Query         gi|254780144|ref|YP_003064557.1| 50S ribosomal protein L12P [Candidatus Liberibacter asiaticus str. psy62]
Match_columns 126
No_of_seqs    114 out of 1829
Neff          5.0 
Searched_HMMs 39220
Date          Sun May 22 11:45:11 2011
Command       /home/congqian_1/programs/hhpred/hhsearch -i 254780144.hhm -d /home/congqian_1/database/cdd/Cdd.hhm 

 No Hit                             Prob E-value P-value  Score    SS Cols Query HMM  Template HMM
  1 TIGR00855 L12 ribosomal protei 100.0       0       0  302.9   9.1  124    1-126     1-131 (131)
  2 CHL00083 rpl12 ribosomal prote 100.0 1.3E-40 2.8E-45  265.5  12.7  125    1-126     1-129 (129)
  3 PRK00157 rplL 50S ribosomal pr 100.0 2.2E-39 5.5E-44  258.3  12.6  122    2-126     3-124 (124)
  4 cd00387 Ribosomal_L7_L12 Ribos 100.0   1E-38 2.6E-43  254.2  13.5  123    2-125     1-127 (127)
  5 COG0222 RplL Ribosomal protein 100.0 1.1E-38 2.8E-43  254.0  12.7  123    1-126     2-124 (124)
  6 KOG1715 consensus              100.0 3.7E-36 9.5E-41  238.8  13.0  123    2-125    58-186 (187)
  7 pfam00542 Ribosomal_L12 Riboso  99.9 2.5E-23 6.4E-28  161.4   8.3   68   57-126     1-68  (68)
  8 PRK06771 hypothetical protein;  88.4    0.31 7.9E-06   28.3   2.2   31   65-96     63-93  (93)
  9 pfam11363 DUF3164 Protein of u  77.6     4.5 0.00011   21.3   4.4   81    5-107    37-119 (195)
 10 CHL00098 tsf elongation factor  67.6     5.7 0.00014   20.6   3.0   17   75-91      5-21  (207)
 11 TIGR00274 TIGR00274 glucokinas  63.8     7.8  0.0002   19.8   3.1   53   71-123   230-286 (291)
 12 PRK12332 tsf elongation factor  60.5     9.5 0.00024   19.3   3.1   24   72-95      5-28  (216)
 13 COG0264 Tsf Translation elonga  58.9      11 0.00028   19.0   3.1   26   71-96      5-30  (296)
 14 PRK09377 tsf elongation factor  58.6      11 0.00027   19.0   3.0   20   73-92      7-26  (288)
 15 LOAD_efts_N consensus           45.1      23 0.00058   17.0   2.9   27   71-97      4-30  (41)
 16 cd04780 HTH_MerR-like_sg5 Heli  40.2      31  0.0008   16.2   3.0   32   70-101    45-81  (95)
 17 cd04774 HTH_YfmP Helix-Turn-He  39.3      29 0.00074   16.4   2.7   26   70-95     44-69  (96)
 18 TIGR00116 tsf translation elon  36.1      26 0.00067   16.6   2.1   29   70-98      4-32  (364)
 19 smart00422 HTH_MERR helix_turn  34.9      39 0.00098   15.6   2.8   25   70-95     45-69  (70)
 20 PRK08172 acyl carrier protein;  34.2      36 0.00092   15.8   2.6   27    7-34     23-49  (75)
 21 COG3797 Uncharacterized protei  30.7      26 0.00066   16.7   1.4   12   22-33     60-71  (178)
 22 PRK12449 acyl carrier protein;  28.7      49  0.0013   15.0   2.6   22   13-34     36-57  (80)
 23 KOG2003 consensus               28.6      49  0.0013   15.0   3.4   28   71-98    693-721 (840)
 24 TIGR01007 eps_fam capsular exo  28.0      50  0.0013   15.0   2.4   58   54-123   127-185 (207)
 25 PRK10753 transcriptional regul  27.3      25 0.00065   16.7   0.8   17   13-29     15-31  (90)
 26 cd00591 HU_IHF Integration hos  27.2      25 0.00063   16.8   0.8   33   72-104     3-35  (87)
 27 pfam02022 Integrase_Zn Integra  26.2      54  0.0014   14.7   2.4   26   75-100    12-37  (40)
 28 pfam04461 DUF520 Protein of un  25.6      56  0.0014   14.7   2.5   64   59-124    45-120 (160)
 29 PRK00285 ihfA integration host  25.1      28 0.00072   16.4   0.7   18   13-30     18-35  (100)
 30 cd04764 HTH_MlrA-like_sg1 Heli  24.6      58  0.0015   14.5   2.6   23   70-93     44-66  (67)
 31 CHL00124 acpP acyl carrier pro  24.4      59  0.0015   14.5   2.6   22   13-34     36-57  (84)
 32 cd04782 HTH_BltR Helix-Turn-He  23.7      61  0.0016   14.4   4.4   27   70-97     45-71  (97)
 33 PRK06720 hypothetical protein;  23.2      61  0.0016   14.4   2.2   14   18-31     79-92  (169)
 34 cd02130 PA_ScAPY_like PA_ScAPY  23.2      62  0.0016   14.4   2.4   23  102-125    98-120 (122)
 35 pfam00216 Bac_DNA_binding Bact  23.1      34 0.00086   16.0   0.8   16   13-28     15-30  (90)
 36 PRK10664 transcriptional regul  22.5      36 0.00092   15.8   0.9   18   13-30     15-32  (90)
 37 PRK05412 nucleotide-binding pr  22.4      65  0.0017   14.3   2.8   65   58-124    44-120 (161)
 38 PTZ00171 acyl carrier protein;  22.1      65  0.0017   14.3   2.8   21   13-33    103-123 (150)
 39 pfam00828 Ribosomal_L18e Ribos  21.7      67  0.0017   14.2   2.6   16  110-125   106-121 (122)

No 1  
>TIGR00855 L12 ribosomal protein L7/L12; InterPro: IPR000206   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 , .   This family of large subunit ribosomal proteins is called the L7/L12 family. L7/L12 is present in each 50S subunit in four copies organised as two dimers. The L8 protein complex consisting of two dimers of L7/L12 and L10 in Escherichia coli ribosomes is assembled on the conserved region of 23 S rRNA termed the GTPase-associated domain . The L7/L12 dimer probably interacts with EF-Tu. L7 and L12 only differ in a single post translational modification of the addition an acetyl group to the N terminus of L7.; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome.
Probab=100.00  E-value=0  Score=302.86  Aligned_cols=124  Identities=62%  Similarity=0.850  Sum_probs=116.2

Q ss_pred             CCCH--HHHHHHHHHCCHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCC--CCCCCCCCCCEEEEE-ECCCCCC-CHHH
Q ss_conf             9718--99999996099999999999999993787100012235544443--222222243115777-4377554-3357
Q gi|254780144|r    1 MSNI--ESIVEKLSSLTLIEAAELSKRLEKEWGVSASAPVSVVAPVAAEA--GSAASEKTEFEVVLK-GFDDPKK-KIAV   74 (126)
Q Consensus         1 maki--~~ive~i~~LTllE~~eLv~~leekfgv~~~~~~~~~~~~~~~~--~~~~~EKt~fdV~L~-~~~~~~~-Ki~v   74 (126)
                      ||++  ++|+++|++||++|++|||+.||++||||+++|+++++.+++++  .++.+|||+|||||+ +++  ++ ||.|
T Consensus         1 Ma~l~~~~i~E~l~~~tvlE~~eLvK~~EE~FGVsAAa~Vaa~a~~aaAa~a~~aaEE~TEF~ViL~~~~a--d~aKi~V   78 (131)
T TIGR00855         1 MAKLSKEQIIEALKSLTVLELSELVKALEEKFGVSAAAPVAAAAAAAAAAAAAAAAEEKTEFDVILKDAGA--DKAKIAV   78 (131)
T ss_pred             CCCCCHHHHHHHHHCCCHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCHHHHHHCCCEEEEECCCCC--CCCCEEE
T ss_conf             97665889999986680333889999875412884243001314433356765433205650588745678--8411321


Q ss_pred             HHHHHH-HCCCCHHHHHHHHHHCCHHHHHCCCHHHHHHHHHHHHHCCCEEEEC
Q ss_conf             877677-6599889999998637977660999899999999999748579939
Q gi|254780144|r   75 IKEVRA-ITDLGLKEAKELVESAPKSLKTGLSKDEANEMKKKLEDAGATVELR  126 (126)
Q Consensus        75 IK~vR~-it~LgLkEAK~lVe~~P~~ike~v~keeAE~ik~~Le~aGa~VeiK  126 (126)
                      ||.||+ ||||||||||+|||++|++||||++|+|||+||++|+++||+|++|
T Consensus        79 iKvVR~~ITGLGLkEAK~LVe~aPk~~KE~v~KeeAE~~KkkLeeaGA~VevK  131 (131)
T TIGR00855        79 IKVVREVITGLGLKEAKDLVEKAPKALKEGVSKEEAEEIKKKLEEAGAKVEVK  131 (131)
T ss_pred             EEEECHHHCCCHHHHHHHHHHHCCCHHHCCCCHHHHHHHHHHHHHCCCEEEEC
T ss_conf             23320002142368899998606801223889768999999997477416629


No 2  
>CHL00083 rpl12 ribosomal protein L12
Probab=100.00  E-value=1.3e-40  Score=265.53  Aligned_cols=125  Identities=58%  Similarity=0.822  Sum_probs=111.2

Q ss_pred             CCCHHHHHHHHHHCCHHHHHHHHHHHHHHHCCCCCCCCC----CCCCCCCCCCCCCCCCCCCEEEEEECCCCCCCHHHHH
Q ss_conf             971899999996099999999999999993787100012----2355444432222222431157774377554335787
Q gi|254780144|r    1 MSNIESIVEKLSSLTLIEAAELSKRLEKEWGVSASAPVS----VVAPVAAEAGSAASEKTEFEVVLKGFDDPKKKIAVIK   76 (126)
Q Consensus         1 maki~~ive~i~~LTllE~~eLv~~leekfgv~~~~~~~----~~~~~~~~~~~~~~EKt~fdV~L~~~~~~~~Ki~vIK   76 (126)
                      ..|+++|+++|++||++|+++|++.|+++|||+++++++    ++++++++++++.+|||+|||+|++|+ +++||+|||
T Consensus         1 S~kv~~ive~i~~LtllE~~eLv~~lee~fgv~~~~~~~~~~~~~~~~~~~~~~~~~ekteF~V~L~~~~-~~kKi~VIK   79 (129)
T CHL00083          1 STKINEIIEKLKSLTLLEAAELVKQIEETFGVDASAPVGGGMMMAAAAAGEAAEAVEEKTEFDVILEEVP-ADKRIAVLK   79 (129)
T ss_pred             CHHHHHHHHHHHHCCHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEEEEEECC-CCCCCEEEE
T ss_conf             9059999999974889999999999999969984432221124677777665442111664689984368-877413552


Q ss_pred             HHHHHCCCCHHHHHHHHHHCCHHHHHCCCHHHHHHHHHHHHHCCCEEEEC
Q ss_conf             76776599889999998637977660999899999999999748579939
Q gi|254780144|r   77 EVRAITDLGLKEAKELVESAPKSLKTGLSKDEANEMKKKLEDAGATVELR  126 (126)
Q Consensus        77 ~vR~it~LgLkEAK~lVe~~P~~ike~v~keeAE~ik~~Le~aGa~VeiK  126 (126)
                      +||++|||||||||+|||++|++||+|+||+|||++|++||++||+|+||
T Consensus        80 ~VR~it~LgLkEAK~lVe~~P~~iKe~vsKeeAe~iK~kLe~aGA~VelK  129 (129)
T CHL00083         80 VVRSLTGLGLKEAKELVESLPKTIKEGVSKEEAEEAKKQLEEAGAKVILK  129 (129)
T ss_pred             HHHHHCCCCHHHHHHHHHCCCHHHHCCCCHHHHHHHHHHHHHCCCEEEEC
T ss_conf             33844699879999998718898862889999999999999859989739


No 3  
>PRK00157 rplL 50S ribosomal protein L7/L12; Reviewed
Probab=100.00  E-value=2.2e-39  Score=258.26  Aligned_cols=122  Identities=61%  Similarity=0.830  Sum_probs=110.6

Q ss_pred             CCHHHHHHHHHHCCHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEEEECCCCCCCHHHHHHHHHH
Q ss_conf             71899999996099999999999999993787100012235544443222222243115777437755433578776776
Q gi|254780144|r    2 SNIESIVEKLSSLTLIEAAELSKRLEKEWGVSASAPVSVVAPVAAEAGSAASEKTEFEVVLKGFDDPKKKIAVIKEVRAI   81 (126)
Q Consensus         2 aki~~ive~i~~LTllE~~eLv~~leekfgv~~~~~~~~~~~~~~~~~~~~~EKt~fdV~L~~~~~~~~Ki~vIK~vR~i   81 (126)
                      .+.++|+|+|++|||+|++||++.|+++|||+++++++++ +++++++++.+|||+|||+|++|+  ++||+|||+||++
T Consensus         3 ~~~~~ive~l~~LTllE~~eLv~~lee~fgv~~~~~~~~~-~~~~~~~~~~eEkteF~V~L~~~~--~~Ki~vIK~VR~i   79 (124)
T PRK00157          3 LTKEQIIEALKEMTVLELSELVKALEEKFGVSAAAPVAAA-AAAAAAAAAAEEKTEFDVVLKSAG--DKKIAVIKAVREI   79 (124)
T ss_pred             CCHHHHHHHHHHCCHHHHHHHHHHHHHHHCCCCCCCCCCC-CCCCCCCCCCCCCCEEEEEEECCC--CCCCEEEEHHHHH
T ss_conf             7699999999718799999999999999699944223567-777766543332666689970388--8765444113855


Q ss_pred             CCCCHHHHHHHHHHCCHHHHHCCCHHHHHHHHHHHHHCCCEEEEC
Q ss_conf             599889999998637977660999899999999999748579939
Q gi|254780144|r   82 TDLGLKEAKELVESAPKSLKTGLSKDEANEMKKKLEDAGATVELR  126 (126)
Q Consensus        82 t~LgLkEAK~lVe~~P~~ike~v~keeAE~ik~~Le~aGa~VeiK  126 (126)
                      |||||+|||+|||++|++||+|++|+|||++|++|+++||+|+||
T Consensus        80 t~LgLkEAK~lVe~~P~~iKe~vsKeeAE~iK~kLe~aGA~VelK  124 (124)
T PRK00157         80 TGLGLKEAKDLVEGAPKAVKEGVSKEEAEEIKKKLEEAGAKVELK  124 (124)
T ss_pred             CCCCHHHHHHHHHCCCHHHHCCCCHHHHHHHHHHHHHCCCEEEEC
T ss_conf             389889999998708888870889999999999999869979729


No 4  
>cd00387 Ribosomal_L7_L12 Ribosomal protein L7/L12. Ribosomal protein L7/L12 refers to the large ribosomal subunit proteins L7 and L12, which are identical except that L7 is acetylated at the N terminus. It is a component of the L7/L12 stalk, which is located at the surface of the ribosome. The stalk base consists of a portion of the 23S rRNA and ribosomal proteins L11 and L10. An extended C-terminal helix of L10 provides the binding site for L7/L12. L7/L12 consists of two domains joined by a flexible hinge, with the helical N-terminal domain (NTD) forming pairs of homodimers that bind to the extended helix of L10. It is the only multimeric ribosomal component, with either four or six copies per ribosome that occur as two or three dimers bound to the L10 helix. L7/L12 is the only ribosomal protein that does not interact directly with rRNA, but instead has indirect interactions through L10. The globular C-terminal domains of L7/L12 are highly mobile. They are exposed to the cytoplasm and
Probab=100.00  E-value=1e-38  Score=254.16  Aligned_cols=123  Identities=66%  Similarity=0.861  Sum_probs=107.3

Q ss_pred             CCHHHHHHHHHHCCHHHHHHHHHHHHHHHCCCCCCCCCCCCCC----CCCCCCCCCCCCCCEEEEEECCCCCCCHHHHHH
Q ss_conf             7189999999609999999999999999378710001223554----444322222224311577743775543357877
Q gi|254780144|r    2 SNIESIVEKLSSLTLIEAAELSKRLEKEWGVSASAPVSVVAPV----AAEAGSAASEKTEFEVVLKGFDDPKKKIAVIKE   77 (126)
Q Consensus         2 aki~~ive~i~~LTllE~~eLv~~leekfgv~~~~~~~~~~~~----~~~~~~~~~EKt~fdV~L~~~~~~~~Ki~vIK~   77 (126)
                      .++++|+|+|++|||+|+++|++.|+++|||++.+++++++++    ++......+|||+|||+|++|+ +++||+|||+
T Consensus         1 ~k~~~ive~i~~LtllE~~eLv~~le~~~gv~~~~~~~~~~~~a~~~~~~~~~~~~Ekt~FdV~L~~~~-~~~KI~vIK~   79 (127)
T cd00387           1 LKVEEIVEALKELTLLEAAELVKALEEKFGVSASAAAAAAAAAAPAAAAAAAAEAEEKTEFDVVLESFG-AAKKIAVIKE   79 (127)
T ss_pred             CCHHHHHHHHHHCCHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEEEEEECC-CCCCCHHHHH
T ss_conf             979999999972889999999999999969996532222345567776655432223765689972068-7664013457


Q ss_pred             HHHHCCCCHHHHHHHHHHCCHHHHHCCCHHHHHHHHHHHHHCCCEEEE
Q ss_conf             677659988999999863797766099989999999999974857993
Q gi|254780144|r   78 VRAITDLGLKEAKELVESAPKSLKTGLSKDEANEMKKKLEDAGATVEL  125 (126)
Q Consensus        78 vR~it~LgLkEAK~lVe~~P~~ike~v~keeAE~ik~~Le~aGa~Vei  125 (126)
                      ||++|||||||||+|||++|++||+|++|+|||++|++|+++||+|+|
T Consensus        80 VR~it~LgLkEAK~lVe~~P~~ike~vsKeeAE~iK~kLe~aGa~Vel  127 (127)
T cd00387          80 VREITGLGLKEAKDLVESAPKVLKEGVSKEEAEEIKKKLEEAGAKVEL  127 (127)
T ss_pred             HHHHCCCCHHHHHHHHHCCCHHHHCCCCHHHHHHHHHHHHHCCCEEEC
T ss_conf             797738987999999870888887189999999999999983898869


No 5  
>COG0222 RplL Ribosomal protein L7/L12 [Translation, ribosomal structure and biogenesis]
Probab=100.00  E-value=1.1e-38  Score=253.97  Aligned_cols=123  Identities=60%  Similarity=0.799  Sum_probs=113.8

Q ss_pred             CCCHHHHHHHHHHCCHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEEEECCCCCCCHHHHHHHHH
Q ss_conf             97189999999609999999999999999378710001223554444322222224311577743775543357877677
Q gi|254780144|r    1 MSNIESIVEKLSSLTLIEAAELSKRLEKEWGVSASAPVSVVAPVAAEAGSAASEKTEFEVVLKGFDDPKKKIAVIKEVRA   80 (126)
Q Consensus         1 maki~~ive~i~~LTllE~~eLv~~leekfgv~~~~~~~~~~~~~~~~~~~~~EKt~fdV~L~~~~~~~~Ki~vIK~vR~   80 (126)
                      |...++|+++|++||++|+++|++.++++|||++++|+++++++ +.++++.+|||+|||+|.+++  ++||.|||+||+
T Consensus         2 ~~~~e~iie~i~~~svlel~eLvk~~eekfgVsaaa~va~a~~~-a~a~~aaeEktefdVvL~~~g--~kKI~VIK~vR~   78 (124)
T COG0222           2 ALTKEQIIEALKELTVLELSELVKALEEKFGVTAAAPVAAAAAG-AAAAEAAEEKTEFDVVLKSAG--GKKIAVIKVVRE   78 (124)
T ss_pred             CCCHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHCCCC-CCCCCCCCCCCEEEEEECCCC--CCHHHHHHHHHH
T ss_conf             67699999999983699999999988998287520034412344-445433344651677731268--760378999999


Q ss_pred             HCCCCHHHHHHHHHHCCHHHHHCCCHHHHHHHHHHHHHCCCEEEEC
Q ss_conf             6599889999998637977660999899999999999748579939
Q gi|254780144|r   81 ITDLGLKEAKELVESAPKSLKTGLSKDEANEMKKKLEDAGATVELR  126 (126)
Q Consensus        81 it~LgLkEAK~lVe~~P~~ike~v~keeAE~ik~~Le~aGa~VeiK  126 (126)
                      +|||||||||++||++|++||||++|+|||++|++||++||+|++|
T Consensus        79 itGLGLKEAKdlVe~aP~~~KE~v~k~eAe~~kkkleeaGa~Ve~k  124 (124)
T COG0222          79 LTGLGLKEAKDLVEGAPKVLKEGVSKEEAEEIKKKLEEAGAKVELK  124 (124)
T ss_pred             HHCCCHHHHHHHHHHCCHHHHCCCCHHHHHHHHHHHHHCCCEEEEC
T ss_conf             7264479999999817088870479989999999999758957629


No 6  
>KOG1715 consensus
Probab=100.00  E-value=3.7e-36  Score=238.75  Aligned_cols=123  Identities=50%  Similarity=0.677  Sum_probs=105.9

Q ss_pred             CCHHHHHHHHHHCCHHHHHHHHHHHHHHHCCCCCCCCCCCCCC------CCCCCCCCCCCCCCEEEEEECCCCCCCHHHH
Q ss_conf             7189999999609999999999999999378710001223554------4443222222243115777437755433578
Q gi|254780144|r    2 SNIESIVEKLSSLTLIEAAELSKRLEKEWGVSASAPVSVVAPV------AAEAGSAASEKTEFEVVLKGFDDPKKKIAVI   75 (126)
Q Consensus         2 aki~~ive~i~~LTllE~~eLv~~leekfgv~~~~~~~~~~~~------~~~~~~~~~EKt~fdV~L~~~~~~~~Ki~vI   75 (126)
                      .||.+|++.|++|||+|+++|+++|+++||++..+.+++++++      ++..++...|+|.|||+|++|++ .+||+||
T Consensus        58 ~KI~~iv~eIssLtLlE~s~L~~~Lk~kl~i~e~~~~~a~~~g~~~~~~~~a~ee~k~ekt~FdVkL~~fda-~~KIkVI  136 (187)
T KOG1715          58 PKISKIVDEISSLTLLETSDLVDLLKKKLNIPELPLAPAAAAGAAAPDAGGAEEEAKKEKTTFDVKLEKFDA-SSKIKVI  136 (187)
T ss_pred             HHHHHHHHHHHHCCHHHHHHHHHHHHHHCCCCCCCCHHHCCCCCCCCCCCCCCCCCCCCCCEEEEEEEECCC-CCHHHHH
T ss_conf             779999999985579999999999998739973322021146688877665432220012257888753376-2213689


Q ss_pred             HHHHHHCCCCHHHHHHHHHHCCHHHHHCCCHHHHHHHHHHHHHCCCEEEE
Q ss_conf             77677659988999999863797766099989999999999974857993
Q gi|254780144|r   76 KEVRAITDLGLKEAKELVESAPKSLKTGLSKDEANEMKKKLEDAGATVEL  125 (126)
Q Consensus        76 K~vR~it~LgLkEAK~lVe~~P~~ike~v~keeAE~ik~~Le~aGa~Vei  125 (126)
                      |+||.+|||||+|||+|||++|+.+|+|++|||||+||.+|+++||+|.|
T Consensus       137 KEVR~~tgL~LkeAKklVE~aP~ilKegvtKeEAEkik~kLea~GakV~l  186 (187)
T KOG1715         137 KEVRALTGLGLKEAKKLVEKAPKILKEGVTKEEAEEIKEKLEAAGAKVVL  186 (187)
T ss_pred             HHHHHHCCCCHHHHHHHHHHCCHHHHCCCCHHHHHHHHHHHHHCCCEEEE
T ss_conf             99987624457999999996509987678788999999999974786850


No 7  
>pfam00542 Ribosomal_L12 Ribosomal protein L7/L12 C-terminal domain.
Probab=99.89  E-value=2.5e-23  Score=161.41  Aligned_cols=68  Identities=69%  Similarity=0.945  Sum_probs=65.8

Q ss_pred             CCEEEEEECCCCCCCHHHHHHHHHHCCCCHHHHHHHHHHCCHHHHHCCCHHHHHHHHHHHHHCCCEEEEC
Q ss_conf             3115777437755433578776776599889999998637977660999899999999999748579939
Q gi|254780144|r   57 EFEVVLKGFDDPKKKIAVIKEVRAITDLGLKEAKELVESAPKSLKTGLSKDEANEMKKKLEDAGATVELR  126 (126)
Q Consensus        57 ~fdV~L~~~~~~~~Ki~vIK~vR~it~LgLkEAK~lVe~~P~~ike~v~keeAE~ik~~Le~aGa~VeiK  126 (126)
                      +|||+|++|+  ++||++||+||++|||||+|||+|||++|++|++|++|+|||++|++|+++||+|+||
T Consensus         1 eFdV~L~~~~--~~Ki~vIK~VR~itglgLkeAK~lVe~~P~~ike~v~keeAe~~k~~Le~aGA~Velk   68 (68)
T pfam00542         1 EFDVVLTSAG--DKKIAVIKVVREITGLGLKEAKDLVEGAPKVIKEGVSKEEAEEIKKKLEEAGAKVELK   68 (68)
T ss_pred             CEEEEECCCC--CCHHHHHHHHHHHCCCCHHHHHHHHHCCCHHHHCCCCHHHHHHHHHHHHHCCCEEEEC
T ss_conf             9069965577--3244999999997699889999998728899983999999999999999859979639


No 8  
>PRK06771 hypothetical protein; Provisional
Probab=88.44  E-value=0.31  Score=28.28  Aligned_cols=31  Identities=29%  Similarity=0.486  Sum_probs=26.9

Q ss_pred             CCCCCCCHHHHHHHHHHCCCCHHHHHHHHHHC
Q ss_conf             37755433578776776599889999998637
Q gi|254780144|r   65 FDDPKKKIAVIKEVRAITDLGLKEAKELVESA   96 (126)
Q Consensus        65 ~~~~~~Ki~vIK~vR~it~LgLkEAK~lVe~~   96 (126)
                      +.+ .+.|..+|.+|+-.|++|-|||..||++
T Consensus        63 v~~-gk~i~AvK~~Re~fG~SLlEaK~YVD~l   93 (93)
T PRK06771         63 MEE-GKTVTAVKRVREAFGFSLLEAKQYVDKL   93 (93)
T ss_pred             HHC-CCEEHHHHHHHHHHCHHHHHHHHHHCCC
T ss_conf             985-7701599999998576799898772049


No 9  
>pfam11363 DUF3164 Protein of unknown function (DUF3164). This family of proteins has no known function.
Probab=77.60  E-value=4.5  Score=21.26  Aligned_cols=81  Identities=20%  Similarity=0.313  Sum_probs=58.6

Q ss_pred             HHHHHHHHHCCHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEEEECCCCCCCHHHHHHHHH-HC-
Q ss_conf             9999999609999999999999999378710001223554444322222224311577743775543357877677-65-
Q gi|254780144|r    5 ESIVEKLSSLTLIEAAELSKRLEKEWGVSASAPVSVVAPVAAEAGSAASEKTEFEVVLKGFDDPKKKIAVIKEVRA-IT-   82 (126)
Q Consensus         5 ~~ive~i~~LTllE~~eLv~~leekfgv~~~~~~~~~~~~~~~~~~~~~EKt~fdV~L~~~~~~~~Ki~vIK~vR~-it-   82 (126)
                      ..-+...+.-+.-++..++....++||+.-..                   +.=+|.|.+| |+..||.+  .+.+ ++ 
T Consensus        37 s~~l~~FK~~~f~di~~fv~l~ae~Yg~k~GG-------------------~KGNvTl~sf-DG~~kv~~--~v~d~i~F   94 (195)
T pfam11363        37 SKQLAEFKAHAFDDIGAFVDLSAEEYGVKVGG-------------------KKGNVTLVSF-DGRYKVQR--AVQERIAF   94 (195)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCC-------------------CCCCEEEEEE-CCCEEEEE--EEEECCCC
T ss_conf             99999999999999999999999995987578-------------------8787788961-68448999--99530255


Q ss_pred             CCCHHHHHHHHHHCCHHHHHCCCHH
Q ss_conf             9988999999863797766099989
Q gi|254780144|r   83 DLGLKEAKELVESAPKSLKTGLSKD  107 (126)
Q Consensus        83 ~LgLkEAK~lVe~~P~~ike~v~ke  107 (126)
                      |=.|.-||.|+|.|=..-.+|-+.+
T Consensus        95 de~lqaAK~LIdeCi~~Ws~ga~~e  119 (195)
T pfam11363        95 DERLQAAKALIDECLTEWSEGARAE  119 (195)
T ss_pred             CHHHHHHHHHHHHHHHHHHCCCCHH
T ss_conf             8689999999999999975479688


No 10 
>CHL00098 tsf elongation factor Ts
Probab=67.58  E-value=5.7  Score=20.65  Aligned_cols=17  Identities=35%  Similarity=0.608  Sum_probs=6.1

Q ss_pred             HHHHHHHCCCCHHHHHH
Q ss_conf             87767765998899999
Q gi|254780144|r   75 IKEVRAITDLGLKEAKE   91 (126)
Q Consensus        75 IK~vR~it~LgLkEAK~   91 (126)
                      ||.+|+.||.|+++.|.
T Consensus         5 VKeLR~~TgagmmdCKk   21 (207)
T CHL00098          5 VKELRDKTGAGMMDCKK   21 (207)
T ss_pred             HHHHHHHHCCCHHHHHH
T ss_conf             99999886987999999


No 11 
>TIGR00274 TIGR00274 glucokinase regulator homolog; InterPro: IPR005488 The glucokinase regulatory protein (GCKR)  is a vertebrate protein that inhibits glucokinase by forming an inactive complex with the enzyme. It is a protein of about 70 Kd which seems to be evolutionary related to a number of uncharacterised bacterial proteins which are about half the size of GCKR..
Probab=63.76  E-value=7.8  Score=19.83  Aligned_cols=53  Identities=32%  Similarity=0.384  Sum_probs=42.7

Q ss_pred             CHHHHHHHHHHCCCCHHHHHHHHHHCCHHHHHC----CCHHHHHHHHHHHHHCCCEE
Q ss_conf             335787767765998899999986379776609----99899999999999748579
Q gi|254780144|r   71 KIAVIKEVRAITDLGLKEAKELVESAPKSLKTG----LSKDEANEMKKKLEDAGATV  123 (126)
Q Consensus        71 Ki~vIK~vR~it~LgLkEAK~lVe~~P~~ike~----v~keeAE~ik~~Le~aGa~V  123 (126)
                      |---|..||.+|+++--+|......+-+-+|..    .+-=++++.|++|+.+||.+
T Consensus       230 ~~Rai~Iv~~lT~~~~~~A~~~L~~a~~~vKlAi~M~~~~l~~~~A~~~Ld~h~G~l  286 (291)
T TIGR00274       230 KERAIRIVKDLTDCSKEEAEETLVAADQNVKLAIVMLLSSLDAEEAKALLDRHGGFL  286 (291)
T ss_pred             HHHHHHHHHHHHHCCHHHHHHHHHHHCCCHHHHHHHHHHCCCHHHHHHHHHHHCCCH
T ss_conf             999999999763004899999999715732346766652368889999999858932


No 12 
>PRK12332 tsf elongation factor Ts; Reviewed
Probab=60.55  E-value=9.5  Score=19.29  Aligned_cols=24  Identities=29%  Similarity=0.505  Sum_probs=13.3

Q ss_pred             HHHHHHHHHHCCCCHHHHHHHHHH
Q ss_conf             357877677659988999999863
Q gi|254780144|r   72 IAVIKEVRAITDLGLKEAKELVES   95 (126)
Q Consensus        72 i~vIK~vR~it~LgLkEAK~lVe~   95 (126)
                      ...||.+|+.||.|+++.|...+.
T Consensus         5 a~~VK~LR~~TgagmmdCKkAL~e   28 (216)
T PRK12332          5 AKLVKELREKTGAGMMDCKKALEE   28 (216)
T ss_pred             HHHHHHHHHHHCCCHHHHHHHHHH
T ss_conf             999999998869879999999998


No 13 
>COG0264 Tsf Translation elongation factor Ts [Translation, ribosomal structure and biogenesis]
Probab=58.88  E-value=11  Score=18.97  Aligned_cols=26  Identities=35%  Similarity=0.534  Sum_probs=15.7

Q ss_pred             CHHHHHHHHHHCCCCHHHHHHHHHHC
Q ss_conf             33578776776599889999998637
Q gi|254780144|r   71 KIAVIKEVRAITDLGLKEAKELVESA   96 (126)
Q Consensus        71 Ki~vIK~vR~it~LgLkEAK~lVe~~   96 (126)
                      ....+|++|+.||-|.++.|...+-+
T Consensus         5 ta~~VKeLRe~TgAGMmdCKkAL~E~   30 (296)
T COG0264           5 TAALVKELREKTGAGMMDCKKALEEA   30 (296)
T ss_pred             CHHHHHHHHHHHCCCHHHHHHHHHHC
T ss_conf             59999999988598689999999984


No 14 
>PRK09377 tsf elongation factor Ts; Provisional
Probab=58.63  E-value=11  Score=18.99  Aligned_cols=20  Identities=35%  Similarity=0.567  Sum_probs=7.2

Q ss_pred             HHHHHHHHHCCCCHHHHHHH
Q ss_conf             57877677659988999999
Q gi|254780144|r   73 AVIKEVRAITDLGLKEAKEL   92 (126)
Q Consensus        73 ~vIK~vR~it~LgLkEAK~l   92 (126)
                      +.||.+|..||.|+++.|+.
T Consensus         7 ~~vK~LR~~Tgagm~dCKkA   26 (288)
T PRK09377          7 ALVKELRERTGAGMMDCKKA   26 (288)
T ss_pred             HHHHHHHHHHCCCHHHHHHH
T ss_conf             99999998869869999999


No 15 
>LOAD_efts_N consensus
Probab=45.09  E-value=23  Score=17.02  Aligned_cols=27  Identities=22%  Similarity=0.272  Sum_probs=21.6

Q ss_pred             CHHHHHHHHHHCCCCHHHHHHHHHHCC
Q ss_conf             335787767765998899999986379
Q gi|254780144|r   71 KIAVIKEVRAITDLGLKEAKELVESAP   97 (126)
Q Consensus        71 Ki~vIK~vR~it~LgLkEAK~lVe~~P   97 (126)
                      .-.-||.+|+-||.|..++|...+..-
T Consensus         4 ~a~~vk~lre~tgagmmdckkAL~e~~   30 (41)
T LOAD_efts_N       4 SAEDIKLLREQTGVSMMDAKKALKENN   30 (41)
T ss_pred             CHHHHHHHHHHHCCCHHHHHHHHHHCC
T ss_conf             899999999882971988999998858


No 16 
>cd04780 HTH_MerR-like_sg5 Helix-Turn-Helix DNA binding domain of putative transcription regulators from the MerR superfamily. Putative helix-turn-helix (HTH) MerR-like transcription regulators (subgroup 5), N-terminal domain. Based on sequence similarity, these proteins are predicted to function as transcription regulators that mediate responses to stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic substrates.
Probab=40.16  E-value=31  Score=16.19  Aligned_cols=32  Identities=19%  Similarity=0.462  Sum_probs=25.2

Q ss_pred             CCHHHHHHHHHHCCCCHHHHHHHHHH-----CCHHHH
Q ss_conf             43357877677659988999999863-----797766
Q gi|254780144|r   70 KKIAVIKEVRAITDLGLKEAKELVES-----APKSLK  101 (126)
Q Consensus        70 ~Ki~vIK~vR~it~LgLkEAK~lVe~-----~P~~ik  101 (126)
                      .++..|+..|...|++|.|.+++.+.     .|+++-
T Consensus        45 ~rL~~Ir~l~~~lG~sL~eIr~lL~~~~d~~~p~~l~   81 (95)
T cd04780          45 ERLRLIRALQQEGGLPISQIKEVLDAIADASLPSTLL   81 (95)
T ss_pred             HHHHHHHHHHHHCCCCHHHHHHHHHCCCCCCCCHHHH
T ss_conf             9999999999936999999999984368899951799


No 17 
>cd04774 HTH_YfmP Helix-Turn-Helix DNA binding domain of the YfmP transcription regulator. Helix-turn-helix (HTH) transcription regulator, YfmP, and related proteins; N-terminal domain. YfmP regulates the multidrug efflux protein, YfmO, and indirectly regulates the expression of the Bacillus subtilis copZA operon encoding a metallochaperone, CopZ, and a CPx-type ATPase efflux protein, CopA. These proteins belong to the MerR superfamily of transcription regulators that promote expression of several stress regulon genes by reconfiguring the spacer between the -35 and -10 promoter elements. Their conserved N-terminal domains contain predicted winged HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules.
Probab=39.26  E-value=29  Score=16.38  Aligned_cols=26  Identities=23%  Similarity=0.471  Sum_probs=23.2

Q ss_pred             CCHHHHHHHHHHCCCCHHHHHHHHHH
Q ss_conf             43357877677659988999999863
Q gi|254780144|r   70 KKIAVIKEVRAITDLGLKEAKELVES   95 (126)
Q Consensus        70 ~Ki~vIK~vR~it~LgLkEAK~lVe~   95 (126)
                      .++..|+..|...|++|.|.+++.|.
T Consensus        44 ~rL~~I~~l~~~lGfsL~eIk~lL~~   69 (96)
T cd04774          44 KRLERILRLREVLGFSLQEVTHFLER   69 (96)
T ss_pred             HHHHHHHHHHHHCCCCHHHHHHHHCC
T ss_conf             99999999999579989999999819


No 18 
>TIGR00116 tsf translation elongation factor Ts; InterPro: IPR001816   Translation elongation factors are responsible for two main processes during protein synthesis on the ribosome , , . EF1A (or EF-Tu) is responsible for the selection and binding of the cognate aminoacyl-tRNA to the A-site (acceptor site) of the ribosome. EF2 (or EF-G) is responsible for the translocation of the peptidyl-tRNA from the A-site to the P-site (peptidyl-tRNA site) of the ribosome, thereby freeing the A-site for the next aminoacyl-tRNA to bind. Elongation factors are responsible for achieving accuracy of translation and both EF1A and EF2 are remarkably conserved throughout evolution.   Elongation factor EF1B (also known as EF-Ts or EF-1beta/gamma/delta) is a nucleotide exchange factor that is required to regenerate EF1A from its inactive form (EF1A-GDP) to its active form (EF1A-GTP). EF1A is then ready to interact with a new aminoacyl-tRNA to begin the cycle again. EF1B is more complex in eukaryotes than in bacteria, and can consist of three subunits: EF1B-alpha (or EF-1beta), EF1B-gamma (or EF-1gamma) and EF1B-beta (or EF-1delta) .   This entry represents EF-Tu (EF1A) proteins found primarily in bacteria, mitochondria and chloroplasts.    More information about these proteins can be found at Protein of the Month: Elongation Factors .; GO: 0003746 translation elongation factor activity, 0006414 translational elongation, 0005622 intracellular.
Probab=36.06  E-value=26  Score=16.62  Aligned_cols=29  Identities=24%  Similarity=0.336  Sum_probs=24.0

Q ss_pred             CCHHHHHHHHHHCCCCHHHHHHHHHHCCH
Q ss_conf             43357877677659988999999863797
Q gi|254780144|r   70 KKIAVIKEVRAITDLGLKEAKELVESAPK   98 (126)
Q Consensus        70 ~Ki~vIK~vR~it~LgLkEAK~lVe~~P~   98 (126)
                      -++..||++|+-|+=|.++-|.....+-.
T Consensus         4 i~a~lVKeLR~~T~AGmMDCKKAL~~~~G   32 (364)
T TIGR00116         4 ITAQLVKELRERTGAGMMDCKKALVEANG   32 (364)
T ss_pred             CCHHHHHHHHHHCCCCCCHHHHHHHHCCC
T ss_conf             77999998874058883136787521268


No 19 
>smart00422 HTH_MERR helix_turn_helix, mercury resistance.
Probab=34.92  E-value=39  Score=15.64  Aligned_cols=25  Identities=32%  Similarity=0.555  Sum_probs=19.3

Q ss_pred             CCHHHHHHHHHHCCCCHHHHHHHHHH
Q ss_conf             43357877677659988999999863
Q gi|254780144|r   70 KKIAVIKEVRAITDLGLKEAKELVES   95 (126)
Q Consensus        70 ~Ki~vIK~vR~it~LgLkEAK~lVe~   95 (126)
                      .++..|+..|+ .|++|++.|++.+-
T Consensus        45 ~~l~~I~~lr~-~G~~l~~Ik~~l~l   69 (70)
T smart00422       45 ERLRFIKRLKE-LGFSLEEIKELLEL   69 (70)
T ss_pred             HHHHHHHHHHH-CCCCHHHHHHHHHC
T ss_conf             99999999999-78999999999962


No 20 
>PRK08172 acyl carrier protein; Validated
Probab=34.17  E-value=36  Score=15.81  Aligned_cols=27  Identities=22%  Similarity=0.388  Sum_probs=19.3

Q ss_pred             HHHHHHHCCHHHHHHHHHHHHHHHCCCC
Q ss_conf             9999960999999999999999937871
Q gi|254780144|r    7 IVEKLSSLTLIEAAELSKRLEKEWGVSA   34 (126)
Q Consensus         7 ive~i~~LTllE~~eLv~~leekfgv~~   34 (126)
                      +++.| +-.=+.+.||+-.||++|||.-
T Consensus        23 fv~DL-gADSLDlvelvMalEeeF~ieI   49 (75)
T PRK08172         23 LVEDL-YADSLDLIDIVFGLSEEFDISC   49 (75)
T ss_pred             HHHHC-CCCHHHHHHHHHHHHHHHCCCC
T ss_conf             35403-8766999999999999988978


No 21 
>COG3797 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=30.73  E-value=26  Score=16.66  Aligned_cols=12  Identities=33%  Similarity=0.567  Sum_probs=5.7

Q ss_pred             HHHHHHHHHCCC
Q ss_conf             999999993787
Q gi|254780144|r   22 LSKRLEKEWGVS   33 (126)
Q Consensus        22 Lv~~leekfgv~   33 (126)
                      |-..++.+||..
T Consensus        60 lE~afe~~fg~~   71 (178)
T COG3797          60 LEAAFEKRFGRH   71 (178)
T ss_pred             HHHHHHHHCCCC
T ss_conf             999999871977


No 22 
>PRK12449 acyl carrier protein; Provisional
Probab=28.70  E-value=49  Score=15.00  Aligned_cols=22  Identities=23%  Similarity=0.351  Sum_probs=17.5

Q ss_pred             HCCHHHHHHHHHHHHHHHCCCC
Q ss_conf             0999999999999999937871
Q gi|254780144|r   13 SLTLIEAAELSKRLEKEWGVSA   34 (126)
Q Consensus        13 ~LTllE~~eLv~~leekfgv~~   34 (126)
                      ++.=+.+.||+-.+|+.||+.-
T Consensus        36 g~DSLd~vElvm~lEdeFgi~I   57 (80)
T PRK12449         36 AVDSIELVEFIINVEDEFHLAI   57 (80)
T ss_pred             CCCHHHHHHHHHHHHHHHCCCC
T ss_conf             9658999999999999979978


No 23 
>KOG2003 consensus
Probab=28.56  E-value=49  Score=14.98  Aligned_cols=28  Identities=43%  Similarity=0.601  Sum_probs=19.7

Q ss_pred             CHHHHH-HHHHHCCCCHHHHHHHHHHCCH
Q ss_conf             335787-7677659988999999863797
Q gi|254780144|r   71 KIAVIK-EVRAITDLGLKEAKELVESAPK   98 (126)
Q Consensus        71 Ki~vIK-~vR~it~LgLkEAK~lVe~~P~   98 (126)
                      -+.-+| .||-.++|||+++|+.-+.+-+
T Consensus       693 dldclkflvri~~dlgl~d~key~~klek  721 (840)
T KOG2003         693 DLDCLKFLVRIAGDLGLKDAKEYADKLEK  721 (840)
T ss_pred             CHHHHHHHHHHHCCCCCHHHHHHHHHHHH
T ss_conf             01999999998400264468999999999


No 24 
>TIGR01007 eps_fam capsular exopolysaccharide family; InterPro: IPR005702    This family describes the capsular exopolysaccharide proteins in bacteria. The exopolysaccharide gene cluster consists of several genes which encode a number of proteins which regulate the exoploysaccharide biosynthesis (EPS). At least 13 genes EpsA to EpsM in streptococcus species seem to direct the EPS proteins and share high homology. ; GO: 0030234 enzyme regulator activity, 0045227 capsule polysaccharide biosynthetic process.
Probab=28.04  E-value=50  Score=14.96  Aligned_cols=58  Identities=22%  Similarity=0.288  Sum_probs=34.6

Q ss_pred             CCCCCEEEEEECCCCCCCHHHHHHHHHHCCCCHHHHHHHHHHCCHHH-HHCCCHHHHHHHHHHHHHCCCEE
Q ss_conf             22431157774377554335787767765998899999986379776-60999899999999999748579
Q gi|254780144|r   54 EKTEFEVVLKGFDDPKKKIAVIKEVRAITDLGLKEAKELVESAPKSL-KTGLSKDEANEMKKKLEDAGATV  123 (126)
Q Consensus        54 EKt~fdV~L~~~~~~~~Ki~vIK~vR~it~LgLkEAK~lVe~~P~~i-ke~v~keeAE~ik~~Le~aGa~V  123 (126)
                      -+..||+++-..+|=.   .||=+  .|.       -..|++.==++ -+.+.|++-++.|++||.+|+.+
T Consensus       127 ~~~~fD~iiiDTPPig---~V~DA--ai~-------a~~~d~~~LV~~A~~~~k~~v~KAK~~LEq~G~~~  185 (207)
T TIGR01007       127 LRKYFDYIIIDTPPIG---TVIDA--AII-------ARAVDASILVTDAGKIKKREVKKAKEQLEQAGSKF  185 (207)
T ss_pred             HHCCCCEEEEEECCCC---HHHHH--HHH-------HHHHCCEEEEEECCCCCHHHHHHHHHHHHHHCCCE
T ss_conf             8716888999518866---67889--999-------98729779887225326467899999998617841


No 25 
>PRK10753 transcriptional regulator HU subunit alpha; Provisional
Probab=27.32  E-value=25  Score=16.72  Aligned_cols=17  Identities=12%  Similarity=0.001  Sum_probs=9.0

Q ss_pred             HCCHHHHHHHHHHHHHH
Q ss_conf             09999999999999999
Q gi|254780144|r   13 SLTLIEAAELSKRLEKE   29 (126)
Q Consensus        13 ~LTllE~~eLv~~leek   29 (126)
                      +||-.++..+++.+-+.
T Consensus        15 ~~sk~~~~~~v~~~~~~   31 (90)
T PRK10753         15 ELSKTQAKAALESTLAA   31 (90)
T ss_pred             CCCHHHHHHHHHHHHHH
T ss_conf             98999999999999999


No 26 
>cd00591 HU_IHF Integration host factor (IHF) and HU are small heterodimeric members of the DNABII protein family that bind and bend DNA, functioning as architectural factors in many cellular processes including transcription, site-specific recombination, and higher-order nucleoprotein complex assembly. The dimer subunits associate to form a compact globular core from which two beta ribbon arms (one from each subunit) protrude. The beta arms track and bind the DNA minor groove.  Despite sequence and structural similarity, IHF and HU can be distinguished by their different DNA substrate preferences.
Probab=27.21  E-value=25  Score=16.79  Aligned_cols=33  Identities=21%  Similarity=0.286  Sum_probs=17.2

Q ss_pred             HHHHHHHHHHCCCCHHHHHHHHHHCCHHHHHCC
Q ss_conf             357877677659988999999863797766099
Q gi|254780144|r   72 IAVIKEVRAITDLGLKEAKELVESAPKSLKTGL  104 (126)
Q Consensus        72 i~vIK~vR~it~LgLkEAK~lVe~~P~~ike~v  104 (126)
                      -.+|+.+..-+|+.-++++.+|+..-..|.+.+
T Consensus         3 ~dLi~~ia~~~~~s~~~~~~~v~~~~~~i~~~L   35 (87)
T cd00591           3 SELIEAIAEKTGLSKKDAEAAVDAFLDVITEAL   35 (87)
T ss_pred             HHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
T ss_conf             999999999869699999999999999999999


No 27 
>pfam02022 Integrase_Zn Integrase Zinc binding domain. Integrase mediates integration of a DNA copy of the viral genome into the host chromosome. Integrase is composed of three domains. This domain is the amino-terminal domain zinc binding domain. The central domain is the catalytic domain pfam00665. The carboxyl terminal domain is a DNA binding domain pfam00552.
Probab=26.24  E-value=54  Score=14.73  Aligned_cols=26  Identities=35%  Similarity=0.350  Sum_probs=20.2

Q ss_pred             HHHHHHHCCCCHHHHHHHHHHCCHHH
Q ss_conf             87767765998899999986379776
Q gi|254780144|r   75 IKEVRAITDLGLKEAKELVESAPKSL  100 (126)
Q Consensus        75 IK~vR~it~LgLkEAK~lVe~~P~~i  100 (126)
                      .+.+|.--|+...+||++|.++|.--
T Consensus        12 ~~~L~~~F~ip~~vAr~IV~~C~~Cq   37 (40)
T pfam02022        12 AKALRHKFGIPRLVAKEIVNSCPKCQ   37 (40)
T ss_pred             HHHHHHHHCCCHHHHHHHHHHCHHHH
T ss_conf             99999892989999999999789976


No 28 
>pfam04461 DUF520 Protein of unknown function (DUF520). Family of uncharacterized proteins.
Probab=25.62  E-value=56  Score=14.66  Aligned_cols=64  Identities=25%  Similarity=0.384  Sum_probs=40.0

Q ss_pred             EEEEEECCCCCCCHHHHHHH-HH-H--CCCCHHHHHHH-HHHCC-------HHHHHCCCHHHHHHHHHHHHHCCCEEE
Q ss_conf             15777437755433578776-77-6--59988999999-86379-------776609998999999999997485799
Q gi|254780144|r   59 EVVLKGFDDPKKKIAVIKEV-RA-I--TDLGLKEAKEL-VESAP-------KSLKTGLSKDEANEMKKKLEDAGATVE  124 (126)
Q Consensus        59 dV~L~~~~~~~~Ki~vIK~v-R~-i--t~LgLkEAK~l-Ve~~P-------~~ike~v~keeAE~ik~~Le~aGa~Ve  124 (126)
                      .+.|..-  .+-|+.-+..+ +. +  -|++++--.-- +|.++       ..|++|++++.|-+|-+.+.+.+-+|.
T Consensus        45 ~i~i~a~--~e~kl~~~~diL~~k~~KR~i~~k~ld~~~~e~asG~~~rq~i~lk~GI~~e~AKkI~K~IK~~klKVq  120 (160)
T pfam04461        45 EITLTAE--SDFQLKQVKDILRTKLIKRGVDLKALDFGKVEKASGKTVKQEVKLKQGIDQELAKKIVKLIKDSKLKVQ  120 (160)
T ss_pred             EEEEEEC--CHHHHHHHHHHHHHHHHHCCCCCCEECCCCCCCCCCCEEEEEEEHHCCCCHHHHHHHHHHHHHCCCCEE
T ss_conf             8999959--789999999999999985399811013587424679879999882204388999999999984488036


No 29 
>PRK00285 ihfA integration host factor subunit alpha; Reviewed
Probab=25.06  E-value=28  Score=16.45  Aligned_cols=18  Identities=33%  Similarity=0.255  Sum_probs=10.1

Q ss_pred             HCCHHHHHHHHHHHHHHH
Q ss_conf             099999999999999993
Q gi|254780144|r   13 SLTLIEAAELSKRLEKEW   30 (126)
Q Consensus        13 ~LTllE~~eLv~~leekf   30 (126)
                      ++|-.++...++.+-+..
T Consensus        18 g~s~~~a~~~v~~~~~~i   35 (100)
T PRK00285         18 GLSKREAKELVELFFEEI   35 (100)
T ss_pred             CCCHHHHHHHHHHHHHHH
T ss_conf             959999999999999999


No 30 
>cd04764 HTH_MlrA-like_sg1 Helix-Turn-Helix DNA binding domain of putative MlrA-like transcription regulators. Putative helix-turn-helix (HTH) MlrA-like transcription regulators (subgroup 1). The MlrA protein, also known as YehV, has been shown to control cell-cell aggregation by co-regulating the expression of curli and extracellular matrix production in Escherichia coli and Salmonella typhimurium. These proteins belong to the MerR superfamily of transcription regulators that promote expression of several stress regulon genes by reconfiguring the spacer between the -35 and -10 promoter elements. Their conserved N-terminal domains contain predicted HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules. Many MlrA-like proteins in this group appear to lack the long dimerization helix seen in the N-terminal domains of typical MerR-like proteins.
Probab=24.61  E-value=58  Score=14.55  Aligned_cols=23  Identities=30%  Similarity=0.455  Sum_probs=18.8

Q ss_pred             CCHHHHHHHHHHCCCCHHHHHHHH
Q ss_conf             433578776776599889999998
Q gi|254780144|r   70 KKIAVIKEVRAITDLGLKEAKELV   93 (126)
Q Consensus        70 ~Ki~vIK~vR~it~LgLkEAK~lV   93 (126)
                      .++..|+..|. .|++|++.|++.
T Consensus        44 ~~l~~I~~l~~-~G~sl~~Ik~~L   66 (67)
T cd04764          44 ELLKKIKTLLE-KGLSIKEIKEIL   66 (67)
T ss_pred             HHHHHHHHHHH-CCCCHHHHHHHH
T ss_conf             99999999999-699899999985


No 31 
>CHL00124 acpP acyl carrier protein; Validated
Probab=24.43  E-value=59  Score=14.53  Aligned_cols=22  Identities=18%  Similarity=0.385  Sum_probs=17.1

Q ss_pred             HCCHHHHHHHHHHHHHHHCCCC
Q ss_conf             0999999999999999937871
Q gi|254780144|r   13 SLTLIEAAELSKRLEKEWGVSA   34 (126)
Q Consensus        13 ~LTllE~~eLv~~leekfgv~~   34 (126)
                      ++-=+...||+-.||++|||.-
T Consensus        36 G~DSLd~vElvm~lE~~F~IeI   57 (84)
T CHL00124         36 GADSLDTVELVMAIEEEFDIEI   57 (84)
T ss_pred             CCCHHHHHHHHHHHHHHHCCCC
T ss_conf             9876999999999999989977


No 32 
>cd04782 HTH_BltR Helix-Turn-Helix DNA binding domain of the BltR transcription regulator. Helix-turn-helix (HTH) multidrug-efflux transporter transcription regulator, BltR (BmrR-like transporter) of Bacillus subtilis, and related proteins; N-terminal domain. Blt, like Bmr, is a membrane protein which causes the efflux of a variety of toxic substances and antibiotics. These regulators are comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain predicted winged HTH motifs that mediate DNA binding, while the C-terminal domains are often unrelated and bind specific coactivator molecules. They share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements.
Probab=23.72  E-value=61  Score=14.44  Aligned_cols=27  Identities=19%  Similarity=0.417  Sum_probs=21.0

Q ss_pred             CCHHHHHHHHHHCCCCHHHHHHHHHHCC
Q ss_conf             4335787767765998899999986379
Q gi|254780144|r   70 KKIAVIKEVRAITDLGLKEAKELVESAP   97 (126)
Q Consensus        70 ~Ki~vIK~vR~it~LgLkEAK~lVe~~P   97 (126)
                      .++..|+..|. .|++|.|.++++++..
T Consensus        45 ~~l~~I~~~r~-lG~sL~eI~~~~~~~~   71 (97)
T cd04782          45 EQLDIILLLKE-LGISLKEIKDYLDNRN   71 (97)
T ss_pred             HHHHHHHHHHH-CCCCHHHHHHHHHCCC
T ss_conf             99999999999-6999999999982799


No 33 
>PRK06720 hypothetical protein; Provisional
Probab=23.21  E-value=61  Score=14.43  Aligned_cols=14  Identities=0%  Similarity=-0.052  Sum_probs=5.9

Q ss_pred             HHHHHHHHHHHHHC
Q ss_conf             99999999999937
Q gi|254780144|r   18 EAAELSKRLEKEWG   31 (126)
Q Consensus        18 E~~eLv~~leekfg   31 (126)
                      ++..+++.+.++||
T Consensus        79 ~v~~~i~~~~~~~g   92 (169)
T PRK06720         79 DWQRVISITLNAFS   92 (169)
T ss_pred             HHHHHHHHHHHHCC
T ss_conf             99999999999759


No 34 
>cd02130 PA_ScAPY_like PA_ScAPY_like: Protease-associated domain containing proteins like Saccharomyces cerevisiae aminopeptidase Y (ScAPY). This group contains various PA domain-containing proteins similar to the S. cerevisiae APY, including Trichophyton rubrum leucine aminopeptidase 1(LAP1). Proteins in this group belong to the peptidase M28 family. ScAPY hydrolyzes amino acid-4-methylcoumaryl-7-amides (MCAs). ScAPY more rapidly hydrolyzes dipeptidyl-MCAs. Hydrolysis of amino acid-MCAs or dipeptides is stimulated by Co2+ while  the hydrolysis of dipeptidyl-MCAs, tripeptides, and longer peptides is inhibited by Co2+. ScAPY is vacuolar and  is activated by proteolytic processing. LAP1 is a secreted leucine aminopeptidase. The significance of the PA domain to these proteins has not been ascertained. It may be a protein-protein interaction domain. At peptidase active sites, the PA domain may participate in substrate binding and/or promoting conformational changes, which influence the stab
Probab=23.15  E-value=62  Score=14.38  Aligned_cols=23  Identities=22%  Similarity=0.518  Sum_probs=19.4

Q ss_pred             HCCCHHHHHHHHHHHHHCCCEEEE
Q ss_conf             099989999999999974857993
Q gi|254780144|r  102 TGLSKDEANEMKKKLEDAGATVEL  125 (126)
Q Consensus       102 e~v~keeAE~ik~~Le~aGa~Vei  125 (126)
                      -++|+++.+.|+.+|+. |.+|+.
T Consensus        98 v~Is~~dG~~L~a~l~~-G~~v~~  120 (122)
T cd02130          98 VGISQEDGKALVAALAN-GGEVSA  120 (122)
T ss_pred             EEECHHHHHHHHHHHHC-CCEEEE
T ss_conf             99619999999999978-997988


No 35 
>pfam00216 Bac_DNA_binding Bacterial DNA-binding protein.
Probab=23.06  E-value=34  Score=15.99  Aligned_cols=16  Identities=13%  Similarity=0.173  Sum_probs=7.6

Q ss_pred             HCCHHHHHHHHHHHHH
Q ss_conf             0999999999999999
Q gi|254780144|r   13 SLTLIEAAELSKRLEK   28 (126)
Q Consensus        13 ~LTllE~~eLv~~lee   28 (126)
                      +||-.++.++++.+-+
T Consensus        15 ~ls~~~~~~~v~~~~~   30 (90)
T pfam00216        15 GLSKKDAEAIVDAFLD   30 (90)
T ss_pred             CCCHHHHHHHHHHHHH
T ss_conf             9699999999999999


No 36 
>PRK10664 transcriptional regulator HU subunit beta; Provisional
Probab=22.50  E-value=36  Score=15.81  Aligned_cols=18  Identities=6%  Similarity=-0.014  Sum_probs=9.7

Q ss_pred             HCCHHHHHHHHHHHHHHH
Q ss_conf             099999999999999993
Q gi|254780144|r   13 SLTLIEAAELSKRLEKEW   30 (126)
Q Consensus        13 ~LTllE~~eLv~~leekf   30 (126)
                      +||-.++...++.+-+..
T Consensus        15 ~ltk~~a~~~v~~~~~~i   32 (90)
T PRK10664         15 DISKAAAGRALDAIIASV   32 (90)
T ss_pred             CCCHHHHHHHHHHHHHHH
T ss_conf             999999999999999999


No 37 
>PRK05412 nucleotide-binding protein; Reviewed
Probab=22.36  E-value=65  Score=14.28  Aligned_cols=65  Identities=23%  Similarity=0.344  Sum_probs=39.2

Q ss_pred             CEEEEEECCCCCCCHHHHHH-HHH-H--CCCCHHHHHH-HHHHC-------CHHHHHCCCHHHHHHHHHHHHHCCCEEE
Q ss_conf             11577743775543357877-677-6--5998899999-98637-------9776609998999999999997485799
Q gi|254780144|r   58 FEVVLKGFDDPKKKIAVIKE-VRA-I--TDLGLKEAKE-LVESA-------PKSLKTGLSKDEANEMKKKLEDAGATVE  124 (126)
Q Consensus        58 fdV~L~~~~~~~~Ki~vIK~-vR~-i--t~LgLkEAK~-lVe~~-------P~~ike~v~keeAE~ik~~Le~aGa~Ve  124 (126)
                      -.+.|.+-+  +-|+.-+.. ++. +  -|++|+--.- -+|.+       ...+++|++++.|-+|-+.+.+.+-+|.
T Consensus        44 ~~i~i~a~~--e~kl~qv~diL~~kl~KR~i~~k~ld~~~~e~asG~~vrq~i~lk~GI~~e~AKkI~k~IK~~klKVq  120 (161)
T PRK05412         44 EEITLTAES--DFQLKQVLDILRSKLIKRGIDLKALDYGKVEKASGKTVKQEVKLKQGIEQELAKKIVKLIKDSKLKVQ  120 (161)
T ss_pred             CEEEEEECC--HHHHHHHHHHHHHHHHHCCCCCCEECCCCCCCCCCCEEEEEEEHHCCCCHHHHHHHHHHHHHCCCCEE
T ss_conf             789999697--89999999999999985399811014688434679879999881204388999999999984488136


No 38 
>PTZ00171 acyl carrier protein; Provisional
Probab=22.12  E-value=65  Score=14.25  Aligned_cols=21  Identities=19%  Similarity=0.389  Sum_probs=14.5

Q ss_pred             HCCHHHHHHHHHHHHHHHCCC
Q ss_conf             099999999999999993787
Q gi|254780144|r   13 SLTLIEAAELSKRLEKEWGVS   33 (126)
Q Consensus        13 ~LTllE~~eLv~~leekfgv~   33 (126)
                      ++.=+++.||+-.||++||+.
T Consensus       103 G~DSLD~vElvm~lEeeF~ie  123 (150)
T PTZ00171        103 GADSLDVVELLIAIEQEFNLT  123 (150)
T ss_pred             CCCHHHHHHHHHHHHHHHCCC
T ss_conf             976799999999999995981


No 39 
>pfam00828 Ribosomal_L18e Ribosomal protein L18e/L15. This family includes eukaryotic L18 as well as prokaryotic L15.
Probab=21.74  E-value=67  Score=14.20  Aligned_cols=16  Identities=38%  Similarity=0.592  Sum_probs=13.1

Q ss_pred             HHHHHHHHHCCCEEEE
Q ss_conf             9999999974857993
Q gi|254780144|r  110 NEMKKKLEDAGATVEL  125 (126)
Q Consensus       110 E~ik~~Le~aGa~Vei  125 (126)
                      +..++++|.+|++|++
T Consensus       106 ~sA~e~Ie~aGG~v~~  121 (122)
T pfam00828       106 KSAREKIEKAGGEVIL  121 (122)
T ss_pred             HHHHHHHHHCCCEEEE
T ss_conf             9999999985998997


Done!