Query         gi|254781211|ref|YP_003065624.1| hypothetical protein CLIBASIA_05590 [Candidatus Liberibacter asiaticus str. psy62]
Match_columns 234
No_of_seqs    1 out of 3
Neff          1.0 
Searched_HMMs 39220
Date          Mon May 30 06:51:33 2011
Command       /home/congqian_1/programs/hhpred/hhsearch -i 254781211.hhm -d /home/congqian_1/database/cdd/Cdd.hhm 

 No Hit                             Prob E-value P-value  Score    SS Cols Query HMM  Template HMM
  1 TIGR01887 dipeptidaselike dipe  65.2     2.5 6.3E-05   23.0   0.8   27  125-151   142-170 (492)
  2 COG2081 Predicted flavoprotein  52.3     3.4 8.5E-05   22.2  -0.4   80  102-193    31-112 (408)
  3 TIGR00019 prfA peptide chain r  46.9     7.3 0.00019   20.0   0.6   14  163-176   134-147 (373)
  4 TIGR00706 SppA_dom signal pept  45.6      17 0.00043   17.6   2.3   50  109-159   143-192 (224)
  5 PHA00666 putative protease      42.1      28 0.00073   16.1  11.7  128   61-200    83-226 (233)
  6 KOG4385 consensus               39.0      15 0.00037   18.0   1.2   59  157-216   394-462 (581)
  7 pfam09715 Plasmod_dom_1 Plasmo  38.9      18 0.00045   17.5   1.6   30  143-172    32-70  (70)
  8 TIGR01748 rhaA L-rhamnose isom  37.7      21 0.00053   17.0   1.8   44   43-118   128-174 (415)
  9 TIGR01286 nifK nitrogenase mol  36.9      30 0.00075   16.0   2.5   54  112-169    29-88  (526)
 10 pfam09077 Phage-MuB_C Mu B tra  36.6      19 0.00047   17.3   1.4   25  139-163     3-27  (78)
 11 COG1154 Dxs Deoxyxylulose-5-ph  36.0      32 0.00082   15.8   2.6   46   60-116   142-187 (627)
 12 KOG4439 consensus               34.2      30 0.00078   15.9   2.2  109   20-129    18-126 (901)
 13 PRK08609 hypothetical protein;  32.9     5.9 0.00015   20.5  -1.6   95  139-233   180-278 (570)
 14 pfam09105 SelB-wing_1 Elongati  30.1      30 0.00076   16.0   1.6   18  113-130    27-44  (61)
 15 TIGR00674 dapA dihydrodipicoli  29.2      27  0.0007   16.2   1.3  142   78-224     3-195 (288)
 16 COG5245 DYN1 Dynein, heavy cha  28.6      47  0.0012   14.7   4.8  102   72-184  1644-1754(3164)
 17 KOG0364 consensus               28.6      28 0.00072   16.1   1.3   31  125-156   178-208 (527)
 18 TIGR02187 GlrX_arch Glutaredox  27.4      41   0.001   15.1   1.9   41   47-88    133-177 (237)
 19 COG2344 AT-rich DNA-binding pr  25.2      41   0.001   15.1   1.6   20  113-132    64-83  (211)
 20 KOG0104 consensus               24.3      55  0.0014   14.2   2.1   32   35-66    592-623 (902)
 21 pfam06640 P_C P protein C-term  23.4      58  0.0015   14.1   3.0   54   12-65     39-110 (227)
 22 TIGR00956 3a01205 Pleiotropic   23.3      40   0.001   15.2   1.2   63   88-150   996-1075(1466)
 23 pfam06798 PrkA PrkA serine pro  23.0      59  0.0015   14.1   4.9   96   88-186    35-147 (254)
 24 pfam04624 Dec-1 Dec-1 repeat.   21.8      28 0.00072   16.1   0.2   12  222-233     8-19  (27)
 25 TIGR00380 cobD cobalamin biosy  20.7      66  0.0017   13.8   3.6   88   99-187   100-194 (322)
 26 COG3110 Uncharacterized protei  20.6      61  0.0015   14.0   1.7   19  212-230   198-216 (216)

No 1  
>TIGR01887 dipeptidaselike dipeptidase, putative; InterPro: IPR010964   Metalloproteases are the most diverse of the four main types of protease, with more than 50 families identified to date. In these enzymes, a divalent cation, usually zinc, activates the water molecule. The metal ion is held in place by amino acid ligands, usually three in number. The known metal ligands are His, Glu, Asp or Lys and at least one other residue is required for catalysis, which may play an electrophillic role. Of the known metalloproteases, around half contain an HEXXH motif, which has been shown in crystallographic studies to form part of the metal-binding site . The HEXXH motif is relatively common, but can be more stringently defined for metalloproteases as 'abXHEbbHbc', where 'a' is most often valine or threonine and forms part of the S1' subsite in thermolysin and neprilysin, 'b' is an uncharged residue, and 'c' a hydrophobic residue. Proline is never found in this site, possibly because it would break the helical structure adopted by this motif in metalloproteases .   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 entry represents bacterial zinc dipeptidases or probably dipeptidases, belonging to the MEROPS peptidase family M20 (clan MH), subfamily M20A. Many of the members are incorrectly annotated as 'Xaa-His' and 'carnosinase' due to the early miss-characterisation of the Lactobacillus delbrueckii PepV enzyme. The entry includes unassigned peptidases and non-peptidase homologues. ; GO: 0008270 zinc ion binding, 0016805 dipeptidase activity.
Probab=65.24  E-value=2.5  Score=23.00  Aligned_cols=27  Identities=37%  Similarity=0.496  Sum_probs=23.5

Q ss_pred             HHHHCCCHHHHHHHHHHHHHH--HCCCHH
Q ss_conf             865077302347799999753--038814
Q gi|254781211|r  125 QTKLGSDYETREKDIARYFRK--EKIPDN  151 (234)
Q Consensus       125 qtklgsdyetrekdiaryfrk--ekipdn  151 (234)
                      .--+|+|=||--++|.|||++  |..|+-
T Consensus       142 R~I~GTDEEsgw~c~~yYf~~~~E~~P~~  170 (492)
T TIGR01887       142 RFIFGTDEESGWKCIDYYFEHLKEEAPDL  170 (492)
T ss_pred             EEEEECCCCCCCCCHHHHHHHCCCCCCCE
T ss_conf             99983465658700787776505888856


No 2  
>COG2081 Predicted flavoproteins [General function prediction only]
Probab=52.32  E-value=3.4  Score=22.15  Aligned_cols=80  Identities=23%  Similarity=0.346  Sum_probs=37.3

Q ss_pred             HHHHHHHHHHHHCCCHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHCCCHH--HHHHHHHHHHHHHHHHHHHHHHHHCCCC
Q ss_conf             99836887788311369999999865077302347799999753038814--7999998632256777999987511211
Q gi|254781211|r  102 LVDHGRKIGEQFGASLEEERKLLQTKLGSDYETREKDIARYFRKEKIPDN--DVQSLISAWGFEKTFNFFDRYAQQNKES  179 (234)
Q Consensus       102 lvdhgrkigeqfgasleeerkllqtklgsdyetrekdiaryfrkekipdn--dvqslisawgfektfnffdryaqqnkes  179 (234)
                      |.||++|+|+          |+|-+--|----|.....+.|.-  .+|.|  -+.|.++.+.-+....||.++...-+|-
T Consensus        31 lid~~~k~Gr----------Kil~sGgGrCN~Tn~~~~~~~ls--~~p~~~~fl~sal~~ft~~d~i~~~e~~Gi~~~e~   98 (408)
T COG2081          31 LIDKGPKLGR----------KILMSGGGRCNFTNSEAPDEFLS--RNPGNGHFLKSALARFTPEDFIDWVEGLGIALKEE   98 (408)
T ss_pred             EEECCCCCCC----------EEEECCCCCCCCCCCCCHHHHHH--HCCCCCHHHHHHHHHCCHHHHHHHHHHCCCEEEEC
T ss_conf             9805864221----------36853788743326505899997--58982067788987279899999998659715774


Q ss_pred             CCCCHHHHCCCCHH
Q ss_conf             23310221245214
Q gi|254781211|r  180 STGDTFVRSEGSQE  193 (234)
Q Consensus       180 stgdtfvrsegsqe  193 (234)
                      +.|--|-.+..++.
T Consensus        99 ~~Gr~Fp~sdkA~~  112 (408)
T COG2081          99 DLGRMFPDSDKASP  112 (408)
T ss_pred             CCCEECCCCCCHHH
T ss_conf             68525578666689


No 3  
>TIGR00019 prfA peptide chain release factor 1; InterPro: IPR004373 This family describes peptide chain release factor 1 (PrfA, RF-1), and excludes the related peptide chain release factor 2 (PrfB, RF-2). RF-1 helps recognise and terminate translation at UAA and UAG stop codons. The mitochondrial release factors are prfA-like, although not included above the trusted cut-off for this model. RF-1 does not have a translational frameshift.; GO: 0016149 translation release factor activity codon specific, 0006415 translational termination, 0005737 cytoplasm.
Probab=46.88  E-value=7.3  Score=19.96  Aligned_cols=14  Identities=29%  Similarity=0.726  Sum_probs=9.4

Q ss_pred             HHHHHHHHHHHHHC
Q ss_conf             56777999987511
Q gi|254781211|r  163 EKTFNFFDRYAQQN  176 (234)
Q Consensus       163 ektfnffdryaqqn  176 (234)
                      ---|+.+-|||...
T Consensus       134 gDLfrMY~rYAE~k  147 (373)
T TIGR00019       134 GDLFRMYSRYAESK  147 (373)
T ss_pred             HHHHHHHHHHHHCC
T ss_conf             87999988887437


No 4  
>TIGR00706 SppA_dom signal peptide peptidase SppA, 36K type; InterPro: IPR004635   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 peptidases belong to MEROPS peptidase family S49 (protease IV family, clan S-). The predicted active site serine for members of this family occurs in a transmembrane domain. This group of sequences represent both long and short forms of the bacterial SppA and homologs found in the archaea and plants.   Signal peptides of secretory proteins seem to serve at least two important biological functions. First, they are required for protein targeting to and translocation across membranes, such as the eubacterial plasma membrane and the endoplasmic reticular membrane of eukaryotes. Second, in addition to their role as determinants for protein targeting and translocation, certain signal peptides have a signaling function.  During or shortly after pre-protein translocation, the signal peptide is removed by signal peptidases. The integral membrane protein, SppA (protease IV), of Escherichia coli was shown experimentally to degrade signal peptides. The member of this family from Bacillus subtilis has only been shown to be required for efficient processing of pre-proteins under conditions of hyper-secretion . ; GO: 0008233 peptidase activity, 0006508 proteolysis.
Probab=45.62  E-value=17  Score=17.61  Aligned_cols=50  Identities=30%  Similarity=0.416  Sum_probs=41.0

Q ss_pred             HHHHHCCCHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHCCCHHHHHHHHHH
Q ss_conf             778831136999999986507730234779999975303881479999986
Q gi|254781211|r  109 IGEQFGASLEEERKLLQTKLGSDYETREKDIARYFRKEKIPDNDVQSLISA  159 (234)
Q Consensus       109 igeqfgasleeerkllqtklgsdyetrekdiaryfrkekipdndvqslisa  159 (234)
                      |+--+-.-.+|||..||+-.-..|+.=-+.|+.+ |..|+|-.+|+.+-.-
T Consensus       143 ~~~~~R~lt~eE~~~lQ~~v~~~Y~~F~~~V~~~-R~nkl~~~~vK~~AdG  192 (224)
T TIGR00706       143 IGSPTRELTPEERKILQSLVNESYEQFVQVVAKG-RNNKLSVEDVKKFADG  192 (224)
T ss_pred             CCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH-CCCCCCHHHHHHHHCC
T ss_conf             8987577629999999998888875789999984-1677897887652068


No 5  
>PHA00666 putative protease
Probab=42.05  E-value=28  Score=16.12  Aligned_cols=128  Identities=20%  Similarity=0.312  Sum_probs=73.7

Q ss_pred             CCCCCEECCCHHH--HHHHHHHHHHHHHHCCHHHHHHHHHHH---HHHHH--------HHHHHHHHCCCHHHHHHHHHHH
Q ss_conf             8321200380020--145678989998862815789999999---99983--------6887788311369999999865
Q gi|254781211|r   61 PIEDYTLSCPDYV--SEAEVTAHIEAFKEAGVDARVAQKVVD---KLVDH--------GRKIGEQFGASLEEERKLLQTK  127 (234)
Q Consensus        61 piedytlscpdyv--seaevtahieafkeagvdarvaqkvvd---klvdh--------grkigeqfgasleeerkllqtk  127 (234)
                      --|.|.+..|.-+  ...-+.+.-+.++|-|..-.-||||||   +++.-        -.++-+++++++.-..+..--+
T Consensus        83 APEkYeF~apEG~elD~e~L~~F~~vA~ELgL~~eQAQkilD~y~k~~~~~q~qQaea~q~~~e~Wa~~~k~D~E~gG~~  162 (233)
T PHA00666         83 APEKYEFQAAEGVELDTGALGAFEPVARELNLTNEQAQKVVDLYTKILPVVQQRQAEAWQKTTEQWAADSKADKEIGGDK  162 (233)
T ss_pred             CCCCCCCCCCCCCCCCHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             97213456886554699999999999998199999999999999735389999999999999999999976538765688


Q ss_pred             HCCCHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHH---HHHHHHHHHHHCCCCCCCCHHHHCCCCHHHHHHHHH
Q ss_conf             0773023477999997530388147999998632256---777999987511211233102212452144322888
Q gi|254781211|r  128 LGSDYETREKDIARYFRKEKIPDNDVQSLISAWGFEK---TFNFFDRYAQQNKESSTGDTFVRSEGSQEADRDFDK  200 (234)
Q Consensus       128 lgsdyetrekdiaryfrkekipdndvqslisawgfek---tfnffdryaqqnkesstgdtfvrsegsqeadrdfdk  200 (234)
                      |......-.+-+.+++-.      .+.+|...-|+-.   ..++|-|....-.|    |.+|.. | .+..|++-.
T Consensus       163 ~~aN~~~Aq~Ald~Fgtp------eL~~lln~tGLGNHPelVr~f~kiGkamsE----D~~V~g-g-~~~~~~~a~  226 (233)
T PHA00666        163 LQENLSAAQRALDQFGTP------ELKEYLNKTGLGNHPELVKVFYKAGKAMSE----DRLVTG-G-NEPKQSDAR  226 (233)
T ss_pred             HHHHHHHHHHHHHHHCCH------HHHHHHHHCCCCCCHHHHHHHHHHHHHHCC----CCEECC-C-CCCCCCHHH
T ss_conf             876799999999985899------999998612777788999999999987522----664107-8-864301789


No 6  
>KOG4385 consensus
Probab=38.98  E-value=15  Score=17.99  Aligned_cols=59  Identities=37%  Similarity=0.539  Sum_probs=40.5

Q ss_pred             HHHHHHHHHHHHHHHHHHHCCC-----CCCCCHHHHCCCCHHH-----HHHHHHHHCCCCCCHHHHCCCH
Q ss_conf             9863225677799998751121-----1233102212452144-----3228886278430033312646
Q gi|254781211|r  157 ISAWGFEKTFNFFDRYAQQNKE-----SSTGDTFVRSEGSQEA-----DRDFDKVFNTPDFGSRVLSGDK  216 (234)
Q Consensus       157 isawgfektfnffdryaqqnke-----sstgdtfvrsegsqea-----drdfdkvfntpdfgsrvlsgdk  216 (234)
                      |-.| |..||-||.|-|-.-|-     -|++..|||-|.-.-+     .|.|.|--.---||+-.|.|+.
T Consensus       394 IY~W-FTrtFAYFRRNaATWKnAVRHNLSLHKCF~RVEnvkgavwtvDe~e~~krr~~k~~g~~sl~~n~  462 (581)
T KOG4385         394 IYNW-FTRTFAYFRRNAATWKNAVRHNLSLHKCFVRVENVKGAVWTVDEREFQKRRPQKITGSPSLIGNM  462 (581)
T ss_pred             HHHH-HHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHCCEEEEEHHHHHHHCCCCCCCCHHHHCCC
T ss_conf             9999-99999999636056767776556788999999987255146324655520675446862131211


No 7  
>pfam09715 Plasmod_dom_1 Plasmodium protein of unknown function (Plasmod_dom_1). These sequences represent an uncharacterized family consisting of a small number of hypothetical proteins of the malaria parasite Plasmodium falciparum (isolate 3D7).
Probab=38.87  E-value=18  Score=17.46  Aligned_cols=30  Identities=37%  Similarity=0.558  Sum_probs=22.3

Q ss_pred             HHHHCCCHHHHHHHHHHH---------HHHHHHHHHHHH
Q ss_conf             753038814799999863---------225677799998
Q gi|254781211|r  143 FRKEKIPDNDVQSLISAW---------GFEKTFNFFDRY  172 (234)
Q Consensus       143 frkekipdndvqslisaw---------gfektfnffdry  172 (234)
                      |-+|-+|+|-+-.+-+|-         -+-|++|||.||
T Consensus        32 ~~~E~V~~n~l~l~~aa~p~~aipi~~Yi~krinF~~~y   70 (70)
T pfam09715        32 FIKEDVIDNSLSLCTAAIPLTAIPIFSYIAKRINFFTKY   70 (70)
T ss_pred             CCHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHCC
T ss_conf             876650453999987414320026699999887777509


No 8  
>TIGR01748 rhaA L-rhamnose isomerase; InterPro: IPR009308   This family consists of several bacterial L-rhamnose isomerase proteins (5.3.1.14 from EC). This enzyme interconverts L-rhamnose and L-rhamnulose. In some species, including Escherichia coli, this is the first step in rhamnose catabolism. Sequential steps are catalyzed by rhamnulose kinase (rhaB), then rhamnulose-1-phosphate aldolase (rhaD) to yield glycerone phosphate and (S)-lactaldehyde. ; GO: 0008740 L-rhamnose isomerase activity, 0030145 manganese ion binding, 0019299 rhamnose metabolic process.
Probab=37.68  E-value=21  Score=17.02  Aligned_cols=44  Identities=36%  Similarity=0.561  Sum_probs=27.9

Q ss_pred             CCCCCCCCCHHHCCCCCCCCCCCEECCCHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHH---HHHHHHHCCCHH
Q ss_conf             8877554430211899998321200380020145678989998862815789999999999836---887788311369
Q gi|254781211|r   43 RNPSSSSSSTEEAGEPKPPIEDYTLSCPDYVSEAEVTAHIEAFKEAGVDARVAQKVVDKLVDHG---RKIGEQFGASLE  118 (234)
Q Consensus        43 rnpssssssteeagepkppiedytlscpdyvseaevtahieafkeagvdarvaqkvvdklvdhg---rkigeqfgasle  118 (234)
                      =||+--|...        --..||||-||-                        .|-+=-++||   |||+|-||-.|-
T Consensus       128 FNPt~FSHp~--------~aDg~TLshpD~------------------------~iR~FWI~HckasRriseYFGkeLG  174 (415)
T TIGR01748       128 FNPTLFSHPL--------AADGYTLSHPDD------------------------EIREFWIEHCKASRRISEYFGKELG  174 (415)
T ss_pred             CCCCCCCCCC--------CCCCCCCCCCCH------------------------HHHHHHHHHHHHHCHHHHHHHHHCC
T ss_conf             3666335420--------005773447882------------------------4679999832330102345313106


No 9  
>TIGR01286 nifK nitrogenase molybdenum-iron protein beta chain; InterPro: IPR005976    The enzyme responsible for nitrogen fixation, the nitrogenase, shows a high degree of conservation of structure, function, and amino acid sequence across wide phylogenetic ranges. All known Mo-nitrogenases consist of two components, component I (also called dinitrogenase, or Fe-Mo protein), an alpha2beta2 tetramer encoded by the nifD and nifK genes, and component II (dinitrogenase reductase, or Fe protein) a homodimer encoded by the nifH gene , . Two operons, nifDK and nifEN, encode a tetrameric (alpha2beta2 and N2E2) enzymatic complex. Nitrogenase contains two unusual rare metal clusters; one of them is the iron molybdenum cofactor (FeMo-co), which is considered to be the site of dinitrogen reduction and whose biosynthesis requires the products of nifNE and of some other nif genes . It has been proposed that NifNE might serve as a scaffold upon which FeMo-co is built and then inserted into component I .; GO: 0016163 nitrogenase activity, 0009399 nitrogen fixation, 0016612 molybdenum-iron nitrogenase complex.
Probab=36.88  E-value=30  Score=16.02  Aligned_cols=54  Identities=30%  Similarity=0.470  Sum_probs=32.9

Q ss_pred             HHCCCHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHCCC---HHHHH---HHHHHHHHHHHHHHH
Q ss_conf             83113699999998650773023477999997530388---14799---999863225677799
Q gi|254781211|r  112 QFGASLEEERKLLQTKLGSDYETREKDIARYFRKEKIP---DNDVQ---SLISAWGFEKTFNFF  169 (234)
Q Consensus       112 qfgasleeerkllqtklgsdyetrekdiaryfrkekip---dndvq---slisawgfektfnff  169 (234)
                      +|-...-.|.---+..+-.-.|-|||..||    |-+-   -.-.|   .++.|-|||+|.-|.
T Consensus        29 ~FE~~~p~~~v~~v~~wT~~wEYrEkNfaR----EALtvNPAKACQPLGAvLAA~GFE~TmpfV   88 (526)
T TIGR01286        29 EFEEKAPKEKVQEVLEWTKTWEYREKNFAR----EALTVNPAKACQPLGAVLAALGFEGTMPFV   88 (526)
T ss_pred             HHCCCCCHHHHHHHHHHHCCHHHHHHHHHH----HHHCCCCHHCCCHHHHHHHHHCCCCCCCCC
T ss_conf             416787345799998741561345454430----221037522034179999971213335752


No 10 
>pfam09077 Phage-MuB_C Mu B transposition protein, C terminal. The C terminal domain of the B transposition protein from Bacteriophage Mu comprises four alpha-helices arranged in a loosely packed bundle, where helix alpha1 runs parallel to alpha3, and anti-parallel to helices alpha2 and alpha4. The domain allows for non-specific binding of Mu to double-stranded DNA, allowing for integration into the bacterial genome, and mediates dimerization of the protein.
Probab=36.60  E-value=19  Score=17.32  Aligned_cols=25  Identities=32%  Similarity=0.587  Sum_probs=19.1

Q ss_pred             HHHHHHHHCCCHHHHHHHHHHHHHH
Q ss_conf             9999753038814799999863225
Q gi|254781211|r  139 IARYFRKEKIPDNDVQSLISAWGFE  163 (234)
Q Consensus       139 iaryfrkekipdndvqslisawgfe  163 (234)
                      |++-++-.|--.+||++++.|||.+
T Consensus         3 igk~~~i~k~kk~Di~Aia~AWgv~   27 (78)
T pfam09077         3 IAKRTGIKKAKKADVKAVAQAWGLQ   27 (78)
T ss_pred             CCHHCCCCCCCHHHHHHHHHHHCCC
T ss_conf             0111002589799999999996899


No 11 
>COG1154 Dxs Deoxyxylulose-5-phosphate synthase [Coenzyme metabolism / Lipid metabolism]
Probab=35.99  E-value=32  Score=15.77  Aligned_cols=46  Identities=26%  Similarity=0.304  Sum_probs=21.1

Q ss_pred             CCCCCCEECCCHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHHHCCC
Q ss_conf             983212003800201456789899988628157899999999998368877883113
Q gi|254781211|r   60 PPIEDYTLSCPDYVSEAEVTAHIEAFKEAGVDARVAQKVVDKLVDHGRKIGEQFGAS  116 (234)
Q Consensus        60 ppiedytlscpdyvseaevtahieafkeagvdarvaqkvvdklvdhgrkigeqfgas  116 (234)
                      +-|-|-.|||-         --.||...+| +. ...+++--|-|.+.-|.+..|+-
T Consensus       142 aVIGDGAlt~G---------mA~EALN~ag-~~-~~~~~iVILNDNeMSIs~nvGal  187 (627)
T COG1154         142 AVIGDGALTGG---------MAFEALNNAG-AD-LKSNLIVILNDNEMSISPNVGAL  187 (627)
T ss_pred             EEECCCCCCCH---------HHHHHHHHHH-HC-CCCCEEEEEECCCCCCCCCCCHH
T ss_conf             99777633001---------7999985332-30-48998999807986458775479


No 12 
>KOG4439 consensus
Probab=34.22  E-value=30  Score=15.93  Aligned_cols=109  Identities=21%  Similarity=0.060  Sum_probs=49.2

Q ss_pred             ECCCCCCCCCCCHHHHHHCCCCCCCCCCCCCCHHHCCCCCCCCCCCEECCCHHHHHHHHHHHHHHHHHCCHHHHHHHHHH
Q ss_conf             00000278688756654308678887755443021189999832120038002014567898999886281578999999
Q gi|254781211|r   20 CERSQRSNPPPSKEEAVQSDPQGRNPSSSSSSTEEAGEPKPPIEDYTLSCPDYVSEAEVTAHIEAFKEAGVDARVAQKVV   99 (234)
Q Consensus        20 cersqrsnpppskeeavqsdpqgrnpssssssteeagepkppiedytlscpdyvseaevtahieafkeagvdarvaqkvv   99 (234)
                      |...+-+--|+||.++++.--+- --.|+-.|++..-...++|..|+.--|--.+..|-+...-+-.--+--+.+-|-|-
T Consensus        18 ~~~d~sssvp~sk~~i~~~~~~~-~~~s~~~s~~~h~ra~s~i~~~~~~~P~~~s~~eS~~~~s~~q~~e~r~~i~q~~~   96 (901)
T KOG4439          18 MIQDQSSSVPKSKQNISRTMLGE-PYDSSECSGENHERARSFILTNKPLRPIEKSDNESAIFRSDSQLEERRKSIKQLVP   96 (901)
T ss_pred             HHHCCCCCCCCCHHHHHCCCCCC-CCCCHHCCCCCHHHCCCHHHCCCCCCCCHHCCCCCCHHHHHHHHHHHHHHHHHHCC
T ss_conf             53023456885200121256788-77611015641432025454168888510002311004578887525564887421


Q ss_pred             HHHHHHHHHHHHHHCCCHHHHHHHHHHHHC
Q ss_conf             999983688778831136999999986507
Q gi|254781211|r  100 DKLVDHGRKIGEQFGASLEEERKLLQTKLG  129 (234)
Q Consensus       100 dklvdhgrkigeqfgasleeerkllqtklg  129 (234)
                      +-+.-|+--++-+-++|-.++-+++.++++
T Consensus        97 ~~~~~~~~~~q~~~~~s~~~~~~~~~~~~~  126 (901)
T KOG4439          97 DILTTEASSRQGWGNASETEELDDLKLHLS  126 (901)
T ss_pred             CCCHHHHHCCCCCCCCCCHHHHCCHHCCCC
T ss_conf             000011101467566763122011011210


No 13 
>PRK08609 hypothetical protein; Provisional
Probab=32.94  E-value=5.9  Score=20.54  Aligned_cols=95  Identities=17%  Similarity=0.217  Sum_probs=47.6

Q ss_pred             HHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCHHHHCCCCHHHHHHHHH-HHCCCCCCHHH--HCCC
Q ss_conf             99997530388147999998632256777999987511211233102212452144322888-62784300333--1264
Q gi|254781211|r  139 IARYFRKEKIPDNDVQSLISAWGFEKTFNFFDRYAQQNKESSTGDTFVRSEGSQEADRDFDK-VFNTPDFGSRV--LSGD  215 (234)
Q Consensus       139 iaryfrkekipdndvqslisawgfektfnffdryaqqnkesstgdtfvrsegsqeadrdfdk-vfntpdfgsrv--lsgd  215 (234)
                      ||--||..+---.|+.-||++-..+....+|-.+..-..--+.|+|.+.-.-........|- +...-.||...  ..|.
T Consensus       180 iaGS~RR~ketvGDIDiLv~s~~p~~v~~~l~~~~~v~evl~~G~tK~s~~~~~~~~i~vDlrvv~~~~fg~aLlyFTGS  259 (570)
T PRK08609        180 RAGSLRRARETVKDLDFIIATDNPKAVREQLLQFPNIVEVIAAGDTKVSLELAYDYTISVDFRLVEPEAFATTLHHFTGS  259 (570)
T ss_pred             EECHHHHCCCCCCCEEEEEECCCHHHHHHHHHCCCCHHHHHHCCCCCEEEEEECCCCCEEEEEEECHHHHHHHHHHHHCC
T ss_conf             60202314665467348995598089999996486256787268860589971588836899980889989999997666


Q ss_pred             HHHHHHHHHHHHHHH-HCC
Q ss_conf             678899999986544-205
Q gi|254781211|r  216 KEATKTLRQWAEKQA-TLN  233 (234)
Q Consensus       216 keatktlrqwaekqa-tln  233 (234)
                      |+-...||++|-++. +||
T Consensus       260 k~hNi~lR~~A~~kG~~Ln  278 (570)
T PRK08609        260 KDHNVRMRQLAKARGEKIS  278 (570)
T ss_pred             HHHHHHHHHHHHHCCCCCC
T ss_conf             9999999999997488503


No 14 
>pfam09105 SelB-wing_1 Elongation factor SelB, winged helix. Members of this family adopt a winged-helix fold, with an alpha/beta structure consisting of three alpha-helices and a twisted three-stranded antiparallel beta-sheet, with an alpha-beta-alpha-alpha-beta-beta connectivity. They are involved in both DNA and RNA binding.
Probab=30.13  E-value=30  Score=15.97  Aligned_cols=18  Identities=50%  Similarity=0.543  Sum_probs=13.5

Q ss_pred             HCCCHHHHHHHHHHHHCC
Q ss_conf             311369999999865077
Q gi|254781211|r  113 FGASLEEERKLLQTKLGS  130 (234)
Q Consensus       113 fgasleeerkllqtklgs  130 (234)
                      -..||||.|||||.-...
T Consensus        27 aslsleetrkllqsmaaa   44 (61)
T pfam09105        27 ASLSLEETRKLLQSMAAA   44 (61)
T ss_pred             HHCCHHHHHHHHHHHHHC
T ss_conf             623489999999999855


No 15 
>TIGR00674 dapA dihydrodipicolinate synthase; InterPro: IPR005263   Dihydropicolinate synthase (DHDPS) is the key enzyme in lysine biosynthesis via the diaminopimelate pathway of prokaryotes, some phycomycetes and higher plants. The enzyme catalyses the condensation of L-aspartate-beta-semialdehyde and pyruvate to dihydropicolinic acid via a ping-pong mechanism in which pyruvate binds to the enzyme by forming a Schiff-base with a lysine residue . Three other proteins are structurally related to DHDPS and probably also act via a similar catalytic mechanism. These are Escherichia coli N-acetylneuraminate lyase (4.1.3.3 from EC, IPR005264 from INTERPRO) (gene nanA), which catalyzes the condensation of N-acetyl-D-mannosamine and pyruvate to form N-acetylneuraminate; Sinorhizobium meliloti protein mosA , which is involved in the biosynthesis of the rhizopine 3-O-methyl-scyllo-inosamine; and E. coli hypothetical protein yjhH. The sequences of DHDPS from different sources are well-conserved. The structure takes the form of a homotetramer, in which 2 monomers are related by an approximate 2-fold symmetry . Each monomer comprises 2 domains: an 8-fold alpha-/beta-barrel, and a C-terminal alpha-helical domain. The fold resembles that of N-acetylneuraminate lyase. The active site lysine is located in the barrel domain, and has access via 2 channels on the C-terminal side of the barrel.   This family represents a subclass of dihydrodipicolinate synthase. ; GO: 0008840 dihydrodipicolinate synthase activity, 0019877 diaminopimelate biosynthetic process.
Probab=29.20  E-value=27  Score=16.22  Aligned_cols=142  Identities=30%  Similarity=0.434  Sum_probs=86.2

Q ss_pred             HHHHHHHHHHCC-HHHHHHHHHHHHHHHHHH-------HHHHHHCCCHHHHHHHHHHHH-------------CCCHHHHH
Q ss_conf             789899988628-157899999999998368-------877883113699999998650-------------77302347
Q gi|254781211|r   78 VTAHIEAFKEAG-VDARVAQKVVDKLVDHGR-------KIGEQFGASLEEERKLLQTKL-------------GSDYETRE  136 (234)
Q Consensus        78 vtahieafkeag-vdarvaqkvvdklvdhgr-------kigeqfgasleeerkllqtkl-------------gsdyetre  136 (234)
                      .||-|--||+-| ||-....++++.++.||-       --||----|.||..+++..-.             ||. -|+|
T Consensus         3 ~~A~iTPFk~~~~VDf~~Le~li~~~~~~G~da~V~~GTTGEs~TLs~EE~~~~i~~~~~~~~~R~pvIaG~GsN-~T~E   81 (288)
T TIGR00674         3 ITALITPFKEDGSVDFAALEKLIDFQIENGTDAIVVVGTTGESATLSHEEHKKVIEFVVDLVKGRVPVIAGTGSN-ATEE   81 (288)
T ss_pred             CCEEECCCCCCCCCCHHHHHHHHHHHHHHCCCEEEECCCCCCCCCCCHHHHHHHHHHHHHHHCCCEEEEECCCCC-HHHH
T ss_conf             840533304988553889999999899707985897135588644688888999999987762877898537732-5899


Q ss_pred             H-HHHHHHHHHCCCHHHHHHHH---HHHHHHHHHHHHHHHHHH--------CCCCCCCCHH-----H------H-CCCCH
Q ss_conf             7-99999753038814799999---863225677799998751--------1211233102-----2------1-24521
Q gi|254781211|r  137 K-DIARYFRKEKIPDNDVQSLI---SAWGFEKTFNFFDRYAQQ--------NKESSTGDTF-----V------R-SEGSQ  192 (234)
Q Consensus       137 k-diaryfrkekipdndvqsli---sawgfektfnffdryaqq--------nkesstgdtf-----v------r-segsq  192 (234)
                      - ..+..++|  ++-.-+-..-   .-=.-|--+..|++-|+.        |--|-||--+     .      + --|..
T Consensus        82 ai~l~~~a~~--~G~dg~L~vtPyYNKP~q~Gl~~HFkaia~~~~lPiiLYNvPsRTg~~l~peTv~rLA~~~~NI~aiK  159 (288)
T TIGR00674        82 AIELTKFAEK--LGVDGFLVVTPYYNKPTQEGLYQHFKAIAEEVDLPIILYNVPSRTGVSLEPETVKRLAEEPNNIVAIK  159 (288)
T ss_pred             HHHHHHHHHH--CCCCEEECCCCCCCCCCCCHHHHHHHHHHHHCCCCEEEECCCCCCCCCCCHHHHHHHHCCCCCEEEEE
T ss_conf             9999999986--89568845887551888213899999999871698898428764101786289999730167706887


Q ss_pred             HHHHHHHHHH----CCC--CCCHHHHCCCHHHHHHHHH
Q ss_conf             4432288862----784--3003331264678899999
Q gi|254781211|r  193 EADRDFDKVF----NTP--DFGSRVLSGDKEATKTLRQ  224 (234)
Q Consensus       193 eadrdfdkvf----ntp--dfgsrvlsgdkeatktlrq  224 (234)
                      ||-.|...+-    -+|  ||  +|||||-+-+--+..
T Consensus       160 Ea~g~l~~~~~i~~~~p~~dF--~vlsGDD~l~l~~~~  195 (288)
T TIGR00674       160 EATGNLERISEIKAITPDDDF--VVLSGDDALTLPILA  195 (288)
T ss_pred             ECCCCHHHHHHHHHHCCCCCE--EEEECCCCHHHHHHH
T ss_conf             268888999999986689853--888478611369998


No 16 
>COG5245 DYN1 Dynein, heavy chain [Cytoskeleton]
Probab=28.64  E-value=47  Score=14.74  Aligned_cols=102  Identities=28%  Similarity=0.277  Sum_probs=63.7

Q ss_pred             HHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHHH-CCCHHH---HHHHHHHHHCCCHHHHHHHHHHHHHH--
Q ss_conf             201456789899988628157899999999998368877883-113699---99999865077302347799999753--
Q gi|254781211|r   72 YVSEAEVTAHIEAFKEAGVDARVAQKVVDKLVDHGRKIGEQF-GASLEE---ERKLLQTKLGSDYETREKDIARYFRK--  145 (234)
Q Consensus        72 yvseaevtahieafkeagvdarvaqkvvdklvdhgrkigeqf-gaslee---erkllqtklgsdyetrekdiaryfrk--  145 (234)
                      |-+-+-...-+||.-++          .-+++|.=+.+-|.| -||.+-   -+.-..+-|-+.|--.-.+..|..|-  
T Consensus      1644 ype~~SL~~Iyea~l~~----------s~l~~~ef~~~se~~~~aSv~ly~~~k~~~k~~lq~~y~y~pReLtR~lr~i~ 1713 (3164)
T COG5245        1644 YPELASLRNIYEAVLMG----------SYLCFDEFNRLSEETMSASVELYLSSKDKTKFFLQMNYGYKPRELTRSLRAIF 1713 (3164)
T ss_pred             CCCHHHHHHHHHHHHHH----------HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHH
T ss_conf             86334499999999998----------88845989887799988889999999886523200000337378889999997


Q ss_pred             ---HCCCHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCH
Q ss_conf             ---038814799999863225677799998751121123310
Q gi|254781211|r  146 ---EKIPDNDVQSLISAWGFEKTFNFFDRYAQQNKESSTGDT  184 (234)
Q Consensus       146 ---ekipdndvqslisawgfektfnffdryaqqnkesstgdt  184 (234)
                         |.-|+..--|||-.|-.|.---|.||..|| ||+|++.+
T Consensus      1714 ~yaeT~~~t~~~slI~~wy~ea~r~~~dRLV~q-kE~st~~q 1754 (3164)
T COG5245        1714 GYAETRIDTPDVSLIIDWYCEAIREKIDRLVQQ-KESSTSRQ 1754 (3164)
T ss_pred             HHHHCCCCCCCHHHHHHHHHHHHHHHHHHHHHH-HHCCHHHH
T ss_conf             677527888748999999988999999999888-74041789


No 17 
>KOG0364 consensus
Probab=28.63  E-value=28  Score=16.15  Aligned_cols=31  Identities=32%  Similarity=0.541  Sum_probs=24.4

Q ss_pred             HHHHCCCHHHHHHHHHHHHHHHCCCHHHHHHH
Q ss_conf             86507730234779999975303881479999
Q gi|254781211|r  125 QTKLGSDYETREKDIARYFRKEKIPDNDVQSL  156 (234)
Q Consensus       125 qtklgsdyetrekdiaryfrkekipdndvqsl  156 (234)
                      -.+.|.+ +.||-||-||.+-||||...++.-
T Consensus       178 vk~V~~~-~g~e~dik~y~kveKvpgg~l~~s  208 (527)
T KOG0364         178 VKTVGVE-NGREIDIKRYAKVEKVPGGLLEDS  208 (527)
T ss_pred             HHHHHHC-CCCEECHHHHCCCCCCCCCCCCCC
T ss_conf             8776404-684420566434565676301344


No 18 
>TIGR02187 GlrX_arch Glutaredoxin-like domain protein; InterPro: IPR011903   Glutaredoxins , , , also known as thioltransferases (disulphide reductases, are small proteins of approximately one hundred amino-acid residues which utilise glutathione and NADPH as cofactors. Oxidized glutathione is regenerated by glutathione reductase. Together these components compose the glutathione system .    Glutaredoxin functions as an electron carrier in the glutathione-dependent synthesis of deoxyribonucleotides by the enzyme ribonucleotide reductase. Like thioredoxin, which functions in a similar way, glutaredoxin possesses an active centre disulphide bond . It exists in either a reduced or an oxidized form where the two cysteine residues are linked in an intramolecular disulphide bond.   Glutaredoxin has been sequenced in a variety of species. On the basis of extensive sequence similarity, it has been proposed  that Vaccinia virus protein O2L is most probably a glutaredoxin. Finally, it must be noted that Bacteriophage T4 thioredoxin seems also to be evolutionary related. In position 5 of the pattern T4 thioredoxin has Val instead of Pro.    This entry of archaeal proteins contains a C-terminal domain with homology to bacterial and eukaryotic glutaredoxins, including a CPYC motif. There is an N-terminal domain which has even more distant homology to glutaredoxins. The name "glutaredoxin" may be inappropriate in the sense of working in tandem with glutathione and glutathione reductase which may not be present in the archaea. The overall domain structure appears to be related to bacterial alkylhydroperoxide reductases, but the homology may be distant enough that the function of this family is wholly different..
Probab=27.36  E-value=41  Score=15.09  Aligned_cols=41  Identities=29%  Similarity=0.400  Sum_probs=24.6

Q ss_pred             CCCCCHHHCCC-CCCCCCC---CEECCCHHHHHHHHHHHHHHHHHC
Q ss_conf             55443021189-9998321---200380020145678989998862
Q gi|254781211|r   47 SSSSSTEEAGE-PKPPIED---YTLSCPDYVSEAEVTAHIEAFKEA   88 (234)
Q Consensus        47 sssssteeage-pkppied---ytlscpdyvseaevtahieafkea   88 (234)
                      -|..+.|+--. -.-||.=   -|-||| |--.|-++||-=|+--.
T Consensus       133 L~~~~~e~l~~kl~~~v~I~vfVTPtCP-YCP~AV~mAH~fA~~~~  177 (237)
T TIGR02187       133 LSEETVEELKSKLDEPVRIEVFVTPTCP-YCPRAVLMAHKFALAND  177 (237)
T ss_pred             CCHHHHHHHHHHCCCCEEEEEEEECCCC-CHHHHHHHHHHHHHHCC
T ss_conf             5089999997337983599999856899-72579999999998354


No 19 
>COG2344 AT-rich DNA-binding protein [General function prediction only]
Probab=25.25  E-value=41  Score=15.10  Aligned_cols=20  Identities=25%  Similarity=0.489  Sum_probs=7.1

Q ss_pred             HCCCHHHHHHHHHHHHCCCH
Q ss_conf             31136999999986507730
Q gi|254781211|r  113 FGASLEEERKLLQTKLGSDY  132 (234)
Q Consensus       113 fgasleeerkllqtklgsdy  132 (234)
                      ||-..+.-+..+..-||-|-
T Consensus        64 ~GYnV~~L~~ff~~~Lg~~~   83 (211)
T COG2344          64 YGYNVKYLRDFFDDLLGQDK   83 (211)
T ss_pred             CCCCHHHHHHHHHHHHCCCC
T ss_conf             78439999999999838774


No 20 
>KOG0104 consensus
Probab=24.32  E-value=55  Score=14.25  Aligned_cols=32  Identities=25%  Similarity=0.364  Sum_probs=11.5

Q ss_pred             HHHCCCCCCCCCCCCCCHHHCCCCCCCCCCCE
Q ss_conf             54308678887755443021189999832120
Q gi|254781211|r   35 AVQSDPQGRNPSSSSSSTEEAGEPKPPIEDYT   66 (234)
Q Consensus        35 avqsdpqgrnpssssssteeagepkppiedyt   66 (234)
                      |-|-+++-...+.+...|+-.-.|-|-+..|.
T Consensus       592 ~s~e~k~e~~t~e~~~~~~~~~~~~p~~~~~~  623 (902)
T KOG0104         592 ASQEDKTEKETSEAQKPTEKKETPAPMVVRLQ  623 (902)
T ss_pred             CCCCCCCCCCCHHCCCCCHHHCCCCCCEEEEE
T ss_conf             21013332000100474111035676226765


No 21 
>pfam06640 P_C P protein C-terminus. This family represents the C-terminus of plant P proteins. The maize P gene is a transcriptional regulator of genes encoding enzymes for flavonoid biosynthesis in the pathway leading to the production of a red phlobaphene pigment, and P proteins are homologous to the DNA-binding domain of myb-like transcription factors. All members of this family contain the pfam00249 domain.
Probab=23.41  E-value=58  Score=14.12  Aligned_cols=54  Identities=33%  Similarity=0.411  Sum_probs=25.0

Q ss_pred             CCCCCCEEECCCCCCCCCCCHHHH----------HHC--------CCCCCCCCCCCCCHHHCCCCCCCCCCC
Q ss_conf             899980230000027868875665----------430--------867888775544302118999983212
Q gi|254781211|r   12 PSTPPVVECERSQRSNPPPSKEEA----------VQS--------DPQGRNPSSSSSSTEEAGEPKPPIEDY   65 (234)
Q Consensus        12 pstppvvecersqrsnpppskeea----------vqs--------dpqgrnpssssssteeagepkppiedy   65 (234)
                      |..+|--...|+.+..+++-+.++          .+|        ||.-..|.|||.||-.+-+-.+--||-
T Consensus        39 pg~spkss~s~sKq~d~d~p~~ea~~~~~~assprhsD~aRSaVVdp~pnQPNsSSGstg~~~~~~~s~EdA  110 (227)
T pfam06640        39 PGRSPKSSASRTKQADADQPGGEAAGDAAAASSPRHSDGARSAVVDPGPNQPNSSSGSTGTAEEGPCSSEDA  110 (227)
T ss_pred             CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEECCCCCCCCCCCCCCCCCCCCCCCCCCC
T ss_conf             998986533334678889987544577776788665676521242799999887778777778998766668


No 22 
>TIGR00956 3a01205 Pleiotropic Drug Resistance (PDR) Family protein; InterPro: IPR005285   ABC transporters belong to the ATP-Binding Cassette (ABC) superfamily, which uses the hydrolysis of ATP to energize diverse biological systems. ABC transporters are minimally constituted of two conserved regions: a highly conserved ATP binding cassette (ABC) and a less conserved transmembrane domain (TMD). These regions can be found on the same protein or on two different ones. Most ABC transporters function as a dimer and therefore are constituted of four domains, two ABC modules and two TMDs.   ABC transporters are involved in the export or import of a wide variety of substrates ranging from small ions to macromolecules. The major function of ABC import systems is to provide essential nutrients to bacteria. They are found only in prokaryotes and their four constitutive domains are usually encoded by independent polypeptides (two ABC proteins and two TMD proteins). Prokaryotic importers require additional extracytoplasmic binding proteins (one or more per systems) for function. In contrast, export systems are involved in the extrusion of noxious substances, the export of extracellular toxins and the targeting of membrane components. They are found in all living organisms and in general the TMD is fused to the ABC module in a variety of combinations. Some eukaryotic exporters encode the four domains on the same polypeptide chain .    The ABC module (approximately two hundred amino acid residues) is known to bind and hydrolyze ATP, thereby coupling transport to ATP hydrolysis in a large number of biological processes. The cassette is duplicated in several subfamilies. Its primary sequence is highly conserved, displaying a typical phosphate-binding loop: Walker A, and a magnesium binding site: Walker B. Besides these two regions, three other conserved motifs are present in the ABC cassette: the switch region which contains a histidine loop, postulated to polarize the attaching water molecule for hydrolysis, the signature conserved motif (LSGGQ) specific to the ABC transporter, and the Q-motif (between Walker A and the signature), which interacts with the gamma phosphate through a water bond. The Walker A, Walker B, Q-loop and switch region form the nucleotide binding site , , .   The 3D structure of a monomeric ABC module adopts a stubby L-shape with two distinct arms. ArmI (mainly beta-strand) contains Walker A and Walker B. The important residues for ATP hydrolysis and/or binding are located in the P-loop. The ATP-binding pocket is located at the extremity of armI. The perpendicular armII contains mostly the alpha helical subdomain with the signature motif. It only seems to be required for structural integrity of the ABC module. ArmII is in direct contact with the TMD. The hinge between armI and armII contains both the histidine loop and the Q-loop, making contact with the gamma phosphate of the ATP molecule. ATP hydrolysis leads to a conformational change that could facilitate ADP release. In the dimer the two ABC cassettes contact each other through hydrophobic interactions at the antiparallel beta-sheet of armI by a two-fold axis , , , , , .   Proteins known to belong to this family are classified in several functional subfamilies depending on the substrate used (for further information see http://www.tcdb.org/tcdb/index.php?tc=3.A.1).    This family includes transporters, whose physiological function is not yet established. These proteins are thought to confer resistance to the chemicals cycloheximide and sulphomethuron methyl, BFA, azole antifungal agents, other antifungal agents: amorolfine and terbinafine. Some of them could serve as an efflux pump of various antibiotics..
Probab=23.30  E-value=40  Score=15.16  Aligned_cols=63  Identities=43%  Similarity=0.592  Sum_probs=40.1

Q ss_pred             CCHHHHHHH---HHHHHHHHHHHHHH---HHHCCCHHHH--HHHHHHHHC-----CCHHHHHHHHHHHHH-HH---CCCH
Q ss_conf             281578999---99999998368877---8831136999--999986507-----730234779999975-30---3881
Q gi|254781211|r   88 AGVDARVAQ---KVVDKLVDHGRKIG---EQFGASLEEE--RKLLQTKLG-----SDYETREKDIARYFR-KE---KIPD  150 (234)
Q Consensus        88 agvdarvaq---kvvdklvdhgrkig---eqfgasleee--rkllqtklg-----sdyetrekdiaryfr-ke---kipd  150 (234)
                      -|.|++-|-   |.+-||+|||+-|=   .|=-|-|=||  |-||--|=|     .|.-..-+.|-.||. +.   |+|+
T Consensus       996 SGLDSQtAWsi~~l~RKLad~GQaILCTIHQPSA~L~~eFDrLLlLqkGG~TvYFGdlG~n~~T~inYFEa~hGA~kCp~ 1075 (1466)
T TIGR00956       996 SGLDSQTAWSICKLLRKLADHGQAILCTIHQPSAILFEEFDRLLLLQKGGQTVYFGDLGENSKTLINYFEAKHGAPKCPE 1075 (1466)
T ss_pred             CCHHHHHHHHHHHHHHHHHHCCCEEEECCCCHHHHHHHHHHHHHHHHCCCEEEEECCCCHHHHHHHHHHHHHCCCCCCCC
T ss_conf             70558999999999998875598388604302489999862897754288068727513135899988866537889858


No 23 
>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=23.02  E-value=59  Score=14.07  Aligned_cols=96  Identities=22%  Similarity=0.344  Sum_probs=42.9

Q ss_pred             CCHHHHHHHHHHHHHHH--HHHHHHHHHCCCHHHHHHHHH-HHHCCCHHHHHH--HHHHHHHH--HCCCHHHHHHH-HHH
Q ss_conf             28157899999999998--368877883113699999998-650773023477--99999753--03881479999-986
Q gi|254781211|r   88 AGVDARVAQKVVDKLVD--HGRKIGEQFGASLEEERKLLQ-TKLGSDYETREK--DIARYFRK--EKIPDNDVQSL-ISA  159 (234)
Q Consensus        88 agvdarvaqkvvdklvd--hgrkigeqfgasleeerkllq-tklgsdyetrek--diaryfrk--ekipdndvqsl-isa  159 (234)
                      .|+..|.+++.+....-  ++...-.-+..--+-+.-+.+ .-+.  -|++++  +.-.+.|+  ..|-.++||.- +.+
T Consensus        35 ~GiS~Rfi~~~ls~a~~~~~~~~~inp~~vl~~Le~~i~~~~~i~--~e~~~~Y~~~i~~vr~eY~e~i~~Evq~A~~~s  112 (254)
T pfam06798        35 DGISPRFIGKALSNALVSDSEERCINPLDVLEELEQGIKDHESIP--EEDRDKYLEFLKVVRKEYNERIKKEVQKAYIES  112 (254)
T ss_pred             CCCCHHHHHHHHHHHHHCCCCCCCCCHHHHHHHHHHHHHCCCCCC--HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHC
T ss_conf             786789999999999843888885789999999999986024378--789999999999999999999999999998644


Q ss_pred             HHHHHHHHHHHHHHHH---------CCCCCCCCHHH
Q ss_conf             3225677799998751---------12112331022
Q gi|254781211|r  160 WGFEKTFNFFDRYAQQ---------NKESSTGDTFV  186 (234)
Q Consensus       160 wgfektfnffdryaqq---------nkesstgdtfv  186 (234)
                      .. +---+.|+||-..         -+...||.-+-
T Consensus       113 ~e-e~~q~lf~~Yid~~~a~~~~~k~kDp~TGe~~~  147 (254)
T pfam06798       113 YE-EAAQNLFDNYLDNVEAYINDEKVKDPLTGEELE  147 (254)
T ss_pred             CH-HHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCC
T ss_conf             39-999999999999999998236215897555216


No 24 
>pfam04624 Dec-1 Dec-1 repeat. The defective chorion-1 gene (dec-1) in Drosophila encodes follicle cell proteins necessary for proper eggshell assembly. Multiple products of the dec-1 gene are formed by alternative RNA splicing and proteolytic processing. Cleavage products include S80 (80 kDa) which is incorporated into the eggshell, and further proteolysis of S80 gives S60 (60 kDa). This repeat is usually found in 12 copies in the central region of the protein. Its function is unknown. Length polymorphisms of Dec-1 have been observed in wild-type strains, and are caused by changes in the numbers of the first five repeats.
Probab=21.81  E-value=28  Score=16.14  Aligned_cols=12  Identities=50%  Similarity=0.961  Sum_probs=9.1

Q ss_pred             HHHHHHHHHHCC
Q ss_conf             999986544205
Q gi|254781211|r  222 LRQWAEKQATLN  233 (234)
Q Consensus       222 lrqwaekqatln  233 (234)
                      -|||.|.||...
T Consensus         8 qRQwsEeQak~q   19 (27)
T pfam04624         8 QRQWSEEQAKIQ   19 (27)
T ss_pred             HHHHHHHHHHHH
T ss_conf             988339999999


No 25 
>TIGR00380 cobD cobalamin biosynthesis protein CobD; InterPro: IPR004485   Cobalamin (vitamin B12) is a structurally complex cofactor, consisting of a modified tetrapyrrole with a centrally chelated cobalt. Cobalamin is usually found in one of two biologically active forms: methylcobalamin and adocobalamin. Most prokaryotes, as well as animals, have cobalamin-dependent enzymes, whereas plants and fungi do not appear to use it. In bacteria and archaea, these include methionine synthase, ribonucleotide reductase, glutamate and methylmalonyl-CoA mutases, ethanolamine ammonia lyase, and diol dehydratase . In mammals, cobalamin is obtained through the diet, and is required for methionine synthase and methylmalonyl-CoA mutase .    There are at least two distinct cobalamin biosynthetic pathways in bacteria :  Aerobic pathway that requires oxygen and in which cobalt is inserted late in the pathway ; found in Pseudomonas denitrificans and Rhodobacter capsulatus. Anaerobic pathway in which cobalt insertion is the first committed step towards cobalamin synthesis ; found in Salmonella typhimurium, Bacillus megaterium, and Propionibacterium freudenreichii shermanii.     Either pathway can be divided into two parts: (1) corrin ring synthesis (differs in aerobic and anaerobic pathways) and (2) adenosylation of corrin ring, attachment of aminopropanol arm, and assembly of the nucleotide loop (common to both pathways) . There are about 30 enzymes involved in either pathway, where those involved in the aerobic pathway are prefixed Cob and those of the anaerobic pathway Cbi. Several of these enzymes are pathway-specific: CbiD, CbiG, and CbiK are specific to the anaerobic route of S. typhimurium, whereas CobE, CobF, CobG, CobN, CobS, CobT, and CobW are unique to the aerobic pathway of P. denitrificans.   This entry represents the CbiB protein, which is involved in cobalamin biosynthesis and porphyrin biosynthesis. It converts cobyric acid to cobinamide by the addition of aminopropanol on the F carboxylic group. It is part of the cob operon .; GO: 0009236 cobalamin biosynthetic process, 0016021 integral to membrane.
Probab=20.68  E-value=66  Score=13.77  Aligned_cols=88  Identities=25%  Similarity=0.283  Sum_probs=59.0

Q ss_pred             HHHHHHHHHHHHHHHCC-CHHHHHHHHHHHHCCCHHHHH-HHHHHHHHHHCCCHHHHHHHHHHHHHH---HHHHHHH--H
Q ss_conf             99999836887788311-369999999865077302347-799999753038814799999863225---6777999--9
Q gi|254781211|r   99 VDKLVDHGRKIGEQFGA-SLEEERKLLQTKLGSDYETRE-KDIARYFRKEKIPDNDVQSLISAWGFE---KTFNFFD--R  171 (234)
Q Consensus        99 vdklvdhgrkigeqfga-sleeerkllqtklgsdyetre-kdiaryfrkekipdndvqslisawgfe---ktfnffd--r  171 (234)
                      +.-|+.|.++.+|..-+ .||.-||-+|.-.+-|-+.-. ..|.+ ---|-+-.|-|.|.+++-=+-   --|.|--  -
T Consensus       100 ~~sL~~~A~~~~E~~k~GDle~AR~~l~~~VSRdt~~Ls~e~i~s-A~vESlaEN~vDgv~apLFY~llGilfGl~GPWP  178 (322)
T TIGR00380       100 VKSLVEAAKKVIESLKEGDLEDARKKLQMIVSRDTEELSEEQILS-AAVESLAENIVDGVTAPLFYALLGILFGLPGPWP  178 (322)
T ss_pred             HHHHHHHHHHCCCCCCCCCCHHHHHHHHHHHCCCCCCCCHHHHHH-HHHHHHHHCHHHHHHHHHHHHHHHHHCCCCCCHH
T ss_conf             999999722026665579826789998764224755345356777-8865533011333378999999998647877147


Q ss_pred             HHHHCCCCCCCCHHHH
Q ss_conf             8751121123310221
Q gi|254781211|r  172 YAQQNKESSTGDTFVR  187 (234)
Q Consensus       172 yaqqnkesstgdtfvr  187 (234)
                      .|---|--+|=|..|-
T Consensus       179 lA~~YravnTLDAMvG  194 (322)
T TIGR00380       179 LAFVYRAVNTLDAMVG  194 (322)
T ss_pred             HHHHHHHHHHHHHHHC
T ss_conf             9999999977532102


No 26 
>COG3110 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=20.64  E-value=61  Score=13.98  Aligned_cols=19  Identities=47%  Similarity=0.711  Sum_probs=15.9

Q ss_pred             HCCCHHHHHHHHHHHHHHH
Q ss_conf             1264678899999986544
Q gi|254781211|r  212 LSGDKEATKTLRQWAEKQA  230 (234)
Q Consensus       212 lsgdkeatktlrqwaekqa  230 (234)
                      .-.|||.-+...+||++|-
T Consensus       198 ~qAd~ETr~rFl~Wa~~Q~  216 (216)
T COG3110         198 QQADKETRKRFLQWAKKQP  216 (216)
T ss_pred             HHCCHHHHHHHHHHHHCCC
T ss_conf             8659999999999864198


Done!