_probs=22.5

Q ss_pred             CEEEEEEEECCCCCCCCC-EEEEEEECCCCCCCCCCEEEECHHHH
Q ss_conf             827999920678776841-02221215678788864479739999
Q gi|254780712|r   16 HHYRIVVANSRSPRDGKF-IEKLGTWNPTLPKENPLRFTMNFERI   59 (116)
Q Consensus        16 p~yrIVvadsr~~Rdgk~-iE~lG~YnP~~~k~~~~~i~l~~eRi   59 (116)
                      +.|-|+=- +..|-+|.+ ...||+|+|..+  ....+.||.+.|
T Consensus       467 ~~YdI~n~-q~~~~~g~~~~~~VG~~~~~~~--~~~~L~in~~~I  508 (510)
T cd06364         467 GNYSIINW-HLSPEDGSVVFKEVGYYNVYAK--KGERLFINESKI  508 (510)
T ss_pred             CEEEEEEE-EECCCCCCEEEEEEEEEECCCC--CCCEEEEECCCC
T ss_conf             41669997-6659999589999679828678--888679850023


No 20 
>COG3785 Uncharacterized conserved protein [Function unknown]
Probab=20.85  E-value=58  Score=15.31  Aligned_cols=17  Identities=12%  Similarity=0.397  Sum_probs=10.9

Q ss_pred             CCCCCEEEEEEEECCCC
Q ss_conf             87888279999206787
Q gi|254780712|r   12 SKSRHHYRIVVANSRSP   28 (116)
Q Consensus        12 ~k~rp~yrIVvadsr~~   28 (116)
                      .+-.||||+++-|.-.+
T Consensus        56 ~rdqPfYHllaEnde~~   72 (116)
T COG3785          56 LRDQPFYHLLAENDETE   72 (116)
T ss_pred             CCCCCCEEEEEECCCCC
T ss_conf             44586101442068861


No 21 
>KOG2806 consensus
Probab=20.66  E-value=78  Score=14.53  Aligned_cols=61  Identities=18%  Similarity=0.212  Sum_probs=38.0

Q ss_pred             CCEEEEEEEECCCCCCCCCEEEEEEECCCCCCCCCCEEEECHH-HHHHHHHCCCCCCHHHHHHH
Q ss_conf             8827999920678776841022212156787888644797399-99999841983568999999
Q gi|254780712|r   15 RHHYRIVVANSRSPRDGKFIEKLGTWNPTLPKENPLRFTMNFE-RIQHWMSKGAQPTDRILFFL   77 (116)
Q Consensus        15 rp~yrIVvadsr~~Rdgk~iE~lG~YnP~~~k~~~~~i~l~~e-Ri~yWL~~GAqpS~~V~~LL   77 (116)
                      -=|..|...|-..|.++.  +..|.--|+..-.....-.+|.| .++||+.+|++|+.-|-.+=
T Consensus       234 ~DfiNi~syDf~gpw~~~--~~tGp~aPl~~~~~~~~~~~Nvd~~~ky~~~~~~~~~Kl~~gip  295 (432)
T KOG2806         234 VDFINIMSYDYYGPWSLP--CFTGPPSPLYKGPSMTNPKMNVDSLLKYWTEKGLPPSKLVLALP  295 (432)
T ss_pred             CCEEEEEEEECCCCCCCC--CCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHCCCCCCCEEEEEC
T ss_conf             785888753015777778--75897776577655566654321344544205788733799964


No 22 
>COG5162 Transcription initiation factor TFIID, subunit TAF10 (also component of histone acetyltransferase SAGA) [Transcription]
Probab=20.52  E-value=78  Score=14.51  Aligned_cols=40  Identities=18%  Similarity=0.430  Sum_probs=28.0

Q ss_pred             CCEEEEEEECCCCCCCCCCEEEECHHHHHHHHHC-CCCCCH-HHHHHHHHCC
Q ss_conf             4102221215678788864479739999999841-983568-9999999729
Q gi|254780712|r   32 KFIEKLGTWNPTLPKENPLRFTMNFERIQHWMSK-GAQPTD-RILFFLDKAG   81 (116)
Q Consensus        32 k~iE~lG~YnP~~~k~~~~~i~l~~eRi~yWL~~-GAqpS~-~V~~LL~~~G   81 (116)
                      -+++.+-+|-|+.|          ..-+.|+|.+ |-..+| +|.+||+...
T Consensus        77 e~l~~mDsy~PliP----------d~v~DYyl~k~Gf~~~D~rvKkLl~L~a  118 (197)
T COG5162          77 ELLQNMDSYTPLIP----------DSVTDYYLEKAGFVTSDQRVKKLLSLLA  118 (197)
T ss_pred             HHHHHCCCCCCCCC----------HHHHHHHHHHCCCEECCHHHHHHHHHHH
T ss_conf             99986125788761----------7999999985484104489999999999


Done!