Query         gi|254780876|ref|YP_003065289.1| hypothetical protein CLIBASIA_03865 [Candidatus Liberibacter asiaticus str. psy62]
Match_columns 210
No_of_seqs    148 out of 458
Neff          5.0 
Searched_HMMs 39220
Date          Mon May 30 03:15:23 2011
Command       /home/congqian_1/programs/hhpred/hhsearch -i 254780876.hhm -d /home/congqian_1/database/cdd/Cdd.hhm 

 No Hit                             Prob E-value P-value  Score    SS Cols Query HMM  Template HMM
  1 pfam04053 Coatomer_WDAD Coatom  83.9     1.5 3.9E-05   22.6   3.8   37   52-88    340-376 (435)
  2 PRK11189 lipoprotein NlpI; Pro  67.1       9 0.00023   17.8   4.5   41   45-85    231-280 (297)
  3 KOG0276 consensus               59.4      12 0.00032   17.0   3.5   39   50-88    665-703 (794)
  4 smart00770 Zn_dep_PLPC Zinc de  59.3      13 0.00032   17.0   5.0   41   45-85    108-148 (241)
  5 pfam00882 Zn_dep_PLPC Zinc dep  53.6      16  0.0004   16.4   5.1   43   43-85     82-124 (223)
  6 pfam10952 DUF2753 Protein of u  47.4      19  0.0005   15.8   3.0   26   52-77      2-27  (140)
  7 pfam08590 DUF1771 Domain of un  39.8      26 0.00065   15.1   6.2   44   49-92     14-57  (66)
  8 TIGR00824 EIIA-man PTS system,  37.0      27  0.0007   14.9   2.3   22   43-64     36-58  (117)
  9 COG1849 Uncharacterized protei  36.5      29 0.00074   14.7   3.2   15   50-64      9-23  (90)
 10 pfam04010 DUF357 Protein of un  35.3      30 0.00077   14.6   3.4   14   69-82     34-47  (75)
 11 pfam10484 MRP-S23 Mitochondria  35.0      30 0.00078   14.6   2.4   31   41-71     31-61  (74)
 12 TIGR00601 rad23 UV excision re  31.4      29 0.00073   14.8   1.7   53   33-90    304-361 (453)
 13 TIGR02933 nifM_nitrog nitrogen  30.7      30 0.00078   14.6   1.7   29   54-82    102-130 (270)
 14 pfam11986 PB1-F2 Influenza A P  29.4      38 0.00096   14.0   2.1   22   67-88     29-50  (90)
 15 CHL00173 cpeA phycoerythrin al  29.1      30 0.00076   14.6   1.4   22   67-88     76-97  (164)
 16 COG1592 Rubrerythrin [Energy p  28.5      39   0.001   13.9   5.5   41   47-87     16-63  (166)
 17 KOG0704 consensus               27.2      20 0.00052   15.7   0.3   26   30-58     82-107 (386)
 18 PTZ00043 cytochrome c oxidase   25.6      42  0.0011   13.7   1.7   44   34-84     63-112 (270)
 19 pfam00502 Phycobilisome Phycob  21.4      51  0.0013   13.2   1.5   20   69-88     73-92  (157)
 20 COG1613 Sbp ABC-type sulfate t  20.9      42  0.0011   13.7   1.0   11   65-75    270-280 (348)
 21 pfam06798 PrkA PrkA serine pro  20.2      57  0.0014   13.0   2.1   38   21-60     37-74  (254)
 22 TIGR02918 TIGR02918 conserved   20.1      14 0.00036   16.7  -1.6   37   45-81    458-496 (511)

No 1  
>pfam04053 Coatomer_WDAD Coatomer WD associated region. This region is composed of WD40 repeats.
Probab=83.89  E-value=1.5  Score=22.55  Aligned_cols=37  Identities=22%  Similarity=0.447  Sum_probs=33.4

Q ss_pred             HHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             9999999998626873678888899999999999998
Q gi|254780876|r   52 ERYSVLARDAMSAGDYVVAENHLQHAEHYNRIVSMAQ   88 (210)
Q Consensus        52 ~ky~~la~da~~~gd~~~~e~~~qha~hy~r~~~~~~   88 (210)
                      .||.+|+..|+..|+--+||..||.+..|-+++--..
T Consensus       340 ~~Wk~Lg~~AL~~g~~~lAe~~~~k~~d~~~LllLy~  376 (435)
T pfam04053       340 HKWKRLGDAALSQGNIKLAEEAYQKAKDFDKLLLLYL  376 (435)
T ss_pred             HHHHHHHHHHHHCCCHHHHHHHHHHHCCHHHHHHHHH
T ss_conf             9999999999974995899999997425345599999


No 2  
>PRK11189 lipoprotein NlpI; Provisional
Probab=67.11  E-value=9  Score=17.84  Aligned_cols=41  Identities=29%  Similarity=0.375  Sum_probs=34.2

Q ss_pred             CCHHHHHHHHHHHHHHHHHCCCHHHHHHHHH---------HHHHHHHHHH
Q ss_conf             8999999999999999862687367888889---------9999999999
Q gi|254780876|r   45 GTAQHIAERYSVLARDAMSAGDYVVAENHLQ---------HAEHYNRIVS   85 (210)
Q Consensus        45 ~~~~~~~~ky~~la~da~~~gd~~~~e~~~q---------ha~hy~r~~~   85 (210)
                      --|++|.|-|.-|||-.+..||.-.|.+||-         +.||=+-+|-
T Consensus       231 ~lAErLcEaYFYLaK~~~~~G~~~~A~~~fKLAla~NVyeFVEhRYA~lE  280 (297)
T PRK11189        231 ELAERLCETYFYLAKYYLSLGDLDEAANLFKLALANNVYNFVEHRYALLE  280 (297)
T ss_pred             HHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHCCCHHHHHHHHHHHH
T ss_conf             99999999999999999987998999999999870482588899999999


No 3  
>KOG0276 consensus
Probab=59.36  E-value=12  Score=16.98  Aligned_cols=39  Identities=18%  Similarity=0.293  Sum_probs=34.6

Q ss_pred             HHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             999999999998626873678888899999999999998
Q gi|254780876|r   50 IAERYSVLARDAMSAGDYVVAENHLQHAEHYNRIVSMAQ   88 (210)
Q Consensus        50 ~~~ky~~la~da~~~gd~~~~e~~~qha~hy~r~~~~~~   88 (210)
                      -..||.+|+.-|+++|+-.||+-.|+||-.|--||....
T Consensus       665 s~~Kw~~Lg~~al~~~~l~lA~EC~~~a~d~~~LlLl~t  703 (794)
T KOG0276         665 SEVKWRQLGDAALSAGELPLASECFLRARDLGSLLLLYT  703 (794)
T ss_pred             CHHHHHHHHHHHHHCCCCHHHHHHHHHHCCHHHHHHHHH
T ss_conf             667799999998641663458999975304355542355


No 4  
>smart00770 Zn_dep_PLPC Zinc dependent phospholipase C (alpha toxin). This domain conveys a zinc dependent phospholipase C activity (EC 3.1.4.3). It is found in a monomeric phospholipase C of Bacillus cereus as well as in the alpha toxin of Clostridium perfringens and Clostridium bifermentans, which is involved in haemolysis and cell rupture. It is also found in a lecithinase of Listeria monocytogenes, which is involved in breaking the 2-membrane vacuoles that surround the bacterium. Structure information: PDB 1ca1.
Probab=59.25  E-value=13  Score=16.95  Aligned_cols=41  Identities=29%  Similarity=0.294  Sum_probs=38.1

Q ss_pred             CCHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Q ss_conf             89999999999999998626873678888899999999999
Q gi|254780876|r   45 GTAQHIAERYSVLARDAMSAGDYVVAENHLQHAEHYNRIVS   85 (210)
Q Consensus        45 ~~~~~~~~ky~~la~da~~~gd~~~~e~~~qha~hy~r~~~   85 (210)
                      -||.....||-.||....-.||.=.|=.||--|-||+-=|+
T Consensus       108 ~~A~~~~~ky~~~A~~~~~~g~~~kA~fyLG~a~Hy~~D~t  148 (241)
T smart00770      108 SNAKDTGRKYFKLALNEWKKGNYKKAFFYLGRACHYLGDLS  148 (241)
T ss_pred             CCHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHCC
T ss_conf             63899999999999999984579999999878888862068


No 5  
>pfam00882 Zn_dep_PLPC Zinc dependent phospholipase C.
Probab=53.57  E-value=16  Score=16.38  Aligned_cols=43  Identities=28%  Similarity=0.248  Sum_probs=38.8

Q ss_pred             CCCCHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Q ss_conf             7889999999999999998626873678888899999999999
Q gi|254780876|r   43 VRGTAQHIAERYSVLARDAMSAGDYVVAENHLQHAEHYNRIVS   85 (210)
Q Consensus        43 ~~~~~~~~~~ky~~la~da~~~gd~~~~e~~~qha~hy~r~~~   85 (210)
                      ..-||.....||-.||....-.|+.-.|-.||--|-||+-=|.
T Consensus        82 ~~~~A~~~~~ky~~~A~~~~~~g~~~ka~fyLG~a~Hy~~D~~  124 (223)
T pfam00882        82 IFPTAKTECRKYFALALNEWRKGNYKKAFFYLGAACHYFGDLN  124 (223)
T ss_pred             CCCCHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHCC
T ss_conf             9985899999999999999983679999999978989887448


No 6  
>pfam10952 DUF2753 Protein of unknown function (DUF2753). This bacterial family of proteins has no known function.
Probab=47.40  E-value=19  Score=15.78  Aligned_cols=26  Identities=38%  Similarity=0.500  Sum_probs=22.5

Q ss_pred             HHHHHHHHHHHHCCCHHHHHHHHHHH
Q ss_conf             99999999986268736788888999
Q gi|254780876|r   52 ERYSVLARDAMSAGDYVVAENHLQHA   77 (210)
Q Consensus        52 ~ky~~la~da~~~gd~~~~e~~~qha   77 (210)
                      ||++-||-.|+..||.+.+--.||-|
T Consensus         2 EkhtLlAd~A~~~~d~~~sIlhYQqA   27 (140)
T pfam10952         2 ERHTLLADEALKNGDPLRSILHYQQA   27 (140)
T ss_pred             CHHHHHHHHHHHCCCHHHHHHHHHHH
T ss_conf             32588888885457689999999999


No 7  
>pfam08590 DUF1771 Domain of unknown function (DUF1771). This domain is always found adjacent to pfam01713.
Probab=39.76  E-value=26  Score=15.06  Aligned_cols=44  Identities=16%  Similarity=0.100  Sum_probs=36.9

Q ss_pred             HHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             99999999999986268736788888999999999999987754
Q gi|254780876|r   49 HIAERYSVLARDAMSAGDYVVAENHLQHAEHYNRIVSMAQAQIQ   92 (210)
Q Consensus        49 ~~~~ky~~la~da~~~gd~~~~e~~~qha~hy~r~~~~~~~~~~   92 (210)
                      .+-.+|.+.|..|...||.-.|-.|...+-.+...+-++..+.-
T Consensus        14 ~~r~~~~~~A~~Ay~~Gd~~~A~~lS~~gk~~~~~~~~~n~~Aa   57 (66)
T pfam08590        14 QKRNELFQKAAEAYKRGDKAAAKELSEEGKKHGEKAEEANRQAA   57 (66)
T ss_pred             HHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             99999999999998828888899999998999999999979999


No 8  
>TIGR00824 EIIA-man PTS system, mannose/fructose/sorbose family, IIA component; InterPro: IPR013789   The phosphoenolpyruvate-dependent sugar phosphotransferase system (PTS) ,  is a major carbohydrate transport system in bacteria. The PTS catalyses the phosphorylation of incoming sugar substrates and coupled with translocation across the cell membrane, makes the PTS a link between the uptake and metabolism of sugars.   The general mechanism of the PTS is the following: a phosphoryl group from phosphoenolpyruvate (PEP) is transferred via a signal transduction pathway, to enzyme I (EI) which in turn transfers it to a phosphoryl carrier, the histidine protein (HPr). Phospho-HPr then transfers the phosphoryl group to a sugar-specific permease, a membrane-bound complex known as enzyme 2 (EII), which transports the sugar to the cell. EII consists of at least three structurally distinct domains IIA, IIB and IIC . These can either be fused together in a single polypeptide chain or exist as two or three interactive chains, formerly called enzymes II (EII) and III (EIII).    The first domain (IIA or EIIA) carries the first permease-specific phosphorylation site, a histidine which is phosphorylated by phospho-HPr. The second domain (IIB or EIIB) is phosphorylated by phospho-IIA on a cysteinyl or histidyl residue, depending on the sugar transported. Finally, the phosphoryl group is transferred from the IIB domain to the sugar substrate concomitantly with the sugar uptake processed by the IIC domain. This third domain (IIC or EIIC) forms the translocation channel and the specific substrate-binding site.    An additional transmembrane domain IID, homologous to IIC, can be found in some PTSs, e.g. for mannose , , , .    The Man family is unique in several respects among PTS permease families. It is the only PTS family in which members possess a IID protein. It is the only PTS family in which the IIB constituent is phosphorylated on a histidyl rather than a cysteyl residue. Its permease members exhibit broad specificity for a range of sugars, rather than being specific for just one or a few sugars.    The mannose permease of Escherichia coli, for example, can transport and phosphorylate glucose, mannose, fructose, glucosamine, N-acetylglucosamine, and other sugars. Other members of this can transport sorbose, fructose and N-acetylglucosamine.    This family is specific for IIA and IIB components..
Probab=36.96  E-value=27  Score=14.88  Aligned_cols=22  Identities=23%  Similarity=0.377  Sum_probs=17.8

Q ss_pred             CCC-CHHHHHHHHHHHHHHHHHC
Q ss_conf             788-9999999999999998626
Q gi|254780876|r   43 VRG-TAQHIAERYSVLARDAMSA   64 (210)
Q Consensus        43 ~~~-~~~~~~~ky~~la~da~~~   64 (210)
                      ++| |+++|++||.++-.|+..-
T Consensus        36 ~~GEn~~~L~~k~~~~l~d~~t~   58 (117)
T TIGR00824        36 VPGENIETLQEKYEKALSDLDTE   58 (117)
T ss_pred             CCCCCHHHHHHHHHHHHHHCCCC
T ss_conf             69989889999999998402668


No 9  
>COG1849 Uncharacterized protein conserved in archaea [Function unknown]
Probab=36.47  E-value=29  Score=14.74  Aligned_cols=15  Identities=27%  Similarity=0.417  Sum_probs=10.3

Q ss_pred             HHHHHHHHHHHHHHC
Q ss_conf             999999999998626
Q gi|254780876|r   50 IAERYSVLARDAMSA   64 (210)
Q Consensus        50 ~~~ky~~la~da~~~   64 (210)
                      -++||..+..+|+..
T Consensus         9 kiekYi~~leeaL~~   23 (90)
T COG1849           9 KIEKYIELLEEALKE   23 (90)
T ss_pred             HHHHHHHHHHHHHHH
T ss_conf             999999989999998


No 10 
>pfam04010 DUF357 Protein of unknown function (DUF357). Members of this family are short (less than 100 amino acid) proteins found in archaebacteria. The function of these proteins is unknown.
Probab=35.32  E-value=30  Score=14.63  Aligned_cols=14  Identities=29%  Similarity=0.396  Sum_probs=7.7

Q ss_pred             HHHHHHHHHHHHHH
Q ss_conf             78888899999999
Q gi|254780876|r   69 VAENHLQHAEHYNR   82 (210)
Q Consensus        69 ~~e~~~qha~hy~r   82 (210)
                      |++.|+.-|.||+.
T Consensus        34 ma~~Y~~Da~~fl~   47 (75)
T pfam04010        34 MAKSYLEDAKYYLE   47 (75)
T ss_pred             HHHHHHHHHHHHHH
T ss_conf             99999999999988


No 11 
>pfam10484 MRP-S23 Mitochondrial ribosomal protein S23. MRP-S23 is one of the proteins that makes up the 55S ribosome in eukaryotes from nematodes to humans. It does not appear to carry any common motifs, either RNA binding or ribosomal protein motifs. All of the mammalian MRPs are encoded in nuclear genes that are evolving more rapidly than those encoding cytoplasmic ribosomal proteins. The MRPs are imported into mitochondria where they assemble coordinately with mitochondrially transcribed rRNAs into ribosomes that are responsible for translating the 13 mRNAs for essential proteins of the oxidative phosphorylation system. MRP-S23 is significantly up-regulated in uterine cancer cells.
Probab=34.96  E-value=30  Score=14.59  Aligned_cols=31  Identities=16%  Similarity=0.284  Sum_probs=22.8

Q ss_pred             CCCCCCHHHHHHHHHHHHHHHHHCCCHHHHH
Q ss_conf             7778899999999999999986268736788
Q gi|254780876|r   41 VKVRGTAQHIAERYSVLARDAMSAGDYVVAE   71 (210)
Q Consensus        41 ~k~~~~~~~~~~ky~~la~da~~~gd~~~~e   71 (210)
                      -+.+-.-|+.++||.+|-....+..+.|-.|
T Consensus        31 ~~~~S~~QqFvq~Y~eLks~g~ldee~lfee   61 (74)
T pfam10484        31 MNNRTQTQQFVQKYQELKSQGALDEEELFEE   61 (74)
T ss_pred             CCCCCHHHHHHHHHHHHHHHCCCCHHHHHHH
T ss_conf             5654188999999999987035568889999


No 12 
>TIGR00601 rad23 UV excision repair protein Rad23; InterPro: IPR004806   All proteins in this family for which functions are known are components of a multiprotein complex used for targeting nucleotide excision repair to specific parts of the genome. Rad23 contains a ubiquitin-like domain that interacts with catalytically active proteasomes and two ubiquitin (Ub)-associated (UBA) sequences that bind Ub. Rad23 interacts with ubiquitinated cellular proteins through the synergistic action of its UBA domains.    In humans, Rad23 complexes with the XPC protein.; GO: 0006289 nucleotide-excision repair, 0005634 nucleus.
Probab=31.39  E-value=29  Score=14.77  Aligned_cols=53  Identities=11%  Similarity=0.174  Sum_probs=38.3

Q ss_pred             CCCCCCCCC-C----CCCCHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             554568777-7----788999999999999999862687367888889999999999999877
Q gi|254780876|r   33 NYDSNGYDV-K----VRGTAQHIAERYSVLARDAMSAGDYVVAENHLQHAEHYNRIVSMAQAQ   90 (210)
Q Consensus        33 ~~~~~~~~~-k----~~~~~~~~~~ky~~la~da~~~gd~~~~e~~~qha~hy~r~~~~~~~~   90 (210)
                      .|-.+-|.+ .    |-+||+-|--=-.+     ++.+++=|.+--.+|-|||+-||+|.-..
T Consensus       304 efLR~~PqFq~lRq~vq~NP~~L~~lL~~-----iG~~nPQL~~~I~~h~E~F~qlL~Epv~~  361 (453)
T TIGR00601       304 EFLRNQPQFQQLRQVVQQNPQLLPPLLQQ-----IGQENPQLLQQISQHPEEFLQLLNEPVEE  361 (453)
T ss_pred             HHCCCCHHHHHHHHHHHCCHHHHHHHHHH-----HCCCCHHHHHHHHHCCHHHHHHHCCCCCH
T ss_conf             21167365676727761266789999997-----34537379999652606788875047313


No 13 
>TIGR02933 nifM_nitrog nitrogen fixation protein NifM; InterPro: IPR014282   Members of this entry are found in a subset of nitrogen-fixing bacteria and are annotated as nitrogen fixation protein NifM. NifM is homologous to peptidyl-prolyl cis-trans isomerases and appears to be an accessory protein for NifH, the Fe protein, also called component II or dinitrogenase reductase, of nitrogenase..
Probab=30.73  E-value=30  Score=14.60  Aligned_cols=29  Identities=28%  Similarity=0.283  Sum_probs=19.3

Q ss_pred             HHHHHHHHHHCCCHHHHHHHHHHHHHHHH
Q ss_conf             99999998626873678888899999999
Q gi|254780876|r   54 YSVLARDAMSAGDYVVAENHLQHAEHYNR   82 (210)
Q Consensus        54 y~~la~da~~~gd~~~~e~~~qha~hy~r   82 (210)
                      ....+.-+---.|--..-.|+-||.||.|
T Consensus       102 L~~v~~q~p~p~~a~V~~wY~~Ha~~F~r  130 (270)
T TIGR02933       102 LASVAEQAPQPDDAEVEAWYRRHAEQFVR  130 (270)
T ss_pred             HHHHHCCCCCCCCHHHHHHHHHHHHHCCC
T ss_conf             99997058999603588998886740577


No 14 
>pfam11986 PB1-F2 Influenza A Proapoptotic protein. PB1-F2 is a protein found in almost all known strains of Influenza A virus - a negative sense ssRNA Orthomyxovirus. It originates from translation of the viral polymerase gene in an alternative reading frame. PB1-F2 consists of two independent structural domains, two closely neighboring short helices at the N terminus, and an extended C-terminal helix. Although the protein has originally been described to induce apoptosis, it has now been shown that PB1-F2 more likely acts as an apoptosis promoter in concert with other apoptosis-inducing agents. PB1-F2 promotes apoptosis by localising to the mitochondria where it destabilizes the membrane. This will cause release of cytochrome C which activates the caspase cascade of apoptosis through the endogenous pathway. In this way it acts like the Bcl-2 protein family which are physiological apoptotic regulators in cells.
Probab=29.36  E-value=38  Score=14.02  Aligned_cols=22  Identities=27%  Similarity=0.309  Sum_probs=15.9

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             3678888899999999999998
Q gi|254780876|r   67 YVVAENHLQHAEHYNRIVSMAQ   88 (210)
Q Consensus        67 ~~~~e~~~qha~hy~r~~~~~~   88 (210)
                      +.-.-|..|--|||+|+++-+-
T Consensus        29 klehpnstqlmdhylr~m~q~~   50 (90)
T pfam11986        29 KLEHPNSTQLMDHYLRTMSQVD   50 (90)
T ss_pred             CCCCCCHHHHHHHHHHHHHHHC
T ss_conf             4678648889999999987721


No 15 
>CHL00173 cpeA phycoerythrin alpha subunit; Provisional
Probab=29.05  E-value=30  Score=14.64  Aligned_cols=22  Identities=18%  Similarity=0.335  Sum_probs=13.2

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             3678888899999999999998
Q gi|254780876|r   67 YVVAENHLQHAEHYNRIVSMAQ   88 (210)
Q Consensus        67 ~~~~e~~~qha~hy~r~~~~~~   88 (210)
                      .....-.+---+||+|++.=+-
T Consensus        76 ~~r~aaClRD~~~yLR~iTY~l   97 (164)
T CHL00173         76 QEKVNKCYRDVDHYMRLVNYCL   97 (164)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHH
T ss_conf             7889999999999999998974


No 16 
>COG1592 Rubrerythrin [Energy production and conversion]
Probab=28.45  E-value=39  Score=13.92  Aligned_cols=41  Identities=20%  Similarity=0.198  Sum_probs=32.8

Q ss_pred             HHHHHHHHHHHHHHHHHCCCHHHHHHH-------HHHHHHHHHHHHHH
Q ss_conf             999999999999998626873678888-------89999999999999
Q gi|254780876|r   47 AQHIAERYSVLARDAMSAGDYVVAENH-------LQHAEHYNRIVSMA   87 (210)
Q Consensus        47 ~~~~~~ky~~la~da~~~gd~~~~e~~-------~qha~hy~r~~~~~   87 (210)
                      -++-..+|+.+|+-|...|..=.++-|       ..||...+++|...
T Consensus        16 Es~a~~rY~~~A~~A~~eG~~~va~lfr~iA~~E~~HA~~~~~~l~~~   63 (166)
T COG1592          16 ESMAVMRYLIFAKVAEEEGYPEIARLFRAIAEAEAVHAKNHLKLLGKL   63 (166)
T ss_pred             HHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHCCC
T ss_conf             099999999999999987788999999999999999999999996300


No 17 
>KOG0704 consensus
Probab=27.18  E-value=20  Score=15.67  Aligned_cols=26  Identities=27%  Similarity=0.148  Sum_probs=11.5

Q ss_pred             CCCCCCCCCCCCCCCCCHHHHHHHHHHHH
Q ss_conf             65555456877777889999999999999
Q gi|254780876|r   30 LVRNYDSNGYDVKVRGTAQHIAERYSVLA   58 (210)
Q Consensus        30 ~~~~~~~~~~~~k~~~~~~~~~~ky~~la   58 (210)
                      .-+.|-+..++.+...   -|++||+.+|
T Consensus        82 ~~~eFL~s~~~~~e~~---~i~eKYns~a  107 (386)
T KOG0704          82 RFREFLSSQGIYKETW---PIREKYNSRA  107 (386)
T ss_pred             HHHHHHHHCCCCCCCC---CHHHHHCCHH
T ss_conf             6789986584502364---4887634488


No 18 
>PTZ00043 cytochrome c oxidase subunit; Provisional
Probab=25.58  E-value=42  Score=13.72  Aligned_cols=44  Identities=25%  Similarity=0.389  Sum_probs=25.4

Q ss_pred             CCCCCCCCCCCC-----CHHHHHHH-HHHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Q ss_conf             545687777788-----99999999-9999999862687367888889999999999
Q gi|254780876|r   34 YDSNGYDVKVRG-----TAQHIAER-YSVLARDAMSAGDYVVAENHLQHAEHYNRIV   84 (210)
Q Consensus        34 ~~~~~~~~k~~~-----~~~~~~~k-y~~la~da~~~gd~~~~e~~~qha~hy~r~~   84 (210)
                      |..+----||||     ++++|..| |.+||+|--.   -|..|-    .+|.+-+|
T Consensus        63 f~~~ywywrir~es~lld~e~lp~ksykqla~dmgm---qiv~e~----~ehm~gll  112 (270)
T PTZ00043         63 YFGSYWYWRIRGESNLMDYEKLPKKSYKQLAVDLGM---QIVNEP----SEHMLGLL  112 (270)
T ss_pred             HHHHHHHHEECCCCCCCCHHHCCHHHHHHHHHHHCC---EECCCC----HHHHHHHH
T ss_conf             665502202205111269566025679999997386---524795----59899999


No 19 
>pfam00502 Phycobilisome Phycobilisome protein.
Probab=21.41  E-value=51  Score=13.22  Aligned_cols=20  Identities=20%  Similarity=0.315  Sum_probs=12.9

Q ss_pred             HHHHHHHHHHHHHHHHHHHH
Q ss_conf             78888899999999999998
Q gi|254780876|r   69 VAENHLQHAEHYNRIVSMAQ   88 (210)
Q Consensus        69 ~~e~~~qha~hy~r~~~~~~   88 (210)
                      -.+-.+---+||+|++.=+-
T Consensus        73 r~~~C~RD~~~~LR~itYai   92 (157)
T pfam00502        73 RMAACLRDIDYYLRLITYAL   92 (157)
T ss_pred             HHHHHHHHHHHHHHHHHHHH
T ss_conf             79998999999999999999


No 20 
>COG1613 Sbp ABC-type sulfate transport system, periplasmic component [Inorganic ion transport and metabolism]
Probab=20.94  E-value=42  Score=13.72  Aligned_cols=11  Identities=45%  Similarity=0.471  Sum_probs=4.7

Q ss_pred             CCHHHHHHHHH
Q ss_conf             87367888889
Q gi|254780876|r   65 GDYVVAENHLQ   75 (210)
Q Consensus        65 gd~~~~e~~~q   75 (210)
                      |-|..||.|++
T Consensus       270 gtr~vAeAyl~  280 (348)
T COG1613         270 GTRKVAEAYLK  280 (348)
T ss_pred             CCHHHHHHHHH
T ss_conf             56899999998


No 21 
>pfam06798 PrkA PrkA serine protein kinase C-terminal domain. This is a family of PrkA bacterial and archaeal serine kinases approximately 630 residues long. This family corresponds to the C-terminal domain.
Probab=20.24  E-value=57  Score=12.96  Aligned_cols=38  Identities=13%  Similarity=-0.070  Sum_probs=14.4

Q ss_pred             CCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHH
Q ss_conf             8877777766555545687777788999999999999999
Q gi|254780876|r   21 SFNRKNLNPLVRNYDSNGYDVKVRGTAQHIAERYSVLARD   60 (210)
Q Consensus        21 ~~~~~~~~~~~~~~~~~~~~~k~~~~~~~~~~ky~~la~d   60 (210)
                      .+-|...+.+...|.+..  ..+--||-.|+.-....-++
T Consensus        37 iS~Rfi~~~ls~a~~~~~--~~~~inp~~vl~~Le~~i~~   74 (254)
T pfam06798        37 ISPRFIGKALSNALVSDS--EERCINPLDVLEELEQGIKD   74 (254)
T ss_pred             CCHHHHHHHHHHHHHCCC--CCCCCCHHHHHHHHHHHHHC
T ss_conf             678999999999984388--88857899999999999860


No 22 
>TIGR02918 TIGR02918 conserved hypothetical protein TIGR02918; InterPro: IPR014267   Members of this entry are found only in Gram-positive bacteria of the Firmicutes lineage, including several species of Staphylococcus, Streptococcus, and Lactobacillus..
Probab=20.13  E-value=14  Score=16.65  Aligned_cols=37  Identities=14%  Similarity=0.016  Sum_probs=16.4

Q ss_pred             CCHHHHHHHHHHHHHHHH--HCCCHHHHHHHHHHHHHHH
Q ss_conf             899999999999999986--2687367888889999999
Q gi|254780876|r   45 GTAQHIAERYSVLARDAM--SAGDYVVAENHLQHAEHYN   81 (210)
Q Consensus        45 ~~~~~~~~ky~~la~da~--~~gd~~~~e~~~qha~hy~   81 (210)
                      ....+|.+++...=-.=.  .++=.-+.+.=|+=|+.|+
T Consensus       458 ~~~~~I~~~lA~~Iv~~Fv~~~~~~~~~~~SY~IA~~Fl  496 (511)
T TIGR02918       458 DDEDEIITALAEKIVEYFVNENDIDAFHEVSYQIAEGFL  496 (511)
T ss_pred             CCHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHHH
T ss_conf             887899999999989861267860026563178886631


Done!