Query         gi|254780367|ref|YP_003064780.1| ribonuclease protein [Candidatus Liberibacter asiaticus str. psy62]
Match_columns 281
No_of_seqs    119 out of 2026
Neff          8.7 
Searched_HMMs 39220
Date          Sun May 29 17:06:57 2011
Command       /home/congqian_1/programs/hhpred/hhsearch -i 254780367.hhm -d /home/congqian_1/database/cdd/Cdd.hhm 

 No Hit                             Prob E-value P-value  Score    SS Cols Query HMM  Template HMM
  1 PRK01637 rbn ribonuclease BN;  100.0       0       0  331.4  35.8  273    1-280     1-274 (284)
  2 COG1295 Rbn Ribonuclease BN fa 100.0       0       0  327.7  35.7  278    3-280    11-292 (303)
  3 PRK04214 rbn ribonuclease BN/u 100.0       0       0  318.9  35.7  263    7-277    14-277 (411)
  4 pfam03631 Ribonuclease_BN Ribo 100.0       0       0  300.6  33.1  254   20-276     1-255 (255)
  5 TIGR00765 yihY_not_rbn YihY fa 100.0 2.1E-29 5.4E-34  157.9  29.5  260   12-274     3-267 (268)
  6 TIGR00766 TIGR00766 ribonuclea  99.7 1.2E-13 3.1E-18   82.6  25.9  260   12-273     3-297 (299)
  7 PRK10999 malF maltose transpor  84.3     2.1 5.4E-05   19.3   4.7   23   34-56    293-315 (520)
  8 PRK09695 glycolate transporter  61.5     9.2 0.00024   16.3  19.2  213   29-251    12-262 (560)
  9 KOG2516 consensus               43.1      19  0.0005   14.7   5.0   80  188-270   285-370 (517)
 10 PRK12721 secretion system appa  39.3      23 0.00058   14.4  18.7   70  208-280   141-212 (349)
 11 pfam03904 DUF334 Domain of unk  31.9      30 0.00078   13.8   8.7   38  163-200   186-223 (229)
 12 PRK10420 L-lactate permease; P  28.3      36 0.00091   13.4  20.7  215   28-252    11-263 (551)
 13 pfam10225 DUF2215 Uncharacteri  23.8      44  0.0011   13.0  12.5   23   17-39     28-50  (247)
 14 TIGR00930 2a30 K-Cl cotranspor  22.5      47  0.0012   12.9  14.8  129   97-257   511-646 (1171)
 15 TIGR02186 alph_Pro_TM conserve  21.5      27 0.00069   14.0   0.1   44  210-253   217-264 (275)

No 1  
>PRK01637 rbn ribonuclease BN; Reviewed
Probab=100.00  E-value=0  Score=331.39  Aligned_cols=273  Identities=16%  Similarity=0.215  Sum_probs=228.0

Q ss_pred             CCHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHH-HHHHHHHHHHHHCCCCHHHHHH
Q ss_conf             912789999999999999985578768899999999999999999999986317567-8999999999733741368999
Q gi|254780367|r    1 MREYFCIVFDIIYDAIEHFVEEDGWAMASHISLSALLSVFPFIVFGANLAGFLGAHQ-FVPTVIDVVFGAWPEVIAKPIT   79 (281)
Q Consensus         1 l~~~~~~~~~~i~~~~~~~~~~~~~~~Aaalaf~~llsl~Plli~~~~i~~~~~~~~-~~~~~~~~i~~~lp~~~~~~i~   79 (281)
                      ||.-.+..|++++++.+|+.+||++.+||++|||+++|++|++++++++.+.++.++ ..+++.+.+.+.+||+..+.+.
T Consensus         1 ~~~~~r~~~~~lk~~~~rf~~d~~~~~AA~lay~~lLSlfP~l~~~~sv~~~~~~~~~~~~~l~~~i~~~~~p~~~~~i~   80 (284)
T PRK01637          1 LRSLLRPLWAFLKLLWQRIDEDNITVLAGHLAYVTLLSLVPLVAVVFSIFSAFPVFSEVSGQLEHFIFANFLPAAGDVVQ   80 (284)
T ss_pred             CHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHCCHHHHHHHH
T ss_conf             91679999999999999988578766999999999999999999999999981135889999999999854745789999


Q ss_pred             HHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             99998520457414999999999999999999999998630236663036767999999999999999999999999999
Q gi|254780367|r   80 DEILQVLAVPAKGLFTISALAAAYFSSNGVEALRISLNRAYRVVEMRSWYITRLISFGYVLLASVTLVIMSFVFVAIPLA  159 (281)
Q Consensus        80 ~~l~~~~~~~~~~~~~i~~~~~l~~as~~~~~l~~~~~~i~~~~~~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  159 (281)
                      +.+++..++ ++..+.+|++.++|++++.+.++++++|++|+++++|++.+++..++......++++..+..........
T Consensus        81 ~~i~~~~~~-~~~~~~~g~~~ll~~a~~~~~~l~~alN~i~~v~~~R~~~~~~~i~~~il~l~~il~~~~l~~~~~l~~~  159 (284)
T PRK01637         81 EYIEQFVAN-SSKMTAVGICGLIVVALMLISSIDKTLNTIWRSKRKRPKVYSFAVYWMILTLGPLLVGASLAISSYLLSL  159 (284)
T ss_pred             HHHHHHHHH-CCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             999999973-3332338899999999999999999999997065554199999999999999999999999999999999


Q ss_pred             HHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCHH
Q ss_conf             99997414652107999999999999999999999998405777675210122189999999999999999998652224
Q gi|254780367|r  160 LAYVRKFFPALGNLLLIIWNGRIYATMLALFIGLIFVHLFLPAAKSKIMSILPGVIFTWISWVVGAVLFTHYIVTFSTYS  239 (281)
Q Consensus       160 ~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~y~~~P~~~~~~~~~~~Ga~~a~v~~~~~~~~f~~y~~~~~~~~  239 (281)
                      ....      ............+.+++++.++.|..+|+++||+|++||+++|||++++++|++.|++|++|+.++++|+
T Consensus       160 ~~~~------~~~~~~~~~~l~~~~~~~l~~~~f~~lY~~lP~~k~~~r~~~~Ga~~ati~w~i~~~~F~~Yv~~f~~y~  233 (284)
T PRK01637        160 RWFE------ASDLSGVIDNLLRILPLLLSWLSFWLLYSVVPNKKVPFRHALVGALVAALLFELGKKGFALYITTFPSYQ  233 (284)
T ss_pred             HHHH------HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCHHH
T ss_conf             9987------3315789999999999999999999999984799753188758899999999999999999998600498


Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCC
Q ss_conf             67899999999999999999999999999999999832379
Q gi|254780367|r  240 TMYAGLASIMTCLVFLYMLGVFFILGAELNASMIIYYWRKK  280 (281)
Q Consensus       240 ~~YGsl~~ii~lllWly~~~~ill~Ga~~na~l~~~~~~~~  280 (281)
                      .+||++|+++++|+|+|+++.++++|||+||+++++|.-|.
T Consensus       234 ~~YGslg~iivlllWlY~s~~i~L~Gaeina~l~~~r~~~~  274 (284)
T PRK01637        234 LIYGALAVIPILFVWVYLSWCIVLLGAEITATLGEYRKLKQ  274 (284)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             99999999999999999999999999999999999998762


No 2  
>COG1295 Rbn Ribonuclease BN family enzyme [Replication, recombination, and repair]
Probab=100.00  E-value=0  Score=327.73  Aligned_cols=278  Identities=30%  Similarity=0.482  Sum_probs=245.4

Q ss_pred             HHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCC-HHHHHHHHHHHHHHCCCCHHHHHHHH
Q ss_conf             27899999999999999855787688999999999999999999999863175-67899999999973374136899999
Q gi|254780367|r    3 EYFCIVFDIIYDAIEHFVEEDGWAMASHISLSALLSVFPFIVFGANLAGFLGA-HQFVPTVIDVVFGAWPEVIAKPITDE   81 (281)
Q Consensus         3 ~~~~~~~~~i~~~~~~~~~~~~~~~Aaalaf~~llsl~Plli~~~~i~~~~~~-~~~~~~~~~~i~~~lp~~~~~~i~~~   81 (281)
                      ......+++++++.+|+.+||++.+|+++|||+++|++|++++.+++.++++. ++..+++...+.+..|++..+.+++.
T Consensus        11 ~~~~~~~~~~~~~~~r~~~d~~~~~aa~layy~lLSl~P~Llv~~sl~~~~~~~~~~~~~~~~~i~~~~P~~~~~~i~~~   90 (303)
T COG1295          11 ILRRGILDLLRRALERFNEDDGSLLAAALAYYTLLSLFPLLLVVFSLLGFFLAHPILLEDLLFIIANLLPEQAADVIEDY   90 (303)
T ss_pred             HHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHCCHHHHHHHHHH
T ss_conf             87888999999999997344365599999999999999999999999999756833688999999863987789999999


Q ss_pred             HHHHHCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             99852045741499999999999999999999999863023666303676799999999999999999999999999999
Q gi|254780367|r   82 ILQVLAVPAKGLFTISALAAAYFSSNGVEALRISLNRAYRVVEMRSWYITRLISFGYVLLASVTLVIMSFVFVAIPLALA  161 (281)
Q Consensus        82 l~~~~~~~~~~~~~i~~~~~l~~as~~~~~l~~~~~~i~~~~~~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  161 (281)
                      +.+...+++++++.+|.+.++|++++++.++++++|++|+++++|++.++++.+...++...+.+.......+.++....
T Consensus        91 l~~~~~~~~~~~~~~g~~~~lwtas~~~~~l~~~lN~i~~~~~~r~~~~~~l~~l~~~i~~~~~l~~~l~l~v~~~~~~~  170 (303)
T COG1295          91 LKNFLSQSRGSLLSLGLVVALWTASNGMSALRDALNKIWRVKPRRSFIRRRLLSLFWTLGTLLPLLFALLLSVVGPIALQ  170 (303)
T ss_pred             HHHHHCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             99997077875499999999999999999999999999768887748999999999999999999999999999999999


Q ss_pred             HHHHHCC--CCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCC-CCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCH
Q ss_conf             9974146--52107999999999999999999999998405777-67521012218999999999999999999865222
Q gi|254780367|r  162 YVRKFFP--ALGNLLLIIWNGRIYATMLALFIGLIFVHLFLPAA-KSKIMSILPGVIFTWISWVVGAVLFTHYIVTFSTY  238 (281)
Q Consensus       162 ~~~~~~~--~~~~~~~~~~~~~~~~~~l~~~~~~~~~y~~~P~~-~~~~~~~~~Ga~~a~v~~~~~~~~f~~y~~~~~~~  238 (281)
                      ......+  ................++++.++.|.++|+++|++ +.+|++++|||++++++|++.|++|++|+.++.+|
T Consensus       171 ~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~f~~ly~~lP~~~~~~~~~~~~Ga~~aai~~~i~~~~f~~Yv~~~~~y  250 (303)
T COG1295         171 ALLLRFGLPFFDVLVLILLRLRLLVSLLLLTLGFFLLYRFLPNVRVLKWRDVLPGALLAAILFELGKYLFGYYLSNFANY  250 (303)
T ss_pred             HHHHHCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCC
T ss_conf             99986055503468999999999999999999999999991787653017878999999999999999999999986033


Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCC
Q ss_conf             467899999999999999999999999999999999832379
Q gi|254780367|r  239 STMYAGLASIMTCLVFLYMLGVFFILGAELNASMIIYYWRKK  280 (281)
Q Consensus       239 ~~~YGsl~~ii~lllWly~~~~ill~Ga~~na~l~~~~~~~~  280 (281)
                      +.+||++|+++++|+|+|+++.++++|||+||++++++.+++
T Consensus       251 ~~~YGalgsvi~lmlw~y~~~~I~l~Gae~~a~~~~~~~~~~  292 (303)
T COG1295         251 SSTYGALGSVIILLLWLYISALIILLGAELNATLSEYKGPRA  292 (303)
T ss_pred             CCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHH
T ss_conf             602667999999999999999999998999999998636144


No 3  
>PRK04214 rbn ribonuclease BN/unknown domain fusion protein; Reviewed
Probab=100.00  E-value=0  Score=318.88  Aligned_cols=263  Identities=18%  Similarity=0.237  Sum_probs=222.7

Q ss_pred             HHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHH-HHHHHHHHHHHHCCCCHHHHHHHHHHHH
Q ss_conf             999999999999985578768899999999999999999999986317567-8999999999733741368999999985
Q gi|254780367|r    7 IVFDIIYDAIEHFVEEDGWAMASHISLSALLSVFPFIVFGANLAGFLGAHQ-FVPTVIDVVFGAWPEVIAKPITDEILQV   85 (281)
Q Consensus         7 ~~~~~i~~~~~~~~~~~~~~~Aaalaf~~llsl~Plli~~~~i~~~~~~~~-~~~~~~~~i~~~lp~~~~~~i~~~l~~~   85 (281)
                      ...++.+...+||.|||++..||++|||+++|+||++++.+++++.++..+ ..+.+.+.+.++++|+..+.+++.+++.
T Consensus        14 r~~~F~r~~~rrF~~dr~~~~AAsLtf~tlLALvPlL~v~~sl~s~fp~f~~~~~~l~~~l~~~l~P~~~~~i~~~l~~f   93 (411)
T PRK04214         14 RTCSFGRFLWRRFLDDRLFQAAASLTFTTLLALVPLATVVFGVLSAFPVFDRWSDAFTDFVFQTFVPGAARSVQNYLNRF   93 (411)
T ss_pred             HHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHCCCCHHHHHHHHHHHH
T ss_conf             89999999999975467988999999999999999999999999875461568999999999864852679999999999


Q ss_pred             HCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             20457414999999999999999999999998630236663036767999999999999999999999999999999974
Q gi|254780367|r   86 LAVPAKGLFTISALAAAYFSSNGVEALRISLNRAYRVVEMRSWYITRLISFGYVLLASVTLVIMSFVFVAIPLALAYVRK  165 (281)
Q Consensus        86 ~~~~~~~~~~i~~~~~l~~as~~~~~l~~~~~~i~~~~~~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  165 (281)
                      .++ .+.++.+|++.++|+++..+.++++++|+||+++++|++.++...++.+..+.++++..+........... ... 
T Consensus        94 ~~~-a~~L~~~G~i~L~~ta~~~l~tie~afN~Iw~v~~~R~~~~r~liy~~lltlgplllg~sl~~~~~l~~~~-~~~-  170 (411)
T PRK04214         94 LED-AGKLTAAGMVMLVVTLLMLLHTIEQTFNSIWRVASARPWVTQFLVYWTVLTLGPLLLGASMAMAAYVFALP-LLR-  170 (411)
T ss_pred             HHH-CCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH-HHH-
T ss_conf             975-02137888999999999999999999999866776671799999999999999999999999999999999-888-


Q ss_pred             HCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHH
Q ss_conf             14652107999999999999999999999998405777675210122189999999999999999998652224678999
Q gi|254780367|r  166 FFPALGNLLLIIWNGRIYATMLALFIGLIFVHLFLPAAKSKIMSILPGVIFTWISWVVGAVLFTHYIVTFSTYSTMYAGL  245 (281)
Q Consensus       166 ~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~y~~~P~~~~~~~~~~~Ga~~a~v~~~~~~~~f~~y~~~~~~~~~~YGsl  245 (281)
                           ...........+..++++.++.|+.+|++.||++++||++++||++++++|++.|.+|++|+.++++|+.+||++
T Consensus       171 -----~~~~~~~~~l~~l~plll~~l~f~lLY~~vPn~~V~~r~Al~Gal~Aallw~l~k~~F~~Yv~~f~sY~~iYGSl  245 (411)
T PRK04214        171 -----TTEGQWLAELARLAPMAVEFLCLVLLYRVVPNRFVPLRHALPGALLTAILLEIVKWGFGFYLGNFQTYQRIYGAF  245 (411)
T ss_pred             -----HHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHH
T ss_conf             -----656689999999999999999999999965888642598999999999999999999999998523099999999


Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHC
Q ss_conf             99999999999999999999999999999832
Q gi|254780367|r  246 ASIMTCLVFLYMLGVFFILGAELNASMIIYYW  277 (281)
Q Consensus       246 ~~ii~lllWly~~~~ill~Ga~~na~l~~~~~  277 (281)
                      |+++++|+|+|++|.++|+|||+.+.+...|.
T Consensus       246 AavpifLlWlYlSW~IvLlGAei~~~l~~~~~  277 (411)
T PRK04214        246 AAVPIFLLWIYLLWVSVLLGAVLTSSLSYWRG  277 (411)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHC
T ss_conf             99999999999999999998999992488762


No 4  
>pfam03631 Ribonuclease_BN Ribonuclease BN-like family. This family contains integral membrane proteins with 5 to 6 predicted transmembrane spans. The family include ribonuclease BN that is involved in tRNA maturation. This family of proteins does not seem to contain any completely conserved polar residues that would be expected in a nuclease enzyme, suggesting that many members of this family may not have this catalytic activity (Bateman A pers. obs.).
Probab=100.00  E-value=0  Score=300.63  Aligned_cols=254  Identities=28%  Similarity=0.451  Sum_probs=228.2

Q ss_pred             HHCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCH-HHHHHHHHHHHHHCCCCHHHHHHHHHHHHHCCCCCCHHHHHH
Q ss_conf             8557876889999999999999999999998631756-789999999997337413689999999852045741499999
Q gi|254780367|r   20 VEEDGWAMASHISLSALLSVFPFIVFGANLAGFLGAH-QFVPTVIDVVFGAWPEVIAKPITDEILQVLAVPAKGLFTISA   98 (281)
Q Consensus        20 ~~~~~~~~Aaalaf~~llsl~Plli~~~~i~~~~~~~-~~~~~~~~~i~~~lp~~~~~~i~~~l~~~~~~~~~~~~~i~~   98 (281)
                      +|||++.+|+++|||+++|++|++++.+++.+.++.+ +..+++.+.+.+.+|++..+.+++.+++..+  ++..+.+|+
T Consensus         1 ~~~~~~~~Aaalay~~llsl~Pll~~~~~i~~~~~~~~~~~~~i~~~l~~~~p~~~~~~i~~~~~~~~~--~~~~~~i~~   78 (255)
T pfam03631         1 QEDDLSLLAAALAYYTLLSLFPLLLVLLALLGLFGGPPALQEQLLDLLAEVLPEEAAELIEDILQRLLT--QASLGLLGL   78 (255)
T ss_pred             CCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHC--CCCCHHHHH
T ss_conf             987388999999999999999999999999998678488999999999987878889999999999980--656199999


Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHH
Q ss_conf             99999999999999999986302366630367679999999999999999999999999999999741465210799999
Q gi|254780367|r   99 LAAAYFSSNGVEALRISLNRAYRVVEMRSWYITRLISFGYVLLASVTLVIMSFVFVAIPLALAYVRKFFPALGNLLLIIW  178 (281)
Q Consensus        99 ~~~l~~as~~~~~l~~~~~~i~~~~~~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  178 (281)
                      +.++|++++++.++|+++|++|+++++|+++++|..++.+.+..++.+..+....+..+..........+ .......+.
T Consensus        79 ~~~l~~a~~~~~~l~~a~~~i~~~~~~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~  157 (255)
T pfam03631        79 GVLLWSASGGFAALRRALNRIYGVKEKRSFLRRRLLSLGLTLLLGLLLLLSLLLSVFLPALLGILLLGLG-LGLATVLLQ  157 (255)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCC-HHHHHHHHH
T ss_conf             9999999999999999999995899888689999999999999999999999999999999999886034-015889999


Q ss_pred             HHHHHHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             99999999999999999984057776752101221899999999999999999986522246789999999999999999
Q gi|254780367|r  179 NGRIYATMLALFIGLIFVHLFLPAAKSKIMSILPGVIFTWISWVVGAVLFTHYIVTFSTYSTMYAGLASIMTCLVFLYML  258 (281)
Q Consensus       179 ~~~~~~~~l~~~~~~~~~y~~~P~~~~~~~~~~~Ga~~a~v~~~~~~~~f~~y~~~~~~~~~~YGsl~~ii~lllWly~~  258 (281)
                      ..+++++++..++.++.+||++|++|++||++++||++++++|+++|.+|++|+.+.++|+.+||++|+++++|+|+|++
T Consensus       158 ~~~~~~~~~~~~~~~~~ly~~lp~~~~~~~~~~~Ga~~~~~~~~~~~~~f~~y~~~~~~~~~~YGsl~~vi~~llWly~~  237 (255)
T pfam03631       158 LLRWLVSLLLLTLLFALLYRFLPNRKVRWRAALPGALLAAVLWLLLSYGFSLYLSNFANYNSTYGSLGALIVLLLWLYLS  237 (255)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHH
T ss_conf             99999999999999999999907998555889999999999999999999999998632147799999999999999999


Q ss_pred             HHHHHHHHHHHHHHHHHH
Q ss_conf             999999999999999983
Q gi|254780367|r  259 GVFFILGAELNASMIIYY  276 (281)
Q Consensus       259 ~~ill~Ga~~na~l~~~~  276 (281)
                      +.++++|||+||+++++|
T Consensus       238 ~~ill~Ga~~~a~l~~~~  255 (255)
T pfam03631       238 ALILLLGAELNAALEERR  255 (255)
T ss_pred             HHHHHHHHHHHHHHHHCC
T ss_conf             999999999999999619


No 5  
>TIGR00765 yihY_not_rbn YihY family protein; InterPro: IPR004664   Members of this entry include ribonuclease BN (rbn) from Escherichia coli and homologues from a number of bacteria, including the largely uncharacterised BrkB (Bordetella spp. resist killing by serum B) from Bordetella pertussis. Some members have an additional C-terminal domain. Paralogs from E. coli (yhjD) and Mycobacterium tuberculosis (Rv3335c) are part of a smaller, related subfamily that form their own cluster. Ribonuclease BN is a homodimer in E. coli and does not contain a nucleic acid component. Bacteriophage T4 encodes several tRNAs that require this host ribonuclease for maturation. However, host tRNAs with the normal universal 3 sequence of CCA do not appear to be substrates. The substrate specificity of RNase BN appears to be very narrow and its biological role is uncertain. It is one of five ribonucleases in E. coli for which any of the five can confer viability, with the order of efficacy being RNase T > RNase PH > RNase D > RNase II > RNase BN.; GO: 0004540 ribonuclease activity.
Probab=100.00  E-value=2.1e-29  Score=157.92  Aligned_cols=260  Identities=20%  Similarity=0.277  Sum_probs=214.6

Q ss_pred             HHHHHHHHH-HCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCC-HHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHCCC
Q ss_conf             999999998-55787688999999999999999999999863175-6789999999997337413689999999852045
Q gi|254780367|r   12 IYDAIEHFV-EEDGWAMASHISLSALLSVFPFIVFGANLAGFLGA-HQFVPTVIDVVFGAWPEVIAKPITDEILQVLAVP   89 (281)
Q Consensus        12 i~~~~~~~~-~~~~~~~Aaalaf~~llsl~Plli~~~~i~~~~~~-~~~~~~~~~~i~~~lp~~~~~~i~~~l~~~~~~~   89 (281)
                      .+...+++. ++++...+++++|+++++++|++....++...++. ++......+.+.++..+...+.+.+.+.+..++ 
T Consensus         3 ~~~~~~~~~g~~~~~~~~~~~~~~~~l~~~p~~~~~~~~~~~~p~~~~~~~~~~~~~~~~~~p~~~~~~~~~~~~~~~~-   81 (268)
T TIGR00765         3 LKLLWRRFDGEDELPSLAGSLAFFTLLSLVPLLLVVFSLFAAFPVFSDLSGELGEFIFPNFAPSLGDLIKDYLEEFVEN-   81 (268)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHC-
T ss_conf             7888887510244555566789999999999999999999987655556778999887655466788899999998630-


Q ss_pred             CCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCHHHHHH--HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHC
Q ss_conf             74149999999999999999999999986302366630367679--9999999999999999999999999999997414
Q gi|254780367|r   90 AKGLFTISALAAAYFSSNGVEALRISLNRAYRVVEMRSWYITRL--ISFGYVLLASVTLVIMSFVFVAIPLALAYVRKFF  167 (281)
Q Consensus        90 ~~~~~~i~~~~~l~~as~~~~~l~~~~~~i~~~~~~r~~~~~~~--~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  167 (281)
                      ...+..+|.+..++.+.....++++..|++|+.+++|++...++  ..+.........+......  ......+......
T Consensus        82 ~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~gp~~~~~~~~~--~~~~~g~~~~~~~  159 (268)
T TIGR00765        82 SNKLTAVGGVSLVVTALLLINNIDSTLNKIWRVKPPRPPLFSRLFAVYWLLLTLGPLLLGLLLAL--SSGYLGRLASLDL  159 (268)
T ss_pred             CCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHH--HHHHHHHHHHHHH
T ss_conf             13214678999999999999889988887763012116899999999999998889999998887--7778776767777


Q ss_pred             CCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCC-HHHHHHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHH
Q ss_conf             6521079999999999999999999999984057776752-101221899999999999999999986522246789999
Q gi|254780367|r  168 PALGNLLLIIWNGRIYATMLALFIGLIFVHLFLPAAKSKI-MSILPGVIFTWISWVVGAVLFTHYIVTFSTYSTMYAGLA  246 (281)
Q Consensus       168 ~~~~~~~~~~~~~~~~~~~l~~~~~~~~~y~~~P~~~~~~-~~~~~Ga~~a~v~~~~~~~~f~~y~~~~~~~~~~YGsl~  246 (281)
                      ..............+..+.+..+..+..+|...|+++.+. ++..+|+.++++.|+..+..|++|+.++.+|...||+++
T Consensus       160 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~p~~~~~~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~  239 (268)
T TIGR00765       160 GAASGLLSLGANLLSGVPLLFTWLLFWLLYTIVPNKKVPLYRHALLGAFLAAVLWELGKWLFTWYVSTFPTYELLYGALA  239 (268)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHH
T ss_conf             77666666777788888899999999999975020244578889989999999999998889888761340677877899


Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             9999999999999999999999999999
Q gi|254780367|r  247 SIMTCLVFLYMLGVFFILGAELNASMII  274 (281)
Q Consensus       247 ~ii~lllWly~~~~ill~Ga~~na~l~~  274 (281)
                      .++.++.|+|+.|.+++.|++.+..+.+
T Consensus       240 ~~~~~~~w~~~~w~~~~~g~~~~~~~~~  267 (268)
T TIGR00765       240 VLPFLLLWLYLSWLLVLLGAELTSTLGE  267 (268)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHCC
T ss_conf             9999999999999999864567654215


No 6  
>TIGR00766 TIGR00766 ribonuclease, putative; InterPro: IPR005274   Members of this family show similarity to ribonuclease BN and include the Escherichia coli protein YhjD is located in the inner membrane . The function of these proteins are unknown. .
Probab=99.71  E-value=1.2e-13  Score=82.58  Aligned_cols=260  Identities=13%  Similarity=0.110  Sum_probs=182.6

Q ss_pred             HHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHHHH----H--HHHCC-C--HHHHHHHHHHHHHHCCCCHHHHHHHHH
Q ss_conf             9999999985578768899999999999999999999----9--86317-5--678999999999733741368999999
Q gi|254780367|r   12 IYDAIEHFVEEDGWAMASHISLSALLSVFPFIVFGAN----L--AGFLG-A--HQFVPTVIDVVFGAWPEVIAKPITDEI   82 (281)
Q Consensus        12 i~~~~~~~~~~~~~~~Aaalaf~~llsl~Plli~~~~----i--~~~~~-~--~~~~~~~~~~i~~~lp~~~~~~i~~~l   82 (281)
                      +.++..+|.++++...+++++|+.+++++|++++.+.    +  .+... .  ++...+..+.......+...+.+.+..
T Consensus         3 ~~~~~~~~~d~~g~~~~~~~~~~~~~~~~p~~~~~~~~gg~~gg~~~~~~~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~   82 (299)
T TIGR00766         3 LVRAGDRFNDRLGNLFGAGLTYFSFLSLIPLLLVGFGAGGFVGGLALHPRLNPPELLGLLEERVRSDVDPALGRTLKNTV   82 (299)
T ss_pred             CCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHCCCHHHHHHHHHHHHHHCCHHHHHHHHHHH
T ss_conf             21000122112002566788999999999999875201200000334320350467888888764101226789999887


Q ss_pred             HHHHCCCCCCHHHHHHHHHHHHHHHHHHHHHHHH----H----HHHCCCCCC-CHHHHHHHHH-HHHHHHHHHHHHHHHH
Q ss_conf             9852045741499999999999999999999999----8----630236663-0367679999-9999999999999999
Q gi|254780367|r   83 LQVLAVPAKGLFTISALAAAYFSSNGVEALRISL----N----RAYRVVEMR-SWYITRLISF-GYVLLASVTLVIMSFV  152 (281)
Q Consensus        83 ~~~~~~~~~~~~~i~~~~~l~~as~~~~~l~~~~----~----~i~~~~~~r-~~~~~~~~~~-~~~~~~~~~~~~~~~~  152 (281)
                      ....+ .+.+++..|.....|.+.++...+++++    +    ++|+.+... ...+.+.... .......+.+......
T Consensus        83 ~~~~~-~~~~~g~~g~~~~~~~g~~w~~~~~~~~~~~~~~~~~~~w~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~  161 (299)
T TIGR00766        83 NTAVD-ARTTVGLVGLAVALYSGLGWLGNLREALRAQSSAQSRDVWERPPAPEEKLWLKYLWDFLSLGGLLLALVVTLAL  161 (299)
T ss_pred             HHHHH-HCCHHHHHHHHHHHHHHHCHHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             66664-11112478899998762011456788875443233444430355403577889999999998899999999998


Q ss_pred             HHHHH---HHHHHHHHHCCC-----CCCH----HHHHHHHHHHHHHHHHHHHHHHHHHHC----CCCCCCCHHHHHHHHH
Q ss_conf             99999---999999741465-----2107----999999999999999999999998405----7776752101221899
Q gi|254780367|r  153 FVAIP---LALAYVRKFFPA-----LGNL----LLIIWNGRIYATMLALFIGLIFVHLFL----PAAKSKIMSILPGVIF  216 (281)
Q Consensus       153 ~~~~~---~~~~~~~~~~~~-----~~~~----~~~~~~~~~~~~~l~~~~~~~~~y~~~----P~~~~~~~~~~~Ga~~  216 (281)
                      .....   ..........+.     ....    .+.+........+....+.+.+++...    |+.+++.+....|.+.
T Consensus       162 ~~~~~~~p~~~~~~~~~~~~~g~~w~~~~~~w~~p~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~~~  241 (299)
T TIGR00766       162 TSLGGARPSAQALIWLALPLNGIDWLRPSVEWLKPTWDLIGLGISVLASLLLLWWLFWWLIGRLPREPPGGKPLLRGGLL  241 (299)
T ss_pred             HHHHCCCHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHH
T ss_conf             86512332578888876145522566666776305789999999999999999999998863112221001355654577


Q ss_pred             HHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             999999999999999986522246789999999999999999999999999999999
Q gi|254780367|r  217 TWISWVVGAVLFTHYIVTFSTYSTMYAGLASIMTCLVFLYMLGVFFILGAELNASMI  273 (281)
Q Consensus       217 a~v~~~~~~~~f~~y~~~~~~~~~~YGsl~~ii~lllWly~~~~ill~Ga~~na~l~  273 (281)
                      ++++++..+.....++....+ ++.-..+|.++.++.+.|+.....++...+.++-+
T Consensus       242 ~~~g~~~~~~~~~~~~~~~~~-~p~g~~~g~~~g~~~~~~~~~~~~~~~~~~~~~~~  297 (299)
T TIGR00766       242 AAVGFELLKFVGTVYLPELLK-SPSGAAFGPVLGLLAFFYFFAWLDLFLTAWAATAD  297 (299)
T ss_pred             HHHHHHHHHHHHHHHHHHHHH-CCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCC
T ss_conf             787689999999988888750-54421356789999999998889999988754115


No 7  
>PRK10999 malF maltose transporter membrane protein; Provisional
Probab=84.32  E-value=2.1  Score=19.31  Aligned_cols=23  Identities=26%  Similarity=0.238  Sum_probs=10.4

Q ss_pred             HHHHHHHHHHHHHHHHHHHCCCH
Q ss_conf             99999999999999998631756
Q gi|254780367|r   34 SALLSVFPFIVFGANLAGFLGAH   56 (281)
Q Consensus        34 ~~llsl~Plli~~~~i~~~~~~~   56 (281)
                      ++++|.+-...+.+.++-.++++
T Consensus       293 fa~~sv~~~~~lGl~lAllln~~  315 (520)
T PRK10999        293 FSLLTVVFTVAVGMVLACLVQWE  315 (520)
T ss_pred             HHHHHHHHHHHHHHHHHHHCCCC
T ss_conf             99999999999999999982875


No 8  
>PRK09695 glycolate transporter; Provisional
Probab=61.50  E-value=9.2  Score=16.25  Aligned_cols=213  Identities=16%  Similarity=0.152  Sum_probs=90.8

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHH-CCCHHH--HHHHH----HHHHHHCCCCHHHHHHHHHHHHHCCC-CCCHHHHHHHH
Q ss_conf             999999999999999999999863-175678--99999----99997337413689999999852045-74149999999
Q gi|254780367|r   29 SHISLSALLSVFPFIVFGANLAGF-LGAHQF--VPTVI----DVVFGAWPEVIAKPITDEILQVLAVP-AKGLFTISALA  100 (281)
Q Consensus        29 aalaf~~llsl~Plli~~~~i~~~-~~~~~~--~~~~~----~~i~~~lp~~~~~~i~~~l~~~~~~~-~~~~~~i~~~~  100 (281)
                      +++-.++++++.|++.++..+..+ .+....  ..-..    ....-.+|  .........+.....- .-...+++.+.
T Consensus        12 ~~~~lsallAllPIl~~~vlL~~~r~~A~~A~~i~~~~t~~iA~~~~~mp--~~~~~~a~~~G~~~~l~pI~~IV~~AIl   89 (560)
T PRK09695         12 GGLGLSALVALIPIIFFFVALAVLRLKGHVAGAITLILSILIAIFAFKMP--IDMAFAAAGYGFIYGLWPIAWIIVAAVF   89 (560)
T ss_pred             CCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCC--HHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             32999999999899999999999983899999999999999999983898--9999999999999998789999999999


Q ss_pred             H--HHHHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHHHH------------HHHHHHHHHHH-------------
Q ss_conf             9--99999999999999986302366630367679999999999------------99999999999-------------
Q gi|254780367|r  101 A--AYFSSNGVEALRISLNRAYRVVEMRSWYITRLISFGYVLLA------------SVTLVIMSFVF-------------  153 (281)
Q Consensus       101 ~--l~~as~~~~~l~~~~~~i~~~~~~r~~~~~~~~~~~~~~~~------------~~~~~~~~~~~-------------  153 (281)
                      +  .---++.+..+++.++++-+  ++|  ++-.+++|+.--..            ...+++.+.+.             
T Consensus        90 ly~~~~~sGa~~~Ir~~~~~Is~--D~r--vQvliIaw~Fg~fiEGaaGFGTPvAI~aplLvaLGF~pl~Aa~i~LI~ns  165 (560)
T PRK09695         90 LYKLTVASGQFDIIRSSVISITD--DQR--LQVLLIGFSFGALLEGAAGFGAPVAITGALLVGLGFKPLYAAGLCLIANT  165 (560)
T ss_pred             HHHHHHHHCCHHHHHHHHHHCCC--CHH--HHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHCCCCHHHHHHHHHHHCC
T ss_conf             99999980979999999974398--637--89999999999999875246760999999999859966999999999804


Q ss_pred             ---HHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             ---99999999997414652107999999999999999999999998405777675210122189999999999999999
Q gi|254780367|r  154 ---VAIPLALAYVRKFFPALGNLLLIIWNGRIYATMLALFIGLIFVHLFLPAAKSKIMSILPGVIFTWISWVVGAVLFTH  230 (281)
Q Consensus       154 ---~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~y~~~P~~~~~~~~~~~Ga~~a~v~~~~~~~~f~~  230 (281)
                         .++..............-+............+++.....+..++..  .+....|+.+|-++++++.+.+.++....
T Consensus       166 ~pvsFGAvGtPi~~~~~~~gl~~~~l~~~~~~~l~~~~~~ip~~~v~~~--~g~~g~~~~~p~aL~~g~~f~i~~~~~a~  243 (560)
T PRK09695        166 APVAFGALGVPILVAGQVTGIDPFHIGAMAGRQLPFLSVLVPFWLVAMM--DGWKGVKETWPAALVAGGSFAVTQFFTSN  243 (560)
T ss_pred             CCCCCHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHH--HCHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             6653021178899988753998899999999999999999999999998--34488888789999999999999999999


Q ss_pred             HHHHHCCHHHHHHHHHHHHHH
Q ss_conf             998652224678999999999
Q gi|254780367|r  231 YIVTFSTYSTMYAGLASIMTC  251 (281)
Q Consensus       231 y~~~~~~~~~~YGsl~~ii~l  251 (281)
                      |+..  ....+-|++-+++..
T Consensus       244 ~~gp--elp~iig~lv~l~~~  262 (560)
T PRK09695        244 YIGP--ELPDITSALVSIVSL  262 (560)
T ss_pred             HCCH--HHHHHHHHHHHHHHH
T ss_conf             5566--078899999999999


No 9  
>KOG2516 consensus
Probab=43.12  E-value=19  Score=14.70  Aligned_cols=80  Identities=16%  Similarity=0.185  Sum_probs=38.8

Q ss_pred             HHHHHHHHHHHHCCCCCCCC------HHHHHHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             99999999984057776752------101221899999999999999999986522246789999999999999999999
Q gi|254780367|r  188 ALFIGLIFVHLFLPAAKSKI------MSILPGVIFTWISWVVGAVLFTHYIVTFSTYSTMYAGLASIMTCLVFLYMLGVF  261 (281)
Q Consensus       188 ~~~~~~~~~y~~~P~~~~~~------~~~~~Ga~~a~v~~~~~~~~f~~y~~~~~~~~~~YGsl~~ii~lllWly~~~~i  261 (281)
                      ...+.|.++|.++|.+.-+.      .-.+.+|..++-+|.-.|...-....-.   .-..-.+..++.-+..+|.+..-
T Consensus       285 l~sL~fi~lySflpHKElRFIIY~~P~~nl~aA~gca~l~~n~kks~~~~~l~l---~v~~hli~n~~~s~~~LyVs~~n  361 (517)
T KOG2516         285 LVSLFFIFLYSFLPHKELRFIIYAFPWFNLAAAIGCARLWNNSKKSKKIFELLL---LVIFHLIINFFISSFFLYVSQYN  361 (517)
T ss_pred             HHHHHHHHHHHHCCCCEEEEEEEEHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH---HHHHHHHHHHHHHHHHHHHHHCC
T ss_conf             888899999870776326787764678899889889999986657899999999---99999999999999999976247


Q ss_pred             HHHHHHHHH
Q ss_conf             999999999
Q gi|254780367|r  262 FILGAELNA  270 (281)
Q Consensus       262 ll~Ga~~na  270 (281)
                      -=.|.+++.
T Consensus       362 YPGg~ALtr  370 (517)
T KOG2516         362 YPGGLALTR  370 (517)
T ss_pred             CCCHHHHHH
T ss_conf             884799999


No 10 
>PRK12721 secretion system apparatus protein SsaU; Reviewed
Probab=39.35  E-value=23  Score=14.40  Aligned_cols=70  Identities=10%  Similarity=0.084  Sum_probs=31.7

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHH--HHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCC
Q ss_conf             1012218999999999999999999865222467899999--999999999999999999999999999832379
Q gi|254780367|r  208 MSILPGVIFTWISWVVGAVLFTHYIVTFSTYSTMYAGLAS--IMTCLVFLYMLGVFFILGAELNASMIIYYWRKK  280 (281)
Q Consensus       208 ~~~~~Ga~~a~v~~~~~~~~f~~y~~~~~~~~~~YGsl~~--ii~lllWly~~~~ill~Ga~~na~l~~~~~~~~  280 (281)
                      |..+.-.+++.+.|...+.-..-.... ...+. -..+..  -....+|....... +.=|.++.-+|+++..|+
T Consensus       141 KsllKv~lv~~i~~~~l~~~~~~~~~l-~~~~~-~~~l~~~~~~~~~l~~~~~~~l-lviai~D~~~Qr~~~~k~  212 (349)
T PRK12721        141 KSLLKVIVLSLIFAFLLYYYAPTFRAL-PYCGS-ACALPVVSTLIKWLWGGVIAFY-LVFGILDYAFQRYKIMKQ  212 (349)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHH-HCCCH-HHHHHHHHHHHHHHHHHHHHHH-HHHHHHHHHHHHHHHHHH
T ss_conf             999999999999999999999999987-54799-9999999999999999999999-999999999999999987


No 11 
>pfam03904 DUF334 Domain of unknown function (DUF334). Staphylococcus aureus plasmid proteins with no characterized function.
Probab=31.93  E-value=30  Score=13.77  Aligned_cols=38  Identities=8%  Similarity=0.029  Sum_probs=23.2

Q ss_pred             HHHHCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHC
Q ss_conf             97414652107999999999999999999999998405
Q gi|254780367|r  163 VRKFFPALGNLLLIIWNGRIYATMLALFIGLIFVHLFL  200 (281)
Q Consensus       163 ~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~y~~~  200 (281)
                      +..............|...+.+|++.....|.++|-+.
T Consensus       186 ia~kIKaSEgf~~~lWYiaYglPYl~~iggFi~Lyewi  223 (229)
T pfam03904       186 IAGKIKASEGFISFLWYIAYGLPYILAIGLFIGLYEWI  223 (229)
T ss_pred             HHHHHHHCHHHHHHHHHHHHCCHHHHHHHHHHHHHHHH
T ss_conf             99887311039999999992559999999999999999


No 12 
>PRK10420 L-lactate permease; Provisional
Probab=28.27  E-value=36  Score=13.45  Aligned_cols=215  Identities=13%  Similarity=0.142  Sum_probs=92.7

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHH-CCCHHH--HHH----HHHHHHHHCCCCHHHHHHHHHHHHHCCC-CCCHHHHHHH
Q ss_conf             8999999999999999999999863-175678--999----9999997337413689999999852045-7414999999
Q gi|254780367|r   28 ASHISLSALLSVFPFIVFGANLAGF-LGAHQF--VPT----VIDVVFGAWPEVIAKPITDEILQVLAVP-AKGLFTISAL   99 (281)
Q Consensus        28 Aaalaf~~llsl~Plli~~~~i~~~-~~~~~~--~~~----~~~~i~~~lp~~~~~~i~~~l~~~~~~~-~~~~~~i~~~   99 (281)
                      .+++-..+++++.|++.+++.+..+ .+....  ..-    .+....-.+|  ........++.....- .-..-+++.+
T Consensus        11 ~g~~~lsallA~lPIl~~~vlL~~~r~~a~~A~~i~~~~a~~iA~~~~~~p--~~~~~aa~~~G~~~al~pI~~II~~Ai   88 (551)
T PRK10420         11 AGNIWLSSLIASLPILFFFFALIKLKLKGYVAASWTVAIALAVALLFYKMP--VANALASVVYGFFYGLWPIAWIIIAAV   88 (551)
T ss_pred             CCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCC--HHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             755899999999999999999999983899999999999999999990899--999999999999999868999999999


Q ss_pred             HH--HHHHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHHHHH------------HHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             99--999999999999999863023666303676799999999999------------9999999999999999999974
Q gi|254780367|r  100 AA--AYFSSNGVEALRISLNRAYRVVEMRSWYITRLISFGYVLLAS------------VTLVIMSFVFVAIPLALAYVRK  165 (281)
Q Consensus       100 ~~--l~~as~~~~~l~~~~~~i~~~~~~r~~~~~~~~~~~~~~~~~------------~~~~~~~~~~~~~~~~~~~~~~  165 (281)
                      ..  .---++.++.+++.++++-+  ++|  ++..+++|+..-..-            ..+++.+.+.-........+.+
T Consensus        89 lly~~~~~tGa~~~Ir~~~~~is~--D~r--vQ~liIaw~Fg~flEGaaGFGTPvAI~AplLvaLGF~pl~Aa~i~LI~n  164 (551)
T PRK10420         89 FVYKISVKTGQFDIIRSSILSITP--DQR--LQMLIVGFCFGAFLEGAAGFGAPVAITAALLVGLGFKPLYAAGLCLIVN  164 (551)
T ss_pred             HHHHHHHHHCCHHHHHHHHHHCCC--CHH--HHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHCCCCHHHHHHHHHHHC
T ss_conf             999999992979999999984499--678--9999999999999987514677199999999986997699999999870


Q ss_pred             H----------------CCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             1----------------465210799999999999999999999999840577767521012218999999999999999
Q gi|254780367|r  166 F----------------FPALGNLLLIIWNGRIYATMLALFIGLIFVHLFLPAAKSKIMSILPGVIFTWISWVVGAVLFT  229 (281)
Q Consensus       166 ~----------------~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~y~~~P~~~~~~~~~~~Ga~~a~v~~~~~~~~f~  229 (281)
                      .                .....+...........++++.....+..++..  +.....|+.+|-++++++.+.+.++...
T Consensus       165 s~pvsFGAvGtPi~~~a~~~gl~~~~l~~~~~~~lp~~~~~i~~~~~~~~--~g~k~~~~~~p~~L~~g~~f~~~~~l~a  242 (551)
T PRK10420        165 TAPVAFGAMGIPILVAGQVTGIDSFEIGQMVGRQLPFLTIIVLFWIMAIM--DGWRGVKETWPAVVVAGGSFAIAQYLSS  242 (551)
T ss_pred             CCCCCCHHHHHHHHHHCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHH--HHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             68762031020343101006988899999999999999999999999995--2178788877999999999999999999


Q ss_pred             HHHHHHCCHHHHHHHHHHHHHHH
Q ss_conf             99986522246789999999999
Q gi|254780367|r  230 HYIVTFSTYSTMYAGLASIMTCL  252 (281)
Q Consensus       230 ~y~~~~~~~~~~YGsl~~ii~ll  252 (281)
                      .|+..  ....+-|++-++....
T Consensus       243 ~~~g~--elp~iig~lv~l~~~~  263 (551)
T PRK10420        243 NFIGP--ELPDIISSLVSLVCLT  263 (551)
T ss_pred             HHCCH--HHHHHHHHHHHHHHHH
T ss_conf             97150--0889999999999999


No 13 
>pfam10225 DUF2215 Uncharacterized conserved protein (DUF2215). This entry is the central 200 residues of a family of proteins conserved from worms to humans. The function is unknown.
Probab=23.78  E-value=44  Score=13.01  Aligned_cols=23  Identities=22%  Similarity=0.167  Sum_probs=9.7

Q ss_pred             HHHHHCCHHHHHHHHHHHHHHHH
Q ss_conf             99985578768899999999999
Q gi|254780367|r   17 EHFVEEDGWAMASHISLSALLSV   39 (281)
Q Consensus        17 ~~~~~~~~~~~Aaalaf~~llsl   39 (281)
                      .+..++-.+++.++.+.=.++++
T Consensus        28 ~~LS~s~~FYY~sgi~lGv~asl   50 (247)
T pfam10225        28 PLLSRSVLFYYSSGIALGVLASL   50 (247)
T ss_pred             HHHCCCHHHHHHHHHHHHHHHHH
T ss_conf             98716718999988999999999


No 14 
>TIGR00930 2a30 K-Cl cotransporter; InterPro: IPR004842 This is a family of K-Cl cotransporters. It includes bumetanide-sensitive sodium-(potassium)-chloride cotransporter, an electrically silent transporter system which is a mediator of sodium and chloride reabsorption. It plays a vital role in the regulation of ionic balance and cell volume. Bumetanide-sensitive sodium-(potassium)-chloride cotransporter belongs to the SLC12A family of transporters.; GO: 0015377 cation:chloride symporter activity, 0006814 sodium ion transport, 0006821 chloride transport, 0016021 integral to membrane.
Probab=22.48  E-value=47  Score=12.88  Aligned_cols=129  Identities=16%  Similarity=0.091  Sum_probs=66.1

Q ss_pred             HHHHHHHHHHHHHHHHHH-HH---HHHHCCCCCCC--HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCC
Q ss_conf             999999999999999999-99---86302366630--3676799999999999999999999999999999997414652
Q gi|254780367|r   97 SALAAAYFSSNGVEALRI-SL---NRAYRVVEMRS--WYITRLISFGYVLLASVTLVIMSFVFVAIPLALAYVRKFFPAL  170 (281)
Q Consensus        97 ~~~~~l~~as~~~~~l~~-~~---~~i~~~~~~r~--~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  170 (281)
                      +++..|.+|-+.++++-+ -+   =+.|++.+.++  +.+..    +++....+..++..                  .+
T Consensus       511 ~AL~sL~sAPrllQAl~~D~I~P~L~~F~~g~gkn~EP~~ay----lLT~~Ia~~filIA------------------~L  568 (1171)
T TIGR00930       511 SALASLVSAPRLLQALCKDNIYPLLQFFGKGYGKNGEPLRAY----LLTFFIALLFILIA------------------EL  568 (1171)
T ss_pred             HHHHHHHHHHHHHHHHHCCCCCCHHHCCCCCCCCCCCCHHHH----HHHHHHHHHHHHHH------------------CC
T ss_conf             888876559999999710572241320465778788727989----99999987876552------------------11


Q ss_pred             CCHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCH-HHHHHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHH
Q ss_conf             10799999999999999999999999840577767521-01221899999999999999999986522246789999999
Q gi|254780367|r  171 GNLLLIIWNGRIYATMLALFIGLIFVHLFLPAAKSKIM-SILPGVIFTWISWVVGAVLFTHYIVTFSTYSTMYAGLASIM  249 (281)
Q Consensus       171 ~~~~~~~~~~~~~~~~l~~~~~~~~~y~~~P~~~~~~~-~~~~Ga~~a~v~~~~~~~~f~~y~~~~~~~~~~YGsl~~ii  249 (281)
                      ....+++.+....--.++.+..|..-+--.|+-|++|| +-++-|++.+++....-.+.+||.+-+          +.++
T Consensus       569 n~iAPiiSnFFL~sYaliNfscF~~~l~~~PgWRP~F~yY~~~lSl~Ga~lC~~iMFl~~W~~alv----------a~~i  638 (1171)
T TIGR00930       569 NTIAPIISNFFLASYALINFSCFHASLLRSPGWRPRFRYYNWWLSLLGAILCVAIMFLISWWAALV----------AIVI  638 (1171)
T ss_pred             CCCCHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH----------HHHH
T ss_conf             211226788999999999999999998528888865167879999999999999999999999999----------9999


Q ss_pred             HHHHHHHH
Q ss_conf             99999999
Q gi|254780367|r  250 TCLVFLYM  257 (281)
Q Consensus       250 ~lllWly~  257 (281)
                      ++++..|.
T Consensus       639 ~~~lY~Yv  646 (1171)
T TIGR00930       639 ALLLYKYV  646 (1171)
T ss_pred             HHHHHHHH
T ss_conf             99987773


No 15 
>TIGR02186 alph_Pro_TM conserved hypothetical protein; InterPro: IPR011734   This family consists of predicted transmembrane proteins of about 270 amino acids. Members are found, so far, only among the Alphaproteobacteria and only once in each genome..
Probab=21.53  E-value=27  Score=14.01  Aligned_cols=44  Identities=14%  Similarity=0.249  Sum_probs=32.0

Q ss_pred             HHH-HHHHH--HHHHHHHHHHHHHHHHHHCCHHH-HHHHHHHHHHHHH
Q ss_conf             122-18999--99999999999999986522246-7899999999999
Q gi|254780367|r  210 ILP-GVIFT--WISWVVGAVLFTHYIVTFSTYST-MYAGLASIMTCLV  253 (281)
Q Consensus       210 ~~~-Ga~~a--~v~~~~~~~~f~~y~~~~~~~~~-~YGsl~~ii~lll  253 (281)
                      ++. |.+++  ...+++.|.|+-..+.+.++-+. +||.+++.++++.
T Consensus       217 LF~~G~Fi~~~~~~L~iVK~GlEQ~v~~aAhq~~L~YGl~av~LA~~T  264 (275)
T TIGR02186       217 LFRDGVFIAEKELALEIVKTGLEQAVTTAAHQNPLIYGLLAVLLAVVT  264 (275)
T ss_pred             EECCCCCHHHHCCCCEEEEECCHHHHHHHHHCCCHHHHHHHHHHHHHH
T ss_conf             805870035322773178745327887665117338999999999861


Done!