Query         gi|254780396|ref|YP_003064809.1| peptidyl-prolyl cis-trans isomerase protein [Candidatus Liberibacter asiaticus str. psy62]
Match_columns 317
No_of_seqs    145 out of 3262
Neff          10.2
Searched_HMMs 39220
Date          Sun May 29 20:14:26 2011
Command       /home/congqian_1/programs/hhpred/hhsearch -i 254780396.hhm -d /home/congqian_1/database/cdd/Cdd.hhm 

 No Hit                             Prob E-value P-value  Score    SS Cols Query HMM  Template HMM
  1 PRK10770 peptidyl-prolyl cis-t 100.0       0       0  314.2  29.2  299   15-317     3-426 (428)
  2 PRK00059 prsA peptidylprolyl i 100.0       0       0  313.8  27.7  292   14-317     5-331 (336)
  3 PRK10788 peptidyl-prolyl cis-t 100.0 2.2E-40 5.6E-45  274.5  25.9  310    1-311     1-394 (622)
  4 PRK03002 prsA peptidylprolyl i 100.0 6.7E-35 1.7E-39  239.7  25.3  242   35-316    22-268 (285)
  5 PRK04405 prsA peptidylprolyl i 100.0 3.2E-33 8.2E-38  229.1  25.6  271   10-316     2-279 (298)
  6 PRK02998 prsA peptidylprolyl i 100.0 8.9E-33 2.3E-37  226.3  25.6  237   40-316    25-268 (283)
  7 PRK03095 prsA peptidylprolyl i 100.0 8.7E-33 2.2E-37  226.4  25.1  239   38-316    22-265 (287)
  8 PRK01326 prsA foldase protein  100.0 7.2E-28 1.8E-32  195.2  24.4  251   35-316    22-283 (310)
  9 PRK12450 foldase protein PrsA; 100.0 4.5E-27 1.2E-31  190.2  25.3  250   37-316    26-286 (309)
 10 pfam09312 SurA_N SurA N-termin  99.8 3.2E-19 8.1E-24  140.5  12.6  108   40-147     2-117 (118)
 11 TIGR02933 nifM_nitrog nitrogen  99.8 2.4E-18 6.1E-23  134.9  16.4  228   80-308    35-269 (270)
 12 COG0760 SurA Parvulin-like pep  99.8 8.2E-17 2.1E-21  125.2  19.9  272   38-316    24-312 (320)
 13 PRK10770 peptidyl-prolyl cis-t  99.7 3.9E-17 9.9E-22  127.3  10.7  172  108-279    82-277 (428)
 14 TIGR02925 cis_trans_EpsD pepti  99.7 4.2E-15 1.1E-19  114.4  17.7  222   18-279     4-233 (236)
 15 pfam00639 Rotamase PPIC-type P  99.4 3.2E-13 8.3E-18  102.5   6.9   92  182-274     1-95  (95)
 16 KOG3259 consensus               99.0 3.9E-10   1E-14   82.9   4.7   68  206-273    94-162 (163)
 17 KOG3258 consensus               98.6 5.8E-08 1.5E-12   69.2   4.8   90  175-276    37-133 (133)
 18 PRK10788 peptidyl-prolyl cis-t  97.7 0.00087 2.2E-08   42.8  10.4   59  252-310   447-508 (622)
 19 pfam05698 Trigger_C Bacterial   96.2   0.067 1.7E-06   30.8   9.0  100   76-175    20-128 (162)
 20 PRK01490 tig trigger factor; P  95.3    0.21 5.3E-06   27.7   9.4   21  238-258   190-211 (435)
 21 COG0544 Tig FKBP-type peptidyl  78.2     4.6 0.00012   19.2   9.5   32  237-268   189-222 (441)
 22 PRK00315 potassium-transportin  49.0      17 0.00043   15.6  11.0   57    1-57      1-57  (195)
 23 COG4856 Uncharacterized protei  34.2      20 0.00051   15.1   1.3   28    3-31      2-29  (403)
 24 PRK03147 thiol-disulfide oxido  33.0      24 0.00061   14.6   1.5   16   42-57     46-61  (176)
 25 PRK11281 potassium efflux prot  32.8      30 0.00078   14.0   7.0   22   47-68     30-51  (1107)
 26 pfam07076 DUF1344 Protein of u  31.7      24 0.00061   14.7   1.3   27   29-55     15-43  (81)
 27 PRK06437 hypothetical protein;  29.2      28 0.00072   14.2   1.3   19   37-55     32-50  (67)
 28 TIGR00115 tig trigger factor;   28.7      36 0.00091   13.6   9.6  105   74-178   309-425 (475)
 29 PRK10626 hypothetical protein;  28.6      36 0.00091   13.6   7.8   70   43-112    55-137 (239)
 30 TIGR01439 lp_hng_hel_AbrB tran  26.1      40   0.001   13.3   2.9   30  242-271    12-42  (44)
 31 smart00342 HTH_ARAC helix_turn  25.5      41   0.001   13.2   4.6   42  106-147     4-46  (84)
 32 COG2104 ThiS Sulfur transfer p  24.2      43  0.0011   13.1   2.4   22   38-59     30-51  (68)
 33 pfam02669 KdpC K+-transporting  23.4      45  0.0011   13.0   8.4   53    4-56      3-55  (188)
 34 pfam02682 AHS1 Allophanate hyd  22.9      28 0.00071   14.2   0.4   19  255-273   167-187 (202)

No 1  
>PRK10770 peptidyl-prolyl cis-trans isomerase SurA; Provisional
Probab=100.00  E-value=0  Score=314.21  Aligned_cols=299  Identities=14%  Similarity=0.213  Sum_probs=240.0

Q ss_pred             HHHHHHHHHHHHHHHHHCCCCCCCCCCEEEEECCEECCHHHHHHHHHHHHHHC--------CHHHHHHHHHHHHHHHHHH
Q ss_conf             99999999999999984023211348269998867868899999999987303--------5035999999999999999
Q gi|254780396|r   15 LLTTYFVLIIFCIVPIVSYKSWAMSSRIRTTINGEVITDGDISKRIALLKLQK--------INGELEKIAVQELIVETLK   86 (317)
Q Consensus        15 ~~~~~~~~~~~~~~~~~~~~~~~~~~~vvA~Vng~~It~~e~~~~~~~~~~~~--------~~~~~~~~~l~~LI~~~l~   86 (317)
                      .++.+++.++++..+.  ++.+...|+|||+|||++||.+||++++.....+.        ....+++++|++||+++|+
T Consensus         3 ~~~~~~~~~~~~~~~~--~a~~~~iD~IvAvVn~~iIl~sdl~~~~~~~~~~~~~~~~~~p~~~~Lr~qvLd~LI~e~Ll   80 (428)
T PRK10770          3 NWKTLLLGIAMIANTS--FAAPQVVDKVAAVVNNGVVLESDVDGLMQSVKLNAQQAGQQLPDDATLRHQILERLIMDQII   80 (428)
T ss_pred             HHHHHHHHHHHHHHHH--HHHHHHCCCEEEEECCCCCCHHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHHHHHHH
T ss_conf             3999999999998475--54055338279999990544999999999999999855899996689999999999999999


Q ss_pred             HHHHHHCCCCCCHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCHHHHHHH
Q ss_conf             86420012234445668999999973134303567777653112455469999998999999998432035558999864
Q gi|254780396|r   87 KQEIEKSGITFDSNTVNYFFVQHARNTGLSAEDFSSFLDKQGIGDNHFKQYLAIQSIWPDVVKNDFMLKYGNLEMEIPAN  166 (317)
Q Consensus        87 ~~~a~~~~i~v~~~~i~~~i~~~~~~~~~~~~~~~~~l~~~g~t~~~~~~~i~~~l~~~~~~~~~~~~~i~~~~~e~~~~  166 (317)
                      .|+|+++|+.+++++|++.+..++++++++.++|.+.|..+|+++..|++.++.+++|+++.+..+.+++.+++.|+..+
T Consensus        81 ~Q~A~~~gi~Vsd~evd~~i~~ia~~~~~s~~q~~~~L~~~G~s~~~~r~~ir~ell~~~l~~~~v~~~i~Vs~~Ev~~~  160 (428)
T PRK10770         81 LQMGQKMGVKISDEQLDQAIANIAKQNNMTLDQMRSRLAYDGLNYNTYRNQIRKEMIISEVRNNEVRRRITILPQEVESL  160 (428)
T ss_pred             HHHHHHCCCCCCHHHHHHHHHHHHHHCCCCHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHH
T ss_conf             99999839986999999999999987488799999999976997899999999999999999998650102478999999


Q ss_pred             HHHHHHHC--CC--------------------------------------------------------------------
Q ss_conf             43211100--11--------------------------------------------------------------------
Q gi|254780396|r  167 KQKMKNIT--VR--------------------------------------------------------------------  176 (317)
Q Consensus       167 ~~~~~~~~--~~--------------------------------------------------------------------  176 (317)
                      +.......  ..                                                                    
T Consensus       161 ~~~~~~~~~~~~e~~l~~Ili~~~~~~~~~~~~~~~~~a~~i~~~i~~G~dF~~lA~~~S~~~~a~~GGdlGw~~~~~lp  240 (428)
T PRK10770        161 AKQIGNQNDASTELNLSHILIPLPENPTSDQVNEAESQARSIVDQARNGADFGKLAIAYSADQQALKGGQMGWGRIQELP  240 (428)
T ss_pred             HHHHHHHCCCCCCEEEEEEEEECCCCCCHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHCCCCHHHCCCCCCCCCCCCCH
T ss_conf             99866422688617899999737888899999999999999999987589989999982657101116864421122130


Q ss_pred             -------------------------------------------CHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHHHHHH-
Q ss_conf             -------------------------------------------002333221024675444799998643578865223-
Q gi|254780396|r  177 -------------------------------------------EYLIRTVLFSIPDNKLQNQGFVQKRIKDAEESRLRL-  212 (317)
Q Consensus       177 -------------------------------------------~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-  212 (317)
                                                                 ++..+||++.+.  ....++.....+.........+ 
T Consensus       241 ~~f~~a~~~l~~Geis~pi~s~~G~HIikl~d~r~~~~~~~~~e~~~rHILi~~~--~~~~~~~a~~~l~~i~~~i~~g~  318 (428)
T PRK10770        241 GIFAQALSTAKKGDIVGPIRSGVGFHILKVNDLRGASQNISVTEVHARHILLKPS--PIMTDEQARAKLEQIAADIKSGK  318 (428)
T ss_pred             HHHHHHHHHCCCCCCCCCEECCCCEEEEEEHHHHCCCCCCCHHHHHHHHHHCCCC--CCCCHHHHHHHHHHHHHHHHCCC
T ss_conf             7899999716898723536417835999724432566541055576667633788--66575999999999999987675


Q ss_pred             HHHHHHHHHHHCCC-CCCCCCCCCCCCHHHCCHHHHHH-CCCCCCCCCCCEEECCEEEEEEEECCCCC-CCCHHHHHHHH
Q ss_conf             32489999852013-22568746752755613676651-12457880123763894899998223578-84457899999
Q gi|254780396|r  213 PKDCNKLEKFASKI-HDVSIGKAQYLLESDLHPQFQNL-LKKSQNNTTNPYVTQKGVEYIAICDKRDL-GGEIALKAYLS  289 (317)
Q Consensus       213 ~~~~~~~~~~~~~~-~~~~~g~lg~~~~~~l~~~~~~~-~~~~~G~is~pv~t~~G~hiikv~~~r~~-~~~~~~~~~i~  289 (317)
                      .+|+..++.+|..+ |+..||+|||+..+.++|.|+.+ +++++|++|+||+|++|||||+|+++|.. ......++.++
T Consensus       319 ~~F~~~A~~~S~D~~Sa~~GGdLgw~~~~~~~p~f~~~~~~l~~GeiS~Pv~t~~G~hii~l~~~R~~d~~~~~~r~~~~  398 (428)
T PRK10770        319 TTFAAAAKEFSQDPGSANQGGDLGWATPDIFDPAFRDALTRLNKGQISAPVHSSFGWHLIELLDTRQVDKTDAAQKDRAY  398 (428)
T ss_pred             CCHHHHHHHHCCCCCHHHCCCCCCCCCCCCCCHHHHHHHHCCCCCCCCCCEECCCEEEEEEEEEECCCCCCCHHHHHHHH
T ss_conf             57999999862795245428836777845479789999970899991656665870699999840367864255899999


Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHCCCCCC
Q ss_conf             9999999999999999999975477509
Q gi|254780396|r  290 AQNTPTKIEKHEAEYVKKLRSNAIIHYY  317 (317)
Q Consensus       290 ~~l~~~~~~~~~~~~l~~Lr~~A~I~~f  317 (317)
                      +.|.+++.++.++.|+.+||+.|+|+++
T Consensus       399 ~~l~~~k~~~~~~~wl~~lR~~ayI~I~  426 (428)
T PRK10770        399 RMLFNRKFSEEAATWMQEQRASAYVKIL  426 (428)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHEEEEEC
T ss_conf             9999999999999999999851179740


No 2  
>PRK00059 prsA peptidylprolyl isomerase; Provisional
Probab=100.00  E-value=0  Score=313.78  Aligned_cols=292  Identities=15%  Similarity=0.161  Sum_probs=230.4

Q ss_pred             HHHHHHHHHHHHHHHHHHCC----CCCCCCCCEEEEECCEECCHHHHHHHHHHHH------HHC------------CHHH
Q ss_conf             99999999999999998402----3211348269998867868899999999987------303------------5035
Q gi|254780396|r   14 KLLTTYFVLIIFCIVPIVSY----KSWAMSSRIRTTINGEVITDGDISKRIALLK------LQK------------INGE   71 (317)
Q Consensus        14 ~~~~~~~~~~~~~~~~~~~~----~~~~~~~~vvA~Vng~~It~~e~~~~~~~~~------~~~------------~~~~   71 (317)
                      +.+.+.+++++|++++++|+    +.....+.+||+|||++||..|+++.+...+      .+.            ....
T Consensus         5 ~ki~~~~ii~~~~~~~vg~~~~~~~~~~~~~~~VA~Vng~~It~~e~~~~~~~~~~~~~l~~q~g~~~~~~~~~~~~~~~   84 (336)
T PRK00059          5 KKIVASLLVGVFIFSAVGCNMVEKTPEAIAKTTVATVGGEKITRGDLDSDPSMKQVLEQLKSQYGDKYEKNEQVKEQLKQ   84 (336)
T ss_pred             HHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCEEEEECCEECCHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCHHHHHHH
T ss_conf             99999999999999983025334676677896489899998489999999999999999998743013557001899999


Q ss_pred             HHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHH----HHHHHCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             999999999999999864200122344456689999----9997313430356777765311245546999999899999
Q gi|254780396|r   72 LEKIAVQELIVETLKKQEIEKSGITFDSNTVNYFFV----QHARNTGLSAEDFSSFLDKQGIGDNHFKQYLAIQSIWPDV  147 (317)
Q Consensus        72 ~~~~~l~~LI~~~l~~~~a~~~~i~v~~~~i~~~i~----~~~~~~~~~~~~~~~~l~~~g~t~~~~~~~i~~~l~~~~~  147 (317)
                      +|+++|++||++.|+.++|+++|+.+++++|++.+.    .+...++++.+.|.+.|..+|+|+..|++.++.+++.+++
T Consensus        85 ~r~qvL~~LI~~~Ll~q~A~~~gl~vsd~ev~~~I~~~~~~~~~~g~f~~~~y~~~L~~~g~t~~~~~~~~r~~l~~~~l  164 (336)
T PRK00059         85 QKKQILESLITEKVLLQKAKELKLIPSDEELNKEVDKQVNEIKKQYNNDEEKFEEALKQTGFTEETFKEYLKNQIIIEKV  164 (336)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHH
T ss_conf             99999999999999999999869984999999999999999988379999999999998699999999999999999999


Q ss_pred             HHHHHHHHCCCCHHHHHHHHHHHHHHCC---CCHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHC
Q ss_conf             9998432035558999864432111001---1002333221024675444799998643578865223324899998520
Q gi|254780396|r  148 VKNDFMLKYGNLEMEIPANKQKMKNITV---REYLIRTVLFSIPDNKLQNQGFVQKRIKDAEESRLRLPKDCNKLEKFAS  224 (317)
Q Consensus       148 ~~~~~~~~i~~~~~e~~~~~~~~~~~~~---~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  224 (317)
                      .. .+.+.+.+|+.|+..||+.+...+.   ..+.++|+++...       +..    .........+.++...+..+|.
T Consensus       165 ~~-~v~~~v~Vsd~Ei~~yY~~nk~~f~~~p~~~~~~~Il~~~~-------~~A----~~i~~~l~~G~dF~~lAk~~S~  232 (336)
T PRK00059        165 IN-EVVKDVKVTDKDAQKYYDENKSTFTEKPNTVHLSHILVKTE-------EEA----KKVKKRLDKGEDFAKVAKEVSQ  232 (336)
T ss_pred             HH-HHHCCCCCCHHHHHHHHHHHHHHHCCCCCEEEEEEEEECCH-------HHH----HHHHHHHHCCCCHHHHHHHHCC
T ss_conf             99-97456865889999999997887337866588998887899-------999----9999998779988999998489


Q ss_pred             CC-CCCCCCCCCCC--CHHHCCHHHHH-HCCCCCCCCCCCEEECCEEEEEEEECCCCCC--CCHHHHHHHHHHHHHHHHH
Q ss_conf             13-22568746752--75561367665-1124578801237638948999982235788--4457899999999999999
Q gi|254780396|r  225 KI-HDVSIGKAQYL--LESDLHPQFQN-LLKKSQNNTTNPYVTQKGVEYIAICDKRDLG--GEIALKAYLSAQNTPTKIE  298 (317)
Q Consensus       225 ~~-~~~~~g~lg~~--~~~~l~~~~~~-~~~~~~G~is~pv~t~~G~hiikv~~~r~~~--~~~~~~~~i~~~l~~~~~~  298 (317)
                      ++ +...||++||+  ..+.+||.|.+ ++.+++|++|+||+|++|||||+|.+++|..  +++.++++|++.|.+++.+
T Consensus       233 D~~s~~~gGdLG~~~~~~~~~~~~f~~a~f~Lk~GeiS~pV~t~~GyhIIkl~~~~~~~~~~feevk~~I~~~L~~qK~~  312 (336)
T PRK00059        233 DPGSKDKGGDLGDVPYSDSNYDKEFMDAAKALKEGEISAPVKTQFGYHIIKAIKKKEYPVKPFDSVKEQIKKQLLQEKQS  312 (336)
T ss_pred             CCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHCCCCCCCCCEEECCEEEEEEEEEECCCCCCCHHHHHHHHHHHHHHHHHH
T ss_conf             95310148866640267665566899999745688868860668867999997215788999999999999999999999


Q ss_pred             HHHHHHHHHHHHHCCCCCC
Q ss_conf             9999999999975477509
Q gi|254780396|r  299 KHEAEYVKKLRSNAIIHYY  317 (317)
Q Consensus       299 ~~~~~~l~~Lr~~A~I~~f  317 (317)
                      +.+.+|+++||++|+|++|
T Consensus       313 ~~~~e~~~~l~~~a~I~i~  331 (336)
T PRK00059        313 EVFKKKIEEWKKDLKVKVY  331 (336)
T ss_pred             HHHHHHHHHHHHHCCEEEC
T ss_conf             9999999999973780754


No 3  
>PRK10788 peptidyl-prolyl cis-trans isomerase (rotamase D); Provisional
Probab=100.00  E-value=2.2e-40  Score=274.45  Aligned_cols=310  Identities=13%  Similarity=0.131  Sum_probs=235.3

Q ss_pred             CHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCEEEEECCEECCHHHHHHHHHHH----HHHCC--------
Q ss_conf             957999999999999999999999999998402321134826999886786889999999998----73035--------
Q gi|254780396|r    1 MTSKVFTSLSDFIKLLTTYFVLIIFCIVPIVSYKSWAMSSRIRTTINGEVITDGDISKRIALL----KLQKI--------   68 (317)
Q Consensus         1 ~~~~~~~~~~~fi~~~~~~~~~~~~~~~~~~~~~~~~~~~~vvA~Vng~~It~~e~~~~~~~~----~~~~~--------   68 (317)
                      |++.++...+.++.++.+.++++.|+++|+.++... ..+++||+|||++||..|+++.+...    ..+..        
T Consensus         1 ML~~iR~~~~~~~~killgliil~Fv~~Gv~~~~~~-~~~~~va~Vng~~Is~~e~~~~~~~~~~~~~~~~G~~~~~~~~   79 (622)
T PRK10788          1 MMDNLRTAANSVVLKIILGLIILSFILTGVGGYLIG-GSNNYAAKVNGQEISRAQLEQAFQSERNRMQQQLGDQFSELAA   79 (622)
T ss_pred             CHHHHHHHCCCHHHHHHHHHHHHHHHHHCCCCCCCC-CCCCEEEEECCEECCHHHHHHHHHHHHHHHHHHHCCCCCCCCC
T ss_conf             928886166098999999999999998224523658-9997489999998489999999999999999872755661121


Q ss_pred             ----HHHHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHH---HHHCCCCCHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             ----03599999999999999986420012234445668999999---97313430356777765311245546999999
Q gi|254780396|r   69 ----NGELEKIAVQELIVETLKKQEIEKSGITFDSNTVNYFFVQH---ARNTGLSAEDFSSFLDKQGIGDNHFKQYLAIQ  141 (317)
Q Consensus        69 ----~~~~~~~~l~~LI~~~l~~~~a~~~~i~v~~~~i~~~i~~~---~~~~~~~~~~~~~~l~~~g~t~~~~~~~i~~~  141 (317)
                          ...+++++|++||++.|+.++|+++|+.++++++.+.|..+   ...+.++.+.|.++|..+|+|+..|.+.+|.+
T Consensus        80 ~e~~~~~l~~qvl~~LI~~~lL~q~A~~lGl~vsd~~v~~~I~~~p~Fq~~G~Fd~~~y~~~L~~~g~t~~~f~~~~r~~  159 (622)
T PRK10788         80 NEGYMKQLRQQVLNRLIDEALLDQYARELGLGISDEQVKQAIFATPAFQTDGKFDNNRYNAILNQMGMTADQYAQALRNQ  159 (622)
T ss_pred             CHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHCCCCCCCCCCCHHHHHHHHHHCCCCHHHHHHHHHHH
T ss_conf             35689999999999999999999999986998799999999984856432699599999999997599999999999999


Q ss_pred             HHHHHHHHHH---------------------------------HHHHCCCCHHHHHHHHHHHHHHCCCCHHHHHHHHHCC
Q ss_conf             8999999998---------------------------------4320355589998644321110011002333221024
Q gi|254780396|r  142 SIWPDVVKND---------------------------------FMLKYGNLEMEIPANKQKMKNITVREYLIRTVLFSIP  188 (317)
Q Consensus       142 l~~~~~~~~~---------------------------------~~~~i~~~~~e~~~~~~~~~~~~~~~~~~~~~~~~~~  188 (317)
                      +..+++....                                 +...+.+++.++..||+.+...+..+...+...+.+.
T Consensus       160 l~~~ql~~~i~~~~~~~~~e~~~~~~~~~q~R~v~~~~i~~~~~~~~~~vtd~el~~yY~~nk~~f~~pe~~~i~yv~l~  239 (622)
T PRK10788        160 LTTQQLINGVAGTDFMLPGETDELAALVLQQRVVREATIDVNALAAKQTVTDQEIQSYYDQNKNNFMAPEQFRVSYIKLD  239 (622)
T ss_pred             HHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHEEEEEEECHHHHCCCCCCCHHHHHHHHHHCHHHHCCCCEEEEEEEEEC
T ss_conf             99999999976426679999999999974211468899746770566899999999999956554068634888999835


Q ss_pred             CCC---CCCHHHHH--------------------------HHHHHHHHHHHHHHHHHHHHHHHHCCC-CCCCCCCCCCCC
Q ss_conf             675---44479999--------------------------864357886522332489999852013-225687467527
Q gi|254780396|r  189 DNK---LQNQGFVQ--------------------------KRIKDAEESRLRLPKDCNKLEKFASKI-HDVSIGKAQYLL  238 (317)
Q Consensus       189 ~~~---~~~~~~~~--------------------------~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~g~lg~~~  238 (317)
                      ...   ...++.+.                          ............+.+|+..++.+|.++ +...||+|||++
T Consensus       240 ~~~~~~~vs~~ei~~~Y~~~~~~~~~pe~r~~~~I~~~~~~~A~~~~~~l~~G~dFa~lA~~~S~D~~Sa~~gGdLG~~~  319 (622)
T PRK10788        240 AATMQQTVSDADIQAYYDQHQDQFTQPERKRYSIIQTKTEDEAKAVLDELKKGADFATLAKEKSTDIISARNGGDMGWLE  319 (622)
T ss_pred             HHHHCCCCCHHHHHHHHHHHHHHCCCCHHEEEEEEECCCHHHHHHHHHHHHCCCCHHHHHHHHCCCCCCCCCCCCCCCCC
T ss_conf             66702458999999999987775177411664301058999999999998769986999998378953212477313426


Q ss_pred             HHHCCHHHHHHCCCCCCCCCCCEEECCEEEEEEEECCCCC--CCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             5561367665112457880123763894899998223578--844578999999999999999999999999975
Q gi|254780396|r  239 ESDLHPQFQNLLKKSQNNTTNPYVTQKGVEYIAICDKRDL--GGEIALKAYLSAQNTPTKIEKHEAEYVKKLRSN  311 (317)
Q Consensus       239 ~~~l~~~~~~~~~~~~G~is~pv~t~~G~hiikv~~~r~~--~~~~~~~~~i~~~l~~~~~~~~~~~~l~~Lr~~  311 (317)
                      ++.+||.|+++....+|++|+||+|++|||||+|++.+|.  .+++.++++|+..|..++..+.+.+..+++.+.
T Consensus       320 ~g~~~~~f~~a~~~~~GevS~pV~t~fG~hiikv~~i~~~~~~~~eevk~eI~~~l~~~~a~~~~~~~~~~~~d~  394 (622)
T PRK10788        320 DATTPDELKNAGLKEKGQLSGVIKSSVGFLIVRLDDIQPAKVKPLSEVRDDIAAKVKQEKALDAYYALQQKVSDA  394 (622)
T ss_pred             CCCCHHHHHHHHHHCCCCCCCCEEECCCEEEEEEECCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             664428999988746798678476078238999832466778998999999999999999999999999999887


No 4  
>PRK03002 prsA peptidylprolyl isomerase; Reviewed
Probab=100.00  E-value=6.7e-35  Score=239.73  Aligned_cols=242  Identities=16%  Similarity=0.219  Sum_probs=195.6

Q ss_pred             CCCCCCCEEEEECCEECCHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHCC
Q ss_conf             21134826999886786889999999998730350359999999999999998642001223444566899999997313
Q gi|254780396|r   35 SWAMSSRIRTTINGEVITDGDISKRIALLKLQKINGELEKIAVQELIVETLKKQEIEKSGITFDSNTVNYFFVQHARNTG  114 (317)
Q Consensus        35 ~~~~~~~vvA~Vng~~It~~e~~~~~~~~~~~~~~~~~~~~~l~~LI~~~l~~~~a~~~~i~v~~~~i~~~i~~~~~~~~  114 (317)
                      +....+.+||+|||..||.+|+.+.+.        ....+++|.+||.+.++.+..     .+++++++.++.....++|
T Consensus        22 ~~~~~~~~VAtv~g~~IT~~df~~~lk--------~~~g~~~l~~mi~~kvl~~~y-----kvs~~ev~~e~~~~k~qyg   88 (285)
T PRK03002         22 GQKNSSATVATATDSTITKSDFEKQLK--------DRYGKDMLYEMMAQDVITKKY-----KVSDDDVDKEVQKAKSQYG   88 (285)
T ss_pred             CCCCCCCEEEEECCCEECHHHHHHHHH--------HHHHHHHHHHHHHHHHHHHHH-----CCCHHHHHHHHHHHHHHHH
T ss_conf             579999779986897873999999999--------887899999999999999861-----2689999999999999987


Q ss_pred             CCCHHHHHHHHHHHHH-HHHHHHHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHCCCCHHHHHHHHHCCCCCCC
Q ss_conf             4303567777653112-455469999998999999998432035558999864432111001100233322102467544
Q gi|254780396|r  115 LSAEDFSSFLDKQGIG-DNHFKQYLAIQSIWPDVVKNDFMLKYGNLEMEIPANKQKMKNITVREYLIRTVLFSIPDNKLQ  193 (317)
Q Consensus       115 ~~~~~~~~~l~~~g~t-~~~~~~~i~~~l~~~~~~~~~~~~~i~~~~~e~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  193 (317)
                         ++|.+.|.++|++ +++|++.++.+++.+..+..      .+++.++..+|.       +...++||++..      
T Consensus        89 ---~~f~~~L~q~glt~e~~~k~qi~~~l~~~~~~k~------~vtd~d~k~~Y~-------pev~~~hIlv~~------  146 (285)
T PRK03002         89 ---DQFKNVLENNGLKDEADFKNQIKFKLAMNEAIKK------SVTEKDVKDHYK-------PEIKASHILVSD------  146 (285)
T ss_pred             ---HHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHC------CCCHHHHHHHCC-------CCEEEEEEEECC------
T ss_conf             ---8999999986997589999999999999999863------288999998618-------763888877789------


Q ss_pred             CHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCC-CCCCCCCCCCCCHHHCCHHHHH-HCCCCCCCCCCCEEECCEEEEEE
Q ss_conf             479999864357886522332489999852013-2256874675275561367665-11245788012376389489999
Q gi|254780396|r  194 NQGFVQKRIKDAEESRLRLPKDCNKLEKFASKI-HDVSIGKAQYLLESDLHPQFQN-LLKKSQNNTTNPYVTQKGVEYIA  271 (317)
Q Consensus       194 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~g~lg~~~~~~l~~~~~~-~~~~~~G~is~pv~t~~G~hiik  271 (317)
                       ++.+.    +.......+.+|...+..+|..+ +...||++||+.++.++|.|.. +|++++|++|+||+|++|||||+
T Consensus       147 -e~~A~----~v~~~l~~G~dF~~lAk~~S~D~~s~~~GG~lg~~~~~~~~~ef~~aaf~L~~GeiS~pv~t~~GyhIIk  221 (285)
T PRK03002        147 -ENEAK----EIKKKLDAGASFEELAKQESQDLLSKEKGGDLGYFNSGRMAPEFETAAYKLKVGQISNPVKSPNGYHIIK  221 (285)
T ss_pred             -HHHHH----HHHHHHHCCCCHHHHHHHHCCCCCHHHCCCCCCCCCCCCCCHHHHHHHHHCCCCCCCCCEEECCEEEEEE
T ss_conf             -99999----9999988799999999996899301004861663589876679999998289988687877478169999


Q ss_pred             EECCCCCCCCHHHHHHHHHHHHHHHHHH--HHHHHHHHHHHHCCCCC
Q ss_conf             8223578844578999999999999999--99999999997547750
Q gi|254780396|r  272 ICDKRDLGGEIALKAYLSAQNTPTKIEK--HEAEYVKKLRSNAIIHY  316 (317)
Q Consensus       272 v~~~r~~~~~~~~~~~i~~~l~~~~~~~--~~~~~l~~Lr~~A~I~~  316 (317)
                      |.++++..++...+++|++.+.+++..+  ..++++.++.++|+|++
T Consensus       222 ~~dk~~~~~~~~~k~~i~~~i~~~k~~d~~~~~~~i~k~~kkanV~i  268 (285)
T PRK03002        222 LTDKKDLKPYDEVKDSIRKNLEEERIADPIFGKKLLQKELKKANIKI  268 (285)
T ss_pred             EEECCCCCCHHHHHHHHHHHHHHHHHHCHHHHHHHHHHHHHHCCCCC
T ss_conf             84168899989999999999999986677999999999998789843


No 5  
>PRK04405 prsA peptidylprolyl isomerase; Provisional
Probab=100.00  E-value=3.2e-33  Score=229.10  Aligned_cols=271  Identities=15%  Similarity=0.147  Sum_probs=207.3

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCEEEEECCEECCHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             99999999999999999999840232113482699988678688999999999873035035999999999999999864
Q gi|254780396|r   10 SDFIKLLTTYFVLIIFCIVPIVSYKSWAMSSRIRTTINGEVITDGDISKRIALLKLQKINGELEKIAVQELIVETLKKQE   89 (317)
Q Consensus        10 ~~fi~~~~~~~~~~~~~~~~~~~~~~~~~~~~vvA~Vng~~It~~e~~~~~~~~~~~~~~~~~~~~~l~~LI~~~l~~~~   89 (317)
                      ..+|+.+.+.+++++.++. +.   +|...+.+||+|||..||..||...+..       .+..+++|.+||..+++.+.
T Consensus         2 ~~~MKK~~l~~~~~~~~l~-La---aCss~~~~Vat~kg~~IT~~e~y~~~k~-------~~~g~~~l~~mi~~kvl~~~   70 (298)
T PRK04405          2 KKKMKKWALAAASAGLLLS-LA---GCSSNNKTVATYKGGKITESQYYKEMKQ-------SSAGKQTLANMIIYRALEKQ   70 (298)
T ss_pred             HHHHHHHHHHHHHHHHHHH-HH---HCCCCCCEEEEECCCCCCHHHHHHHHHC-------CHHHHHHHHHHHHHHHHHHH
T ss_conf             0678999999999999999-98---7179997699863987259999999864-------42367999999999999998


Q ss_pred             HHHCCCCCCHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHH
Q ss_conf             20012234445668999999973134303567777653112455469999998999999998432035558999864432
Q gi|254780396|r   90 IEKSGITFDSNTVNYFFVQHARNTGLSAEDFSSFLDKQGIGDNHFKQYLAIQSIWPDVVKNDFMLKYGNLEMEIPANKQK  169 (317)
Q Consensus        90 a~~~~i~v~~~~i~~~i~~~~~~~~~~~~~~~~~l~~~g~t~~~~~~~i~~~l~~~~~~~~~~~~~i~~~~~e~~~~~~~  169 (317)
                         +|-.|++.+|+..+..+..++|   ++|...|+++|+|++.|++.++.+++.+..+.    ..+.+++.+++.+|..
T Consensus        71 ---yg~kVsdkeV~~~~~~~k~qyg---~~f~~~L~q~g~te~~~K~~ik~~~l~~~a~k----~~~kvTd~~~k~~y~~  140 (298)
T PRK04405         71 ---YGKKVSTKKVNKQYNSYKKQYG---SSFDSVLSQNGMTTSSFKQNLRTNLLSEAALK----DLKKITTAQLKKAWKS  140 (298)
T ss_pred             ---HCCCCCHHHHHHHHHHHHHHHH---HHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHH----HCCCCCHHHHHHHHHH
T ss_conf             ---7460679999999999999971---88999999859987999999999999999998----5489888999999985


Q ss_pred             HHHHCCCCHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCC-CCCCCCCCCCCCC--HHHCCHHH
Q ss_conf             11100110023332210246754447999986435788652233248999985201-3225687467527--55613676
Q gi|254780396|r  170 MKNITVREYLIRTVLFSIPDNKLQNQGFVQKRIKDAEESRLRLPKDCNKLEKFASK-IHDVSIGKAQYLL--ESDLHPQF  246 (317)
Q Consensus       170 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~g~lg~~~--~~~l~~~~  246 (317)
                      +.    +.+.++||++..       ++.+.    +.......+.+|...++.+|.. .+..+||+|||+.  .+.|||+|
T Consensus       141 ~~----p~v~~~hIlv~~-------e~~A~----~v~~~l~~G~dF~~lAk~~S~D~~sk~~GG~Lg~f~~~~~~m~~~f  205 (298)
T PRK04405        141 YQ----PKVTVQHILVSK-------KSTAE----TVIKKLKDGKDFAKLAKKYSTDTATKNKGGKLPAFDSTDTTLDSTF  205 (298)
T ss_pred             CC----CCEEEEEEEECC-------HHHHH----HHHHHHHCCCCHHHHHHHHCCCCCCCCCCCCCCEECCCCCCCCHHH
T ss_conf             49----865889988678-------99999----9999987899789999983889865556862540407998617699


Q ss_pred             HH-HCCCCCCCCC-CCEEECCEEEEEEEECCCCCCCCHHHHHHHHHHHHHHHHHH--HHHHHHHHHHHHCCCCC
Q ss_conf             65-1124578801-23763894899998223578844578999999999999999--99999999997547750
Q gi|254780396|r  247 QN-LLKKSQNNTT-NPYVTQKGVEYIAICDKRDLGGEIALKAYLSAQNTPTKIEK--HEAEYVKKLRSNAIIHY  316 (317)
Q Consensus       247 ~~-~~~~~~G~is-~pv~t~~G~hiikv~~~r~~~~~~~~~~~i~~~l~~~~~~~--~~~~~l~~Lr~~A~I~~  316 (317)
                      ++ +|++++|++| .||+|++|||||++.++++...+...+++|+.++.+++..+  ..++.+.++.++|+|.+
T Consensus       206 ~~aaf~Lk~geis~~PvkT~~GYhIIK~~~~~~k~~~~~~K~~l~~~i~~~k~~D~~~~~~vi~k~lk~anVki  279 (298)
T PRK04405        206 KTAAFKLKNGEYTTTPVKTTYGYEVIKMIKHPAKGKFTDHKKELTKQIYAKWASDSTVMQNVISKVLKKANVSI  279 (298)
T ss_pred             HHHHHCCCCCCCCCCCEECCCCEEEEEEECCCCCCCHHHHHHHHHHHHHHHHHHCHHHHHHHHHHHHHHCCCCC
T ss_conf             99997488998168845216733999983457779889999999999999873087999999999999779871


No 6  
>PRK02998 prsA peptidylprolyl isomerase; Reviewed
Probab=100.00  E-value=8.9e-33  Score=226.29  Aligned_cols=237  Identities=14%  Similarity=0.192  Sum_probs=192.0

Q ss_pred             CCEEEEECCEECCHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHCCCCCHH
Q ss_conf             82699988678688999999999873035035999999999999999864200122344456689999999731343035
Q gi|254780396|r   40 SRIRTTINGEVITDGDISKRIALLKLQKINGELEKIAVQELIVETLKKQEIEKSGITFDSNTVNYFFVQHARNTGLSAED  119 (317)
Q Consensus        40 ~~vvA~Vng~~It~~e~~~~~~~~~~~~~~~~~~~~~l~~LI~~~l~~~~a~~~~i~v~~~~i~~~i~~~~~~~~~~~~~  119 (317)
                      +..||+++|..||.+|+...+..        ...+++|.+||..+++.+.-     .|++.+++..++....+.|   ++
T Consensus        25 ~~~vat~kgg~IT~~e~y~~lk~--------~~g~~~l~~li~~kvl~~~y-----kVsdkev~~~~~~~k~qyG---~~   88 (283)
T PRK02998         25 SDNVVTSKVGNITEKELSKELRQ--------KYGESTLYQMVLSKALLDKY-----KVSDEEAKKQVEEAKDKMG---DN   88 (283)
T ss_pred             CCCEEEECCCCCCHHHHHHHHHH--------HHHHHHHHHHHHHHHHHHHC-----CCCHHHHHHHHHHHHHHHH---HH
T ss_conf             98179843992839999999999--------99999999999999999983-----6889999999999999997---89


Q ss_pred             HHHHHHHHHH-HHHHHHHHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHCCCCHHHHHHHHHCCCCCCCCHHHH
Q ss_conf             6777765311-245546999999899999999843203555899986443211100110023332210246754447999
Q gi|254780396|r  120 FSSFLDKQGI-GDNHFKQYLAIQSIWPDVVKNDFMLKYGNLEMEIPANKQKMKNITVREYLIRTVLFSIPDNKLQNQGFV  198 (317)
Q Consensus       120 ~~~~l~~~g~-t~~~~~~~i~~~l~~~~~~~~~~~~~i~~~~~e~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  198 (317)
                      |...|.++|+ +++.|++.++.+++.++.+.      ..+++.++..+|.       +...++||++..       ++. 
T Consensus        89 F~~~L~q~g~t~e~~~k~~i~~~l~~~~a~k------~~vtd~~~k~~y~-------p~~~~~hIlv~~-------e~~-  147 (283)
T PRK02998         89 FKSTLEQVGLKNEDELKEKMKPEIAFEKAIK------ATVTEKDVKDNYK-------PEMKVSHILVKD-------EKT-  147 (283)
T ss_pred             HHHHHHHCCCCCHHHHHHHHHHHHHHHHHHH------CCCCHHHHHHHCC-------CCEEEEEEEECC-------HHH-
T ss_conf             9999998699828999999999999999875------5188899998649-------864889989898-------999-


Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHCCC-CCCCCCCCCCCCHHHCCHHHHH-HCCCCCCCCCCCEEECCEEEEEEEECCC
Q ss_conf             9864357886522332489999852013-2256874675275561367665-1124578801237638948999982235
Q gi|254780396|r  199 QKRIKDAEESRLRLPKDCNKLEKFASKI-HDVSIGKAQYLLESDLHPQFQN-LLKKSQNNTTNPYVTQKGVEYIAICDKR  276 (317)
Q Consensus       199 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~g~lg~~~~~~l~~~~~~-~~~~~~G~is~pv~t~~G~hiikv~~~r  276 (317)
                         +.+.......+.+|...+..+|..+ +...||++||+..+.++|.|+. +|.+++|++|+||+|++|||||+|.+++
T Consensus       148 ---A~~v~~~L~~G~dF~~lAk~yS~D~~s~~~GG~Lg~~~~g~~~~~f~~Aaf~L~~G~vS~PVkt~~GyHIIkv~dk~  224 (283)
T PRK02998        148 ---AKEVKEKVNNGEDFAALAKQYSEDTGSKEQGGEISGFAPGQTVKEFEEAAYKLDAGQVSEPVKTTYGYHIIKVTDKK  224 (283)
T ss_pred             ---HHHHHHHHHCCCCHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHCCCCCCCCCCEEECCEEEEEEEECCC
T ss_conf             ---99999998779989999999589966443588667679998078999999759999948877878867999980168


Q ss_pred             CCCCCHHHHHHHHHHHHHHHHHHHH----HHHHHHHHHHCCCCC
Q ss_conf             7884457899999999999999999----999999997547750
Q gi|254780396|r  277 DLGGEIALKAYLSAQNTPTKIEKHE----AEYVKKLRSNAIIHY  316 (317)
Q Consensus       277 ~~~~~~~~~~~i~~~l~~~~~~~~~----~~~l~~Lr~~A~I~~  316 (317)
                      +.+++...++.|+.+|.+++.++..    ++.+.++.++|+|.+
T Consensus       225 ~~~~~~~~K~~l~~~i~~~k~~d~~~~~~~~vi~~~lkkanV~i  268 (283)
T PRK02998        225 ELKPFDEVKDSIRKDLEQQRLQDTTGKWKQQVVNDLLKDADIKV  268 (283)
T ss_pred             CCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCC
T ss_conf             89999999999999999999755478999999999998779876


No 7  
>PRK03095 prsA peptidylprolyl isomerase; Reviewed
Probab=100.00  E-value=8.7e-33  Score=226.36  Aligned_cols=239  Identities=14%  Similarity=0.186  Sum_probs=194.3

Q ss_pred             CCCCEEEEECCEECCHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHCCCCC
Q ss_conf             34826999886786889999999998730350359999999999999998642001223444566899999997313430
Q gi|254780396|r   38 MSSRIRTTINGEVITDGDISKRIALLKLQKINGELEKIAVQELIVETLKKQEIEKSGITFDSNTVNYFFVQHARNTGLSA  117 (317)
Q Consensus        38 ~~~~vvA~Vng~~It~~e~~~~~~~~~~~~~~~~~~~~~l~~LI~~~l~~~~a~~~~i~v~~~~i~~~i~~~~~~~~~~~  117 (317)
                      ..+..||+++|..||.+|+...+.        ....+++|.+||.++++.+..     .|++.+|+..++...++.|   
T Consensus        22 ~~~~~vat~kgg~IT~~e~y~~~k--------~~~g~~~l~~mi~~kvl~~~y-----kVsdkeV~~~~~~~k~qyG---   85 (287)
T PRK03095         22 SSSDKIVTSKAGDITKDEFYEQMK--------TQAGKQVLNNMVMEKVLIKNY-----KVEDKEVDKKYDEMKKQYG---   85 (287)
T ss_pred             CCCCEEEEECCCCCCHHHHHHHHH--------HHHHHHHHHHHHHHHHHHHHC-----CCCHHHHHHHHHHHHHHHH---
T ss_conf             998758984698272999999999--------888999999999999999964-----8789999999999999987---


Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHCCCCHHHHHHHHHCCCCCCCCHHH
Q ss_conf             35677776531124554699999989999999984320355589998644321110011002333221024675444799
Q gi|254780396|r  118 EDFSSFLDKQGIGDNHFKQYLAIQSIWPDVVKNDFMLKYGNLEMEIPANKQKMKNITVREYLIRTVLFSIPDNKLQNQGF  197 (317)
Q Consensus       118 ~~~~~~l~~~g~t~~~~~~~i~~~l~~~~~~~~~~~~~i~~~~~e~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  197 (317)
                      ++|...|.++|++++.|++.||.+++.++.+..      .+++.++..+|.       +.+.++||++.       .++.
T Consensus        86 ~~F~~~L~q~glt~e~~K~~ir~~l~~~~a~~~------~itd~e~k~~y~-------p~v~~~hIlv~-------~e~~  145 (287)
T PRK03095         86 DQFDTLLKQQGIKEETLKTGVRAQLAQEKAIEK------TITDKELKENYK-------PEIKASHILVK-------DEAT  145 (287)
T ss_pred             HHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHC------CCCHHHHHHHCC-------CCEEEEEEEEC-------CHHH
T ss_conf             999999998799989999999999999999864------288999998649-------86489998889-------9999


Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHCCC-CCCCCCCCCCCCHHHCCHHHHH-HCCCCCCCCCCCEEECCEEEEEEEECC
Q ss_conf             99864357886522332489999852013-2256874675275561367665-112457880123763894899998223
Q gi|254780396|r  198 VQKRIKDAEESRLRLPKDCNKLEKFASKI-HDVSIGKAQYLLESDLHPQFQN-LLKKSQNNTTNPYVTQKGVEYIAICDK  275 (317)
Q Consensus       198 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~g~lg~~~~~~l~~~~~~-~~~~~~G~is~pv~t~~G~hiikv~~~  275 (317)
                      +.    +.......+.+|...++.+|..+ +...||++||+..+.++|.|+. +|.+++|++|+||+|++|||||+|+++
T Consensus       146 Ak----~i~~~l~~G~dF~~lAk~~S~D~~s~~~GG~lg~~~~~~~~~~f~~aaf~Lk~geiS~Pvkt~~GyhIIk~~~k  221 (287)
T PRK03095        146 AK----KVKEELGQGKSFEELAKQYSEDTGSKEKGGDLGFFGPGKMVKEFEDAAYKLKKDEVSEPVKSQFGYHIIKVTDI  221 (287)
T ss_pred             HH----HHHHHHHCCCCHHHHHHHHCCCCCHHHCCCCCCCCCCCCCHHHHHHHHHCCCCCCCCCCEEECCEEEEEEEEEC
T ss_conf             99----99999987998999999967996502039715657987625999999972899985886760883599998414


Q ss_pred             CCC-CCCHHHHHHHHHHHHHHHHHH--HHHHHHHHHHHHCCCCC
Q ss_conf             578-844578999999999999999--99999999997547750
Q gi|254780396|r  276 RDL-GGEIALKAYLSAQNTPTKIEK--HEAEYVKKLRSNAIIHY  316 (317)
Q Consensus       276 r~~-~~~~~~~~~i~~~l~~~~~~~--~~~~~l~~Lr~~A~I~~  316 (317)
                      ++. .++...+.+|+..|.+++..+  ...+.+.++.++|+|.+
T Consensus       222 ~~k~~~~~~~K~~lk~~i~~~k~~D~~~~~~vi~k~lkkanV~i  265 (287)
T PRK03095        222 KEPEKSFEQSKADIKKELVQKKAQDGEFMNDLMMKEIKKADVKV  265 (287)
T ss_pred             CCCCCCHHHHHHHHHHHHHHHHHHCHHHHHHHHHHHHHHCCCCC
T ss_conf             78899989999999999999986476999999999999779861


No 8  
>PRK01326 prsA foldase protein PrsA; Reviewed
Probab=99.97  E-value=7.2e-28  Score=195.23  Aligned_cols=251  Identities=14%  Similarity=0.163  Sum_probs=191.8

Q ss_pred             CCCCCCCEEEEECCEECCHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHCC
Q ss_conf             21134826999886786889999999998730350359999999999999998642001223444566899999997313
Q gi|254780396|r   35 SWAMSSRIRTTINGEVITDGDISKRIALLKLQKINGELEKIAVQELIVETLKKQEIEKSGITFDSNTVNYFFVQHARNTG  114 (317)
Q Consensus        35 ~~~~~~~vvA~Vng~~It~~e~~~~~~~~~~~~~~~~~~~~~l~~LI~~~l~~~~a~~~~i~v~~~~i~~~i~~~~~~~~  114 (317)
                      +....+..||+..|..||..|+...+.       .....+++|.+||-.+++..   ++|-.|++.+|+..++....++|
T Consensus        22 s~~~~~~~vat~kgg~IT~~e~Y~~~K-------~~~~g~q~l~~mi~~kvLe~---~Yg~kVsdkeV~~~~~~~k~qyG   91 (310)
T PRK01326         22 SKTNDNTKVISMKGDTITVSDFYNEVK-------NNEVAQQAMLNLVISRVFEK---QYGDKVSDKEVEKAYHKTAKQYG   91 (310)
T ss_pred             CCCCCCCEEEEECCCCEEHHHHHHHHH-------CCCHHHHHHHHHHHHHHHHH---HHCCCCCHHHHHHHHHHHHHHHH
T ss_conf             699988068982499342999999984-------66428999999999999999---86261789999999999999986


Q ss_pred             CCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHCCCCHHHHHHHHHCCCCCCCC
Q ss_conf             43035677776531124554699999989999999984320355589998644321110011002333221024675444
Q gi|254780396|r  115 LSAEDFSSFLDKQGIGDNHFKQYLAIQSIWPDVVKNDFMLKYGNLEMEIPANKQKMKNITVREYLIRTVLFSIPDNKLQN  194 (317)
Q Consensus       115 ~~~~~~~~~l~~~g~t~~~~~~~i~~~l~~~~~~~~~~~~~i~~~~~e~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  194 (317)
                         ++|...|.++|++++.|++.||.+++.+..+....  +..+++.+++.+|...    .+...++||++.       .
T Consensus        92 ---~~F~~~L~q~g~T~e~~K~qir~~lL~e~A~k~~a--k~~iTd~~lK~~y~~y----~p~v~a~hIlv~-------~  155 (310)
T PRK01326         92 ---ASFSAALAQAGLTPETYKRQIRTSKLVEYAVKEAA--KKELTDEEYKKAYESY----TPEVTVQIITLD-------N  155 (310)
T ss_pred             ---HHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHH--HCCCCHHHHHHHHHHC----CCCEEEEEEEEC-------C
T ss_conf             ---89999999869988999999999899999999875--3437889999999734----985378998725-------6


Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCHH-HCCHHHHH-HCCCCCCCCCCCEEE------CCE
Q ss_conf             7999986435788652233248999985201322568746752755-61367665-112457880123763------894
Q gi|254780396|r  195 QGFVQKRIKDAEESRLRLPKDCNKLEKFASKIHDVSIGKAQYLLES-DLHPQFQN-LLKKSQNNTTNPYVT------QKG  266 (317)
Q Consensus       195 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~lg~~~~~-~l~~~~~~-~~~~~~G~is~pv~t------~~G  266 (317)
                      ++.+.....+...   .+..|...+++.+.  +...||++||...+ .+|+.|+. ||.|++|++|.|+.+      ++|
T Consensus       156 e~~Ak~vi~~l~a---~G~dFa~lAKe~St--~k~~GG~l~f~~~~~~~~~~f~~AAfkLk~gevS~~v~t~~p~~~q~g  230 (310)
T PRK01326        156 EDKAKSVLEEAKA---EGADFAQIAKEKTT--TKEKKVEYKFDSGATNVPTDVKKAAFSLDEGGVSDVISVLDPTSYQKK  230 (310)
T ss_pred             HHHHHHHHHHHHC---CCCCHHHHHHHCCC--CCCCCCCCCCCCCCCCCCHHHHHHHHCCCCCCCCCCEECCCCCCCCCE
T ss_conf             8889999999863---78748999865257--855697345478998076999999870668984661124787655540


Q ss_pred             EEEEEEECCCCCCC-CHHHHHHHHHHHHHHHHHHH--HHHHHHHHHHHCCCCC
Q ss_conf             89999822357884-45789999999999999999--9999999997547750
Q gi|254780396|r  267 VEYIAICDKRDLGG-EIALKAYLSAQNTPTKIEKH--EAEYVKKLRSNAIIHY  316 (317)
Q Consensus       267 ~hiikv~~~r~~~~-~~~~~~~i~~~l~~~~~~~~--~~~~l~~Lr~~A~I~~  316 (317)
                      ||||++.++.+.++ +...+++|+..|.+++..+.  .+..+.++-++|+|.+
T Consensus       231 YhIIK~~~k~eK~~~~~~~K~~lk~~i~~~k~~D~~~~~~vi~k~lKkanVkI  283 (310)
T PRK01326        231 YYIVKVTKKTEKKSDWQDYKKRLKAIILAQKSKDMNFQNKVIAKALDKANVKI  283 (310)
T ss_pred             EEEEEEECCCCCCCCHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHCCCCC
T ss_conf             69999736766677789999999999999862277999999999999769873


No 9  
>PRK12450 foldase protein PrsA; Reviewed
Probab=99.96  E-value=4.5e-27  Score=190.17  Aligned_cols=250  Identities=13%  Similarity=0.125  Sum_probs=190.8

Q ss_pred             CCCCCEEEEECCEECCHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHCCCC
Q ss_conf             13482699988678688999999999873035035999999999999999864200122344456689999999731343
Q gi|254780396|r   37 AMSSRIRTTINGEVITDGDISKRIALLKLQKINGELEKIAVQELIVETLKKQEIEKSGITFDSNTVNYFFVQHARNTGLS  116 (317)
Q Consensus        37 ~~~~~vvA~Vng~~It~~e~~~~~~~~~~~~~~~~~~~~~l~~LI~~~l~~~~a~~~~i~v~~~~i~~~i~~~~~~~~~~  116 (317)
                      ...+..||+..|..||..||...+.       .....+++|.+||-++++.   .++|-.|++.+|+.+++....+.|  
T Consensus        26 ~~~~~~v~t~kgg~IT~~efy~~~K-------~t~~gq~~L~~mi~~KvLe---~kYg~kVsdkeVd~~~~~~k~qyG--   93 (309)
T PRK12450         26 SHNNTKLVSMKGDTITVSDFYNETK-------NTELAQKAMLSLVISRVFE---TQYANKVSDKEVEKAYKQTADQYG--   93 (309)
T ss_pred             CCCCCEEEEECCCCCCHHHHHHHHH-------CCCHHHHHHHHHHHHHHHH---HHHCCCCCHHHHHHHHHHHHHHHH--
T ss_conf             9998368983599240999999985-------3415899999999999999---985351788999999999999986--


Q ss_pred             CHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHCCCCHHHHHHHHHCCCCCCCCHH
Q ss_conf             03567777653112455469999998999999998432035558999864432111001100233322102467544479
Q gi|254780396|r  117 AEDFSSFLDKQGIGDNHFKQYLAIQSIWPDVVKNDFMLKYGNLEMEIPANKQKMKNITVREYLIRTVLFSIPDNKLQNQG  196 (317)
Q Consensus       117 ~~~~~~~l~~~g~t~~~~~~~i~~~l~~~~~~~~~~~~~i~~~~~e~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  196 (317)
                       ++|...|.++|+|++.|++.||.+++.+..+.... ....+++.++..+|...    .+...++||+..        .+
T Consensus        94 -~~F~~~L~q~GlT~e~~K~~ir~~ll~~~Avk~~~-k~~~vTdk~~K~~y~~y----~p~v~a~hIlv~--------dE  159 (309)
T PRK12450         94 -TSFKTVLAQSGLTPETYKKQIRLTKLVEYAVKEQA-KNETISKKDYRQAYDAY----TPTMTAEIMQFE--------KE  159 (309)
T ss_pred             -HHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHH-HHCCCCHHHHHHHHHHC----CCCEEEEEEECC--------CH
T ss_conf             -89999999879987999999999889999999865-30256829999999844----986146544134--------28


Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCC-CCHHHCCHHHHH-HCCCCCCCCCC------CEEECCEEE
Q ss_conf             9998643578865223324899998520132256874675-275561367665-11245788012------376389489
Q gi|254780396|r  197 FVQKRIKDAEESRLRLPKDCNKLEKFASKIHDVSIGKAQY-LLESDLHPQFQN-LLKKSQNNTTN------PYVTQKGVE  268 (317)
Q Consensus       197 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~lg~-~~~~~l~~~~~~-~~~~~~G~is~------pv~t~~G~h  268 (317)
                      ..++...+...  ..+..|...+++.+.  +...+|+.+| ...+.+|+.|+. +|.+++|++|.      ||++++|||
T Consensus       160 ~tAk~V~~~l~--a~G~dFa~LAKe~St--~~~~k~~~~fd~~~~~~~~ef~~AAfkLk~GevS~~i~~~~Pvkt~~GYh  235 (309)
T PRK12450        160 EDAKAALEAVK--AEGADFAAIAKEKTI--AADKKTTYTFDSGETTLPAEVVRAASGLKEGNRSEIITALDPATSKRTYH  235 (309)
T ss_pred             HHHHHHHHHHH--CCCCCHHHHHHHHCC--CCCCCCCCCCCCCCCCCCHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCEE
T ss_conf             77999999986--478658999877245--65568876777789756289999987166887144223688720157638


Q ss_pred             EEEEECCCCCCC-CHHHHHHHHHHHHHHHHHHH--HHHHHHHHHHHCCCCC
Q ss_conf             999822357884-45789999999999999999--9999999997547750
Q gi|254780396|r  269 YIAICDKRDLGG-EIALKAYLSAQNTPTKIEKH--EAEYVKKLRSNAIIHY  316 (317)
Q Consensus       269 iikv~~~r~~~~-~~~~~~~i~~~l~~~~~~~~--~~~~l~~Lr~~A~I~~  316 (317)
                      ||+++++.+..+ +...++.|+..|.+++.++.  ...-+.++-++|+|.+
T Consensus       236 IIK~t~k~eK~~~~~~~K~~lk~~i~~~k~~d~~~~~~vi~k~lKkanVkI  286 (309)
T PRK12450        236 IIKVTKKATKKADWKAYQKRLKDIIVTGKLKDPDFQNKVIAKALDKANVKI  286 (309)
T ss_pred             EEEEECCCCCCCCHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHCCCCC
T ss_conf             999815755456689999999999999871287999999999999779876


No 10 
>pfam09312 SurA_N SurA N-terminal domain. This domain is found at the N-terminus of the chaperone SurA. It is a helical domain of unknown function. The C-terminus of the SurA protein folds back and forms part of this domain also but is not included in the current alignment.
Probab=99.82  E-value=3.2e-19  Score=140.50  Aligned_cols=108  Identities=20%  Similarity=0.397  Sum_probs=99.9

Q ss_pred             CCEEEEECCEECCHHHHHHHHHHHHHHC--------CHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHH
Q ss_conf             8269998867868899999999987303--------50359999999999999998642001223444566899999997
Q gi|254780396|r   40 SRIRTTINGEVITDGDISKRIALLKLQK--------INGELEKIAVQELIVETLKKQEIEKSGITFDSNTVNYFFVQHAR  111 (317)
Q Consensus        40 ~~vvA~Vng~~It~~e~~~~~~~~~~~~--------~~~~~~~~~l~~LI~~~l~~~~a~~~~i~v~~~~i~~~i~~~~~  111 (317)
                      ++|||+|||+|||.+|+++++..+..+.        ....+++++|+.||+++|+.++|+++|+.|++++|++++..+++
T Consensus         2 D~IvAiVN~~iIt~~el~~~~~~~~~~~~~~~~~~~~~~~l~~~vL~~LI~~~L~~q~A~~~gi~vsd~evd~~i~~ia~   81 (118)
T pfam09312         2 DRIVAVVNDGVILQSELDRRVKTVKRQLAKQGTQLPPDAVLRRQVLERLILERIQLQMAERTGIRVDDEQLNQAIARIAQ   81 (118)
T ss_pred             CEEEEEECCCCCCHHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHH
T ss_conf             72688889926489999999999999998658999928999999999999999999999985999989999999999998


Q ss_pred             HCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             313430356777765311245546999999899999
Q gi|254780396|r  112 NTGLSAEDFSSFLDKQGIGDNHFKQYLAIQSIWPDV  147 (317)
Q Consensus       112 ~~~~~~~~~~~~l~~~g~t~~~~~~~i~~~l~~~~~  147 (317)
                      ++++|.++|.+.|.+.|+++++|++.++.+++|+++
T Consensus        82 ~n~~s~~~~~~~L~~~G~~~~~~r~~ir~qil~~kl  117 (118)
T pfam09312        82 QNNMTLDQLRAALAADGLSYDEFREQIRKEMLISRL  117 (118)
T ss_pred             HCCCCHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHH
T ss_conf             859899999999998499999999999999999970


No 11 
>TIGR02933 nifM_nitrog nitrogen fixation protein NifM; InterPro: IPR014282   Members of this entry are found in a subset of nitrogen-fixing bacteria and are annotated as nitrogen fixation protein NifM. NifM is homologous to peptidyl-prolyl cis-trans isomerases and appears to be an accessory protein for NifH, the Fe protein, also called component II or dinitrogenase reductase, of nitrogenase..
Probab=99.81  E-value=2.4e-18  Score=134.94  Aligned_cols=228  Identities=12%  Similarity=0.103  Sum_probs=191.4

Q ss_pred             HHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCC
Q ss_conf             99999998642001223444566899999997313430356777765311245546999999899999999843203555
Q gi|254780396|r   80 LIVETLKKQEIEKSGITFDSNTVNYFFVQHARNTGLSAEDFSSFLDKQGIGDNHFKQYLAIQSIWPDVVKNDFMLKYGNL  159 (317)
Q Consensus        80 LI~~~l~~~~a~~~~i~v~~~~i~~~i~~~~~~~~~~~~~~~~~l~~~g~t~~~~~~~i~~~l~~~~~~~~~~~~~i~~~  159 (317)
                      ..-+.-+.+.+.+-+++|++..++..-..+++.+. +.+.+...|.+.+++..+-.+-+.+++.+...+...-..-..++
T Consensus        35 ~~~E~Av~~~~~~~~~~i~p~~le~~Wahiasrye-s~~~L~~~L~~~~l~A~~~~a~l~h~~~l~~~L~~v~~q~p~p~  113 (270)
T TIGR02933        35 RHIEQAVVEAADESAVDIPPSLLEEVWAHIASRYE-SAQALAAELDEQELAAAEREALLAHHVRLEAQLASVAEQAPQPD  113 (270)
T ss_pred             HHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHCCC-CHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHCCCCCCC
T ss_conf             89999999736522464788889999999873156-77899987133048930179999999999999999970589996


Q ss_pred             HHHHHHHHHHHHHHCCCC--HHHHHHHHHCCCC--CCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCC
Q ss_conf             899986443211100110--0233322102467--544479999864357886522332489999852013225687467
Q gi|254780396|r  160 EMEIPANKQKMKNITVRE--YLIRTVLFSIPDN--KLQNQGFVQKRIKDAEESRLRLPKDCNKLEKFASKIHDVSIGKAQ  235 (317)
Q Consensus       160 ~~e~~~~~~~~~~~~~~~--~~~~~~~~~~~~~--~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~lg  235 (317)
                      +++|..+|..+...|..+  ...+|+++.+.++  ....++...+...-......+-+.|+..+..+|..|++=.||-||
T Consensus       114 ~a~V~~wY~~Ha~~F~rPeQrltrHLLlTv~edfPen~~eAv~~ri~al~rrL~~~~~~FA~~A~rhS~CPtAl~gG~LG  193 (270)
T TIGR02933       114 DAEVEAWYRRHAEQFVRPEQRLTRHLLLTVNEDFPENDREAVRERILALLRRLRAKRAAFAELAERHSHCPTALEGGLLG  193 (270)
T ss_pred             CHHHHHHHHHHHHHCCCHHHHHHHHHHEECCCCCCCCCCHHHHHHHHHHHHHHCCCHHHHHHHHHHHCCCCCHHCCCCEE
T ss_conf             03588998886740577134422233201158779888178999999999874688567899987627786202278204


Q ss_pred             CCCHHHCCHHHHH-HCCCCCCCCCCCEEECCEEEEEEEECCCCCCCC--HHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             5275561367665-112457880123763894899998223578844--578999999999999999999999999
Q gi|254780396|r  236 YLLESDLHPQFQN-LLKKSQNNTTNPYVTQKGVEYIAICDKRDLGGE--IALKAYLSAQNTPTKIEKHEAEYVKKL  308 (317)
Q Consensus       236 ~~~~~~l~~~~~~-~~~~~~G~is~pv~t~~G~hiikv~~~r~~~~~--~~~~~~i~~~l~~~~~~~~~~~~l~~L  308 (317)
                      |+.+|-|=|.+++ +|.|..|+.|.||+|+-|||++.++..||..+.  +.+-..++++|..++.+..-++|+..|
T Consensus       194 Wv~RG~LYp~Ld~aLF~L~~G~LS~~~es~lGwHlL~CE~irp~~pl~~~~aL~~~rd~L~~r~q~~~QRqWL~qL  269 (270)
T TIGR02933       194 WVSRGLLYPQLDAALFQLAEGELSAPIESELGWHLLLCEAIRPARPLEKEEALERARDRLLLRQQKEYQRQWLVQL  269 (270)
T ss_pred             EECCCCCCHHHHHHHHHHHCCCCCCCHHCHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHC
T ss_conf             4307766600789999986068886011101467787530486567898789899999999999888677998621


No 12 
>COG0760 SurA Parvulin-like peptidyl-prolyl isomerase [Posttranslational modification, protein turnover, chaperones]
Probab=99.79  E-value=8.2e-17  Score=125.24  Aligned_cols=272  Identities=20%  Similarity=0.109  Sum_probs=157.6

Q ss_pred             CCCCEEEEECCEECCHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHCCCCC
Q ss_conf             34826999886786889999999998730350359999999999999998642001223444566899999997313430
Q gi|254780396|r   38 MSSRIRTTINGEVITDGDISKRIALLKLQKINGELEKIAVQELIVETLKKQEIEKSGITFDSNTVNYFFVQHARNTGLSA  117 (317)
Q Consensus        38 ~~~~vvA~Vng~~It~~e~~~~~~~~~~~~~~~~~~~~~l~~LI~~~l~~~~a~~~~i~v~~~~i~~~i~~~~~~~~~~~  117 (317)
                      ....+++.+++.+++................... +..+.+.+++..+..+.+...+..++...+.+.+...........
T Consensus        24 ~~~~~~~~~~~~~v~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  102 (320)
T COG0760          24 SASLVAGVVNAGAVAKVGAQEISAKEKLNAQQKE-RNIALEQLGEQLLLLQAAAELGIKISQQVVAQLIAEIAVLDKLAK  102 (320)
T ss_pred             CCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             0024554300578987547766326899987311-666999999999877767777777779999987766899889899


Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH--HHHCCCCHHHHHH--HHHHHHHH--CCCCHHHHHHHHHCCCCC
Q ss_conf             35677776531124554699999989999999984--3203555899986--44321110--011002333221024675
Q gi|254780396|r  118 EDFSSFLDKQGIGDNHFKQYLAIQSIWPDVVKNDF--MLKYGNLEMEIPA--NKQKMKNI--TVREYLIRTVLFSIPDNK  191 (317)
Q Consensus       118 ~~~~~~l~~~g~t~~~~~~~i~~~l~~~~~~~~~~--~~~i~~~~~e~~~--~~~~~~~~--~~~~~~~~~~~~~~~~~~  191 (317)
                      ..+.......+.....+....+....+........  .......+.+...  .+......  ....+..+|+++...  .
T Consensus       103 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~~~--~  180 (320)
T COG0760         103 ELLLGLSDEQGKQLIAEKPAFQDVEGKFDARAYLKRLRIKGLTEEQEAEALRDKLQNKQQGKKVTEVQARHILVKAE--A  180 (320)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCH--H
T ss_conf             99998887652214547899999999899999999987603765469999999998876310034554543103324--6


Q ss_pred             CCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCC-CCCCCCCCHHHCCHHHHH-HCCCCCCCCCCCEEECCEEEE
Q ss_conf             444799998643578865223324899998520132256-874675275561367665-112457880123763894899
Q gi|254780396|r  192 LQNQGFVQKRIKDAEESRLRLPKDCNKLEKFASKIHDVS-IGKAQYLLESDLHPQFQN-LLKKSQNNTTNPYVTQKGVEY  269 (317)
Q Consensus       192 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~g~lg~~~~~~l~~~~~~-~~~~~~G~is~pv~t~~G~hi  269 (317)
                      ...+ ...........   ....+...+..++.++++.. ||.+||...+.++|.|.+ ++.+++|++|+|++|++||||
T Consensus       181 ~a~~-~~~~~~~~~~~---~~~~f~~~a~~~s~~~~~~~~g~~~~~~~~~~~~p~f~~a~~~~~~g~~~~pv~t~~g~~i  256 (320)
T COG0760         181 KAKE-ALALLKKGVRE---AKADFAELAKKQSEDPSSKNGGGLLGWNKKGQLVPEFRKAAFILKVGEVSAPVKTSFGYHI  256 (320)
T ss_pred             HHHH-HHHHHHHHHHH---CCCCHHHHHHHHCCCHHHHCCCCCCCCCCCCCCCHHHHHHHHHCCCCCCCCCEEECCEEEE
T ss_conf             5699-99998732422---0034799999836682542057633324567667889999975667871675567665899


Q ss_pred             EEEECCCCCCC-CHHHHHHHH----HH----HHHHHHHHHHHHHHHHHHHHCCCCC
Q ss_conf             99822357884-457899999----99----9999999999999999997547750
Q gi|254780396|r  270 IAICDKRDLGG-EIALKAYLS----AQ----NTPTKIEKHEAEYVKKLRSNAIIHY  316 (317)
Q Consensus       270 ikv~~~r~~~~-~~~~~~~i~----~~----l~~~~~~~~~~~~l~~Lr~~A~I~~  316 (317)
                      ++|+++++... +...+....    ..    ...++.......+++.+++.+.+.+
T Consensus       257 i~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  312 (320)
T COG0760         257 IKVEKKRDAKLDFPEVKAVKEISLKQELLQKAALEKLLKGEQKSFDKLLKEAAIDI  312 (320)
T ss_pred             EEEECCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             83103455334534889999998999999999999998766666889888651567


No 13 
>PRK10770 peptidyl-prolyl cis-trans isomerase SurA; Provisional
Probab=99.73  E-value=3.9e-17  Score=127.28  Aligned_cols=172  Identities=10%  Similarity=0.131  Sum_probs=101.3

Q ss_pred             HHHHHCCC--CCHHHHH----HHHHHHHHHHHHHHHHHHH----------HHHHHHHHHHHHHHCCCCHHHHHHHHHHHH
Q ss_conf             99973134--3035677----7765311245546999999----------899999999843203555899986443211
Q gi|254780396|r  108 QHARNTGL--SAEDFSS----FLDKQGIGDNHFKQYLAIQ----------SIWPDVVKNDFMLKYGNLEMEIPANKQKMK  171 (317)
Q Consensus       108 ~~~~~~~~--~~~~~~~----~l~~~g~t~~~~~~~i~~~----------l~~~~~~~~~~~~~i~~~~~e~~~~~~~~~  171 (317)
                      +.++..|+  ++++..+    ...+++++.++|++.+..+          +..+.+........+.....-.....+...
T Consensus        82 Q~A~~~gi~Vsd~evd~~i~~ia~~~~~s~~q~~~~L~~~G~s~~~~r~~ir~ell~~~l~~~~v~~~i~Vs~~Ev~~~~  161 (428)
T PRK10770         82 QMGQKMGVKISDEQLDQAIANIAKQNNMTLDQMRSRLAYDGLNYNTYRNQIRKEMIISEVRNNEVRRRITILPQEVESLA  161 (428)
T ss_pred             HHHHHCCCCCCHHHHHHHHHHHHHHCCCCHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHH
T ss_conf             99998399869999999999999874887999999999769978999999999999999999986501024789999999


Q ss_pred             HHCCCCHH------HHHHHHHCCCCCCCCH-HHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCHHHCCH
Q ss_conf             10011002------3332210246754447-9999864357886522332489999852013225687467527556136
Q gi|254780396|r  172 NITVREYL------IRTVLFSIPDNKLQNQ-GFVQKRIKDAEESRLRLPKDCNKLEKFASKIHDVSIGKAQYLLESDLHP  244 (317)
Q Consensus       172 ~~~~~~~~------~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~lg~~~~~~l~~  244 (317)
                      ........      +.|+++.++.++.... ................+..|...+..+|.++++..||++||+..+.+|+
T Consensus       162 ~~~~~~~~~~~e~~l~~Ili~~~~~~~~~~~~~~~~~a~~i~~~i~~G~dF~~lA~~~S~~~~a~~GGdlGw~~~~~lp~  241 (428)
T PRK10770        162 KQIGNQNDASTELNLSHILIPLPENPTSDQVNEAESQARSIVDQARNGADFGKLAIAYSADQQALKGGQMGWGRIQELPG  241 (428)
T ss_pred             HHHHHHCCCCCCEEEEEEEEECCCCCCHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHCCCCHHHCCCCCCCCCCCCCHH
T ss_conf             98664226886178999997378888999999999999999999875899899999826571011168644211221307


Q ss_pred             HHHHH-CCCCCCCCCCCEEECCEEEEEEEECCCCCC
Q ss_conf             76651-124578801237638948999982235788
Q gi|254780396|r  245 QFQNL-LKKSQNNTTNPYVTQKGVEYIAICDKRDLG  279 (317)
Q Consensus       245 ~~~~~-~~~~~G~is~pv~t~~G~hiikv~~~r~~~  279 (317)
                      .|..+ +.+++|++|+||+|++||||++|.++|...
T Consensus       242 ~f~~a~~~l~~Geis~pi~s~~G~HIikl~d~r~~~  277 (428)
T PRK10770        242 IFAQALSTAKKGDIVGPIRSGVGFHILKVNDLRGAS  277 (428)
T ss_pred             HHHHHHHHCCCCCCCCCEECCCCEEEEEEHHHHCCC
T ss_conf             899999716898723536417835999724432566


No 14 
>TIGR02925 cis_trans_EpsD peptidyl-prolyl cis-trans isomerase, EpsD family; InterPro: IPR014274   Proteins in this entry include EpsD from Methylobacillus sp. 12S and belong to the peptidyl-prolyl cis-trans isomerase family. They are located at loci associated with exopolysaccharide biosynthesis and are encoded near a homologue of EpsH (IPR013426 from INTERPRO)..
Probab=99.70  E-value=4.2e-15  Score=114.42  Aligned_cols=222  Identities=11%  Similarity=0.059  Sum_probs=150.2

Q ss_pred             HHHHHHHHHHHHHHCCCCCCCCCCEEEEECCEECCHHHHHHHHHHHHHHC-----CHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             99999999999984023211348269998867868899999999987303-----5035999999999999999864200
Q gi|254780396|r   18 TYFVLIIFCIVPIVSYKSWAMSSRIRTTINGEVITDGDISKRIALLKLQK-----INGELEKIAVQELIVETLKKQEIEK   92 (317)
Q Consensus        18 ~~~~~~~~~~~~~~~~~~~~~~~~vvA~Vng~~It~~e~~~~~~~~~~~~-----~~~~~~~~~l~~LI~~~l~~~~a~~   92 (317)
                      ++|.+++.++.++.-......++.|+|+|||.+||.++++..+.......     .....|+++|++||+++|..+.|.+
T Consensus         4 ~~~~ll~~~La~C~~~~~~~~asQVAA~VNG~EIsv~QlNy~l~r~p~~~~~~PEda~~~r~~~Ld~LVdqel~~~kA~E   83 (236)
T TIGR02925         4 VLLVLLVGALAACGEKEAKESASQVAAKVNGKEISVHQLNYALQRIPNLGADSPEDAARARRQVLDRLVDQELVVEKALE   83 (236)
T ss_pred             HHHHHHHHHHHCCCCHHCCCCCCCEEEEECCEECCHHHHHHHHHHCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             78769998751244001027888538888682111889999997144678887021589999999999999999999886


Q ss_pred             CCCCCCHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHH
Q ss_conf             12234445668999999973134303567777653112455469999998999999998432035558999864432111
Q gi|254780396|r   93 SGITFDSNTVNYFFVQHARNTGLSAEDFSSFLDKQGIGDNHFKQYLAIQSIWPDVVKNDFMLKYGNLEMEIPANKQKMKN  172 (317)
Q Consensus        93 ~~i~v~~~~i~~~i~~~~~~~~~~~~~~~~~l~~~g~t~~~~~~~i~~~l~~~~~~~~~~~~~i~~~~~e~~~~~~~~~~  172 (317)
                      .+++-+++.+...                              +.-+++++..-++.+.+.....+|+.|+..||..+..
T Consensus        84 ~KLDRsP~V~~A~------------------------------~~A~r~IlArAYl~~~~g~~~~Ps~~e~~~Y~~~HP~  133 (236)
T TIGR02925        84 EKLDRSPDVVMAL------------------------------EAAKREILARAYLEQLVGAQSKPSPEEIKEYFQEHPE  133 (236)
T ss_pred             HCCCCCHHHHHHH------------------------------HHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHH
T ss_conf             0046785789999------------------------------9988989999999987447988788889888610056


Q ss_pred             HCCCCHHHHHHHHHCC-CCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCHHHCCHHHHHHC-
Q ss_conf             0011002333221024-67544479999864357886522332489999852013225687467527556136766511-
Q gi|254780396|r  173 ITVREYLIRTVLFSIP-DNKLQNQGFVQKRIKDAEESRLRLPKDCNKLEKFASKIHDVSIGKAQYLLESDLHPQFQNLL-  250 (317)
Q Consensus       173 ~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~lg~~~~~~l~~~~~~~~-  250 (317)
                      .|......+..-+.++ ......+     .+......+....+..+-.+.-......    ..--.+..++|..+-..+ 
T Consensus       134 LFA~RK~Y~lqEi~~pG~~~~~~d-----~Lr~~~~~~k~L~d~~~WLKa~~~~f~~----~~~~r~AEQ~P~~~L~~l~  204 (236)
T TIGR02925       134 LFAERKLYNLQEIALPGPDKELLD-----ELRAMVENSKPLEDILAWLKAKNVKFKA----SSAARSAEQLPAEILAKLA  204 (236)
T ss_pred             HHHHCCCCCHHEEEECCCCCHHHH-----HHHHHHHCCCCHHHHHHHHHCCCCCCCC----CCCCCCHHCCCHHHHHHHH
T ss_conf             676066311111441597820358-----9999975388877899997048983023----5323660114656657844


Q ss_pred             CCCCCCCCCCEEECCEE-EEEEEECCCCCC
Q ss_conf             24578801237638948-999982235788
Q gi|254780396|r  251 KKSQNNTTNPYVTQKGV-EYIAICDKRDLG  279 (317)
Q Consensus       251 ~~~~G~is~pv~t~~G~-hiikv~~~r~~~  279 (317)
                      .+++|. .-+|..++++ ||++|.+-...+
T Consensus       205 ~lk~G~-~l~~~~p~~~s~~~~~~~aq~~P  233 (236)
T TIGR02925       205 KLKDGA-VLVVQGPNNVSLILRVADAQAAP  233 (236)
T ss_pred             CCCCCC-EEEEECCCCEEEEEEEECCCCCC
T ss_conf             289782-48887788737987740000265


No 15 
>pfam00639 Rotamase PPIC-type PPIASE domain. Rotamases increase the rate of protein folding by catalysing the interconversion of cis-proline and trans-proline.
Probab=99.43  E-value=3.2e-13  Score=102.46  Aligned_cols=92  Identities=13%  Similarity=0.245  Sum_probs=68.3

Q ss_pred             HHHHHCCCCCCCCHHHHHHHHHHHHHHHHHHH-HHHHHHHHHHC-CCCCCCCCCCCCCCHHHCCHHHHH-HCCCCCCCCC
Q ss_conf             32210246754447999986435788652233-24899998520-132256874675275561367665-1124578801
Q gi|254780396|r  182 TVLFSIPDNKLQNQGFVQKRIKDAEESRLRLP-KDCNKLEKFAS-KIHDVSIGKAQYLLESDLHPQFQN-LLKKSQNNTT  258 (317)
Q Consensus       182 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~-~~~~~~~g~lg~~~~~~l~~~~~~-~~~~~~G~is  258 (317)
                      ||++..+.+.. ..+.+.+.+........... .|...+..+|. ..+...||++||+..+++++.|.+ ++++++|++|
T Consensus         1 HIli~~~~~~~-~~~~a~~~a~~i~~~i~~g~~~F~~la~~~S~d~~s~~~gG~lG~~~~~~l~~~~~~~~~~l~~G~is   79 (95)
T pfam00639         1 HILIKPPESSE-DKAAAKAKAEEILEQLQSGEDTFAELAREYSDDCPSAANGGDLGWFTRGQLPPEFEDAVFSLKEGEIS   79 (95)
T ss_pred             CEEEECCCCCC-HHHHHHHHHHHHHHHHHCCCCHHHHHHHHHCCCCCCCCCCCEECCCCCCCCCHHHHHHHHCCCCCCCC
T ss_conf             97770899834-89999999999999999192079999998388745324586622115888865699997346765378


Q ss_pred             CCEEECCEEEEEEEEC
Q ss_conf             2376389489999822
Q gi|254780396|r  259 NPYVTQKGVEYIAICD  274 (317)
Q Consensus       259 ~pv~t~~G~hiikv~~  274 (317)
                      +||+|++|||||+|.|
T Consensus        80 ~pi~s~~G~hIikl~d   95 (95)
T pfam00639        80 GPVKTPFGYHIIKVTD   95 (95)
T ss_pred             CCEEECCEEEEEEEEC
T ss_conf             8889799889999969


No 16 
>KOG3259 consensus
Probab=99.00  E-value=3.9e-10  Score=82.94  Aligned_cols=68  Identities=10%  Similarity=0.045  Sum_probs=57.7

Q ss_pred             HHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCHHHCCHHHHH-HCCCCCCCCCCCEEECCEEEEEEEE
Q ss_conf             8865223324899998520132256874675275561367665-1124578801237638948999982
Q gi|254780396|r  206 EESRLRLPKDCNKLEKFASKIHDVSIGKAQYLLESDLHPQFQN-LLKKSQNNTTNPYVTQKGVEYIAIC  273 (317)
Q Consensus       206 ~~~~~~~~~~~~~~~~~~~~~~~~~~g~lg~~~~~~l~~~~~~-~~~~~~G~is~pv~t~~G~hiikv~  273 (317)
                      .........+...+...++..+...||||||+.+++|.+.|++ +|.|++|++|+||.|+.|+|||+-.
T Consensus        94 ~~l~~g~~~f~elA~q~SdCSSaKRGGDLG~fgrgqMqk~FEdaafaL~~ge~SgiV~t~SG~HiI~R~  162 (163)
T KOG3259          94 EDLKSGSGDFEELAKQRSDCSSAKRGGDLGFFGRGQMQKPFEDAAFALKVGEMSGIVDTDSGVHIIYRT  162 (163)
T ss_pred             HHHHCCCCCHHHHHHHHCCHHHHCCCCCCCCCCCCCCCCCCHHHHHHCCCCCCCCCEECCCCEEEEEEC
T ss_conf             876057432899987534713323477655435423245301012202556416722169853898855


No 17 
>KOG3258 consensus
Probab=98.60  E-value=5.8e-08  Score=69.21  Aligned_cols=90  Identities=17%  Similarity=0.169  Sum_probs=60.5

Q ss_pred             CCCHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCHHHCCHHHHH-HCCCC
Q ss_conf             11002333221024675444799998643578865223324899998520132256874675275561367665-11245
Q gi|254780396|r  175 VREYLIRTVLFSIPDNKLQNQGFVQKRIKDAEESRLRLPKDCNKLEKFASKIHDVSIGKAQYLLESDLHPQFQN-LLKKS  253 (317)
Q Consensus       175 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~lg~~~~~~l~~~~~~-~~~~~  253 (317)
                      ...+.+||++-..       .    -.+.+..........|...+.++|... ...||||||.+++.|.-.|++ +|++.
T Consensus        37 gtaVKvRHiLCEK-------q----GKi~EA~eKLk~G~~F~evAA~YSEdk-ar~GGDLGW~~RG~MvGPFQdaAFalp  104 (133)
T KOG3258          37 GTAVKVRHILCEK-------Q----GKINEAMEKLKSGMKFNEVAAQYSEDK-ARQGGDLGWMTRGSMVGPFQDAAFALP  104 (133)
T ss_pred             CCEEEEEEEEEHH-------H----CHHHHHHHHHHCCCCHHHHHHHHCCCC-CCCCCCCCCEECCCCCCCHHHHHHCCC
T ss_conf             6368877752111-------0----669999999873350689999863172-003785353455632362254453166


Q ss_pred             CC------CCCCCEEECCEEEEEEEECCC
Q ss_conf             78------801237638948999982235
Q gi|254780396|r  254 QN------NTTNPYVTQKGVEYIAICDKR  276 (317)
Q Consensus       254 ~G------~is~pv~t~~G~hiikv~~~r  276 (317)
                      .+      -.+.||+|.+|||||.|+.++
T Consensus       105 vs~~~~pv~TdpP~KtkfGYHiImvEGrK  133 (133)
T KOG3258         105 VSTVDKPVYTDPPVKTKFGYHIIMVEGRK  133 (133)
T ss_pred             CCCCCCCCCCCCCCCCCCCEEEEEECCCC
T ss_conf             56567763148983123325899852669


No 18 
>PRK10788 peptidyl-prolyl cis-trans isomerase (rotamase D); Provisional
Probab=97.67  E-value=0.00087  Score=42.76  Aligned_cols=59  Identities=10%  Similarity=0.070  Sum_probs=40.4

Q ss_pred             CCCCCCCCCEEEC-CEEEEEEEECCCCC--CCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             4578801237638-94899998223578--84457899999999999999999999999997
Q gi|254780396|r  252 KSQNNTTNPYVTQ-KGVEYIAICDKRDL--GGEIALKAYLSAQNTPTKIEKHEAEYVKKLRS  310 (317)
Q Consensus       252 ~~~G~is~pv~t~-~G~hiikv~~~r~~--~~~~~~~~~i~~~l~~~~~~~~~~~~l~~Lr~  310 (317)
                      ..+|..|++++.+ +++.+++|.+..|.  .+.+.++++|+..+..++..+..++..+++..
T Consensus       447 ~~~g~~sd~i~~~~~~~~v~rv~~~~p~~~~~l~eVk~~V~~~~~~~~~~~~a~~~a~~ll~  508 (622)
T PRK10788        447 GAPGSNSDIITVDGDRAFVLRISEHKPEAVKPLADVRDQVTALVKHQKAEQQAKVDAEKLLV  508 (622)
T ss_pred             CCCCCCCCCEEECCCEEEEEEEECCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             36777787279669809999984668787899999999999999999999999999999999


No 19 
>pfam05698 Trigger_C Bacterial trigger factor protein (TF) C-terminus. In the E. coli cytosol, a fraction of the newly synthesized proteins requires the activity of molecular chaperones for folding to the native state. The major chaperones implicated in this folding process are the ribosome-associated Trigger Factor (TF), and the DnaK and GroEL chaperones with their respective co-chaperones. Trigger Factor is an ATP-independent chaperone and displays chaperone and peptidyl-prolyl-cis-trans-isomerase (PPIase) activities in vitro. It is composed of at least three domains, an N-terminal domain which mediates association with the large ribosomal subunit, a central substrate binding and PPIase domain with homology to FKBP proteins, and a C-terminal domain of unknown function. The positioning of TF at the peptide exit channel, together with its ability to interact with nascent chains as short as 57 residues renders TF a prime candidate for being the first chaperone that binds to the nascent p
Probab=96.15  E-value=0.067  Score=30.83  Aligned_cols=100  Identities=13%  Similarity=0.101  Sum_probs=54.8

Q ss_pred             HHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHC----CCCCHHHHHHHHHHHHHHHHHHHHHHHH----HHHHHH
Q ss_conf             99999999999864200122344456689999999731----3430356777765311245546999999----899999
Q gi|254780396|r   76 AVQELIVETLKKQEIEKSGITFDSNTVNYFFVQHARNT----GLSAEDFSSFLDKQGIGDNHFKQYLAIQ----SIWPDV  147 (317)
Q Consensus        76 ~l~~LI~~~l~~~~a~~~~i~v~~~~i~~~i~~~~~~~----~~~~~~~~~~l~~~g~t~~~~~~~i~~~----l~~~~~  147 (317)
                      ..+..+...++........+.+++..|++.+..+....    ..+.-.+.+++...|.+.+.+++.++.+    +.+.-+
T Consensus        20 ~~~~~~~~~i~~~L~~~~~~evP~~~v~~e~~~~~~~~~~~~~~~g~~~e~~~~~~~~~~e~~~~~~~~~A~~~vk~~li   99 (162)
T pfam05698        20 ATAEELKEAILDKLVENAEIELPESLVEEEIDRLLRQFLQQLQGQGLDLEEYLSLSGSSEEELREEFKEEAEKRVKLGLI   99 (162)
T ss_pred             HHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHH
T ss_conf             99999999999999987889999999999999999999999876699888887652564788878889999999999999


Q ss_pred             HHHHH-HHHCCCCHHHHHHHHHHHHHHCC
Q ss_conf             99984-32035558999864432111001
Q gi|254780396|r  148 VKNDF-MLKYGNLEMEIPANKQKMKNITV  175 (317)
Q Consensus       148 ~~~~~-~~~i~~~~~e~~~~~~~~~~~~~  175 (317)
                      +.... ..++.+++.++..........++
T Consensus       100 l~~Ia~~e~i~vs~eev~~~i~~~a~~~~  128 (162)
T pfam05698       100 LEEIAKEEKIEVTDEEIKEEIEELASQYG  128 (162)
T ss_pred             HHHHHHHCCCCCCHHHHHHHHHHHHHHCC
T ss_conf             99999880899899999999999998869


No 20 
>PRK01490 tig trigger factor; Provisional
Probab=95.33  E-value=0.21  Score=27.72  Aligned_cols=21  Identities=14%  Similarity=0.275  Sum_probs=13.6

Q ss_pred             CHHHCCHHHHH-HCCCCCCCCC
Q ss_conf             75561367665-1124578801
Q gi|254780396|r  238 LESDLHPQFQN-LLKKSQNNTT  258 (317)
Q Consensus       238 ~~~~l~~~~~~-~~~~~~G~is  258 (317)
                      ..+.+.|.|.+ +..+++|+-.
T Consensus       190 g~~~~i~gf~~~LiG~k~Gd~~  211 (435)
T PRK01490        190 GSGRMIPGFEEQLVGMKAGEEK  211 (435)
T ss_pred             CCCCCCHHHHHHHCCCCCCCEE
T ss_conf             5887755599985468778621


No 21 
>COG0544 Tig FKBP-type peptidyl-prolyl cis-trans isomerase (trigger factor) [Posttranslational modification, protein turnover, chaperones]
Probab=78.16  E-value=4.6  Score=19.19  Aligned_cols=32  Identities=13%  Similarity=0.194  Sum_probs=20.5

Q ss_pred             CCHHHCCHHHHH-HCCCCCCCCCCC-EEECCEEE
Q ss_conf             275561367665-112457880123-76389489
Q gi|254780396|r  237 LLESDLHPQFQN-LLKKSQNNTTNP-YVTQKGVE  268 (317)
Q Consensus       237 ~~~~~l~~~~~~-~~~~~~G~is~p-v~t~~G~h  268 (317)
                      +.++++-|.|++ ++.++.|+.-.. +.-+-.||
T Consensus       189 lGs~~fipgFe~~LvG~k~Ge~k~i~vtFP~~y~  222 (441)
T COG0544         189 LGSGRFIPGFEDQLVGMKAGEEKDIKVTFPEDYH  222 (441)
T ss_pred             ECCCCCHHHHHHHHCCCCCCCEEEEEEECCCCCC
T ss_conf             7078744428864136857975689887166530


No 22 
>PRK00315 potassium-transporting ATPase subunit C; Reviewed
Probab=49.02  E-value=17  Score=15.60  Aligned_cols=57  Identities=14%  Similarity=-0.061  Sum_probs=36.0

Q ss_pred             CHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCEEEEECCEECCHHHHH
Q ss_conf             957999999999999999999999999998402321134826999886786889999
Q gi|254780396|r    1 MTSKVFTSLSDFIKLLTTYFVLIIFCIVPIVSYKSWAMSSRIRTTINGEVITDGDIS   57 (317)
Q Consensus         1 ~~~~~~~~~~~fi~~~~~~~~~~~~~~~~~~~~~~~~~~~~vvA~Vng~~It~~e~~   57 (317)
                      |...++.++..++-++.+..++..++.+++.-..-+..+++-+.++||++|-..-+-
T Consensus         1 M~k~l~~al~~~l~~~vl~G~~YPl~vtgiaq~~fp~qAnGSli~~~G~vvGS~LIg   57 (195)
T PRK00315          1 MMKGLRPALVLFLFLLLITGGAYPLLTTGLGQWWFPWQANGSLIRDDGKVRGSALIG   57 (195)
T ss_pred             CHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCEEEECCEEHHHHHHC
T ss_conf             958899999999999999999999999999998675658887570799972138758


No 23 
>COG4856 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=34.20  E-value=20  Score=15.14  Aligned_cols=28  Identities=21%  Similarity=0.469  Sum_probs=18.3

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             79999999999999999999999999984
Q gi|254780396|r    3 SKVFTSLSDFIKLLTTYFVLIIFCIVPIV   31 (317)
Q Consensus         3 ~~~~~~~~~fi~~~~~~~~~~~~~~~~~~   31 (317)
                      +|++.+ .|+++++.++|.++||+.+...
T Consensus         2 dK~lns-~W~irIiaff~A~~Lfl~vn~~   29 (403)
T COG4856           2 DKFLNS-PWLIRIIAFFFAILLFLYVNNN   29 (403)
T ss_pred             CCHHCC-CHHHHHHHHHHHHHHHEEECCC
T ss_conf             612037-3768899999999863052031


No 24 
>PRK03147 thiol-disulfide oxidoreductase; Provisional
Probab=32.98  E-value=24  Score=14.64  Aligned_cols=16  Identities=25%  Similarity=0.410  Sum_probs=12.2

Q ss_pred             EEEEECCEECCHHHHH
Q ss_conf             6999886786889999
Q gi|254780396|r   42 IRTTINGEVITDGDIS   57 (317)
Q Consensus        42 vvA~Vng~~It~~e~~   57 (317)
                      .+-.++|++++.+|+.
T Consensus        46 ~l~~l~G~~v~lsd~k   61 (176)
T PRK03147         46 VLTDLEGKKIELKDLK   61 (176)
T ss_pred             EEECCCCCEEEHHHHC
T ss_conf             6278998987189969


No 25 
>PRK11281 potassium efflux protein KefA; Provisional
Probab=32.78  E-value=30  Score=14.00  Aligned_cols=22  Identities=32%  Similarity=0.490  Sum_probs=13.4

Q ss_pred             CCEECCHHHHHHHHHHHHHHCC
Q ss_conf             8678688999999999873035
Q gi|254780396|r   47 NGEVITDGDISKRIALLKLQKI   68 (317)
Q Consensus        47 ng~~It~~e~~~~~~~~~~~~~   68 (317)
                      +++.-|..+++++++.+.....
T Consensus        30 ~~~lPt~~~iq~~L~~l~~~~~   51 (1107)
T PRK11281         30 NGDLPTEADVQAQLDKLNKQKD   51 (1107)
T ss_pred             CCCCCCHHHHHHHHHHHHCCCC
T ss_conf             1699999999999998626779


No 26 
>pfam07076 DUF1344 Protein of unknown function (DUF1344). This family consists of several short, hypothetical bacterial proteins of around 80 residues in length. Members of this family are found in Rhizobium, Agrobacterium and Brucella species. The function of this family is unknown.
Probab=31.68  E-value=24  Score=14.67  Aligned_cols=27  Identities=15%  Similarity=0.020  Sum_probs=12.4

Q ss_pred             HHHCCCCCCCCCCEEEEEC--CEECCHHH
Q ss_conf             9840232113482699988--67868899
Q gi|254780396|r   29 PIVSYKSWAMSSRIRTTIN--GEVITDGD   55 (317)
Q Consensus        29 ~~~~~~~~~~~~~vvA~Vn--g~~It~~e   55 (317)
                      ++.+....+...++++.||  +..||.+|
T Consensus        15 ~~s~~A~a~d~Eg~I~~Vd~~~~tiTLdD   43 (81)
T pfam07076        15 AMSTPAFAADAEGTIASVDKDSLSITLDD   43 (81)
T ss_pred             HCCCHHHHHHCCCEEEEECCCCCEEEECC
T ss_conf             51106554430013455457763799569


No 27 
>PRK06437 hypothetical protein; Provisional
Probab=29.19  E-value=28  Score=14.21  Aligned_cols=19  Identities=11%  Similarity=0.181  Sum_probs=14.2

Q ss_pred             CCCCCEEEEECCEECCHHH
Q ss_conf             1348269998867868899
Q gi|254780396|r   37 AMSSRIRTTINGEVITDGD   55 (317)
Q Consensus        37 ~~~~~vvA~Vng~~It~~e   55 (317)
                      ..++..|++|||.|.|...
T Consensus        32 ldee~yvvIvNGsP~~~D~   50 (67)
T PRK06437         32 LDEEEYVVIVNGSPVLEDH   50 (67)
T ss_pred             CCCCCEEEEECCCCCCCCC
T ss_conf             9921079998698544445


No 28 
>TIGR00115 tig trigger factor; InterPro: IPR005215   The trigger factor is found in several prokaryotes, and is involved in protein export. Trigger factor is a ribosome-associated molecular chaperone and is the first chaperone to interact with nascent polypeptide. It acts as a chaperone by maintaining the newly synthesised protein in an open conformation. Trigger factor can bind at the same time as the signal recognition particle (SRP), but is excluded by the SRP receptor (FtsY). The central domain of trigger factor has peptidyl-prolyl cis/trans isomerase activity .; GO: 0015031 protein transport.
Probab=28.69  E-value=36  Score=13.56  Aligned_cols=105  Identities=11%  Similarity=0.019  Sum_probs=64.5

Q ss_pred             HHHHHHHHHHH-HHHHHHHHCCCC--CCHHHHHHHHHHHHHHCCC----CCHHHHHHHHHHHHHHHHHHHHHHHHHH---
Q ss_conf             99999999999-998642001223--4445668999999973134----3035677776531124554699999989---
Q gi|254780396|r   74 KIAVQELIVET-LKKQEIEKSGIT--FDSNTVNYFFVQHARNTGL----SAEDFSSFLDKQGIGDNHFKQYLAIQSI---  143 (317)
Q Consensus        74 ~~~l~~LI~~~-l~~~~a~~~~i~--v~~~~i~~~i~~~~~~~~~----~~~~~~~~l~~~g~t~~~~~~~i~~~l~---  143 (317)
                      ++.++..+... ++.+..+...+.  ++...|+++++.+.++...    ..-.+.+++...+.+....+++.+.+..   
T Consensus       309 k~~~~~~~~~~k~i~~l~e~~~~DP~~P~~~I~~E~drll~~~~~~~~~~~~~~~~~~~~s~~~~~~~~~~~~~ea~~~~  388 (475)
T TIGR00115       309 KQELDNQEKNQKLIEKLSEKNTIDPYLPESMIEQEIDRLLRNQKQRAQRYGMNLEQLLQLSRESLEELKDRNKKEALKNV  388 (475)
T ss_pred             HHHHHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHCCHHHHHHHHHHHHHHHHHHH
T ss_conf             99999999989999989873157887507899999999999999999971888899973125689998763288898756


Q ss_pred             -HHHHHHHHH-HHHCCCCHHHHHHHHHHHHHHCCCCH
Q ss_conf             -999999984-32035558999864432111001100
Q gi|254780396|r  144 -WPDVVKNDF-MLKYGNLEMEIPANKQKMKNITVREY  178 (317)
Q Consensus       144 -~~~~~~~~~-~~~i~~~~~e~~~~~~~~~~~~~~~~  178 (317)
                       ...++.... ..++.+++.++...+.........++
T Consensus       389 k~~l~~~~~Ad~Ekikv~~~ev~~~~~~~~~~~~~~~  425 (475)
T TIGR00115       389 KSALIMEAIADEEKIKVTEEEVKSELEEEAEAVEYPS  425 (475)
T ss_pred             HHHHHHHHHHCHHCCCCCHHHHHHHHHHHHHHHCCCH
T ss_conf             8998899871220378876899999999999828971


No 29 
>PRK10626 hypothetical protein; Provisional
Probab=28.64  E-value=36  Score=13.56  Aligned_cols=70  Identities=16%  Similarity=0.109  Sum_probs=31.8

Q ss_pred             EEEECCEECCHHHHHHHHHH-HHHHC--C----------HHHHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHH
Q ss_conf             99988678688999999999-87303--5----------03599999999999999986420012234445668999999
Q gi|254780396|r   43 RTTINGEVITDGDISKRIAL-LKLQK--I----------NGELEKIAVQELIVETLKKQEIEKSGITFDSNTVNYFFVQH  109 (317)
Q Consensus        43 vA~Vng~~It~~e~~~~~~~-~~~~~--~----------~~~~~~~~l~~LI~~~l~~~~a~~~~i~v~~~~i~~~i~~~  109 (317)
                      -..+||++|+.+.=++.... ++...  .          .-...+.+||..|-+.+=..-.-+..++.-+....+.++++
T Consensus        55 ~l~~nGk~v~Ls~~Qrq~a~~YQ~~lR~dLPwi~~~a~~~l~~ar~aLDkViv~~lG~~Snvr~rlt~l~~ql~qqm~ri  134 (239)
T PRK10626         55 NVMRNGKQYTLNAAQREQAKDYQAELRSDLPWIDEGAKSRLEKARVALDKIIVQELGESSNMRSRLTKLDAQLKQQMNRI  134 (239)
T ss_pred             CEEECCEEEECCHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             76887876301899999999999999871816557789899999999999999985640168889999999999999999


Q ss_pred             HHH
Q ss_conf             973
Q gi|254780396|r  110 ARN  112 (317)
Q Consensus       110 ~~~  112 (317)
                      ...
T Consensus       135 ie~  137 (239)
T PRK10626        135 IET  137 (239)
T ss_pred             HHH
T ss_conf             971


No 30 
>TIGR01439 lp_hng_hel_AbrB transcriptional regulator, AbrB family; InterPro: IPR006339   This DNA-binding domain is found in proteins like AbrB, a transition state regulator in Bacillus subtilis, whose DNA-binding domain structure in solution was determined by NMR. The domain binds DNA as a dimer in what is termed a looped-hinge helix fold. Some members of the family have two copies of the domain in tandem. The domain is found usually at the N-terminus of a small protein. .
Probab=26.08  E-value=40  Score=13.27  Aligned_cols=30  Identities=7%  Similarity=0.131  Sum_probs=25.2

Q ss_pred             CCHHHHHHCCCCCCCCCCCEEECCE-EEEEE
Q ss_conf             1367665112457880123763894-89999
Q gi|254780396|r  242 LHPQFQNLLKKSQNNTTNPYVTQKG-VEYIA  271 (317)
Q Consensus       242 l~~~~~~~~~~~~G~is~pv~t~~G-~hiik  271 (317)
                      .|....+.+++++|+....+.+.+| .+|..
T Consensus        12 IPK~iR~~lgl~eGd~l~~~~~~d~~i~l~p   42 (44)
T TIGR01439        12 IPKEIREKLGLKEGDKLEVIRVEDGEIILRP   42 (44)
T ss_pred             ECHHHHHHCCCCCCCEEEEEEECCCEEEEEE
T ss_conf             2738964069999987889882798798983


No 31 
>smart00342 HTH_ARAC helix_turn_helix, arabinose operon control protein.
Probab=25.49  E-value=41  Score=13.20  Aligned_cols=42  Identities=12%  Similarity=0.226  Sum_probs=31.0

Q ss_pred             HHHHHHHCCCCCHHHHHHHHHH-HHHHHHHHHHHHHHHHHHHH
Q ss_conf             9999973134303567777653-11245546999999899999
Q gi|254780396|r  106 FVQHARNTGLSAEDFSSFLDKQ-GIGDNHFKQYLAIQSIWPDV  147 (317)
Q Consensus       106 i~~~~~~~~~~~~~~~~~l~~~-g~t~~~~~~~i~~~l~~~~~  147 (317)
                      ++.+++..+.|...+...+.+. |.++.+|...+|-+.+...+
T Consensus         4 l~~lA~~~~~S~~~l~~~f~~~~g~s~~~~i~~~Rl~~a~~~L   46 (84)
T smart00342        4 LEDLAEALGMSPRHLQRLFKKETGTTPKQYLRDRRLERARRLL   46 (84)
T ss_pred             HHHHHHHHCCCHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHH
T ss_conf             9999998890999999999998893999999999999999999


No 32 
>COG2104 ThiS Sulfur transfer protein involved in thiamine biosynthesis [Coenzyme metabolism]
Probab=24.23  E-value=43  Score=13.05  Aligned_cols=22  Identities=14%  Similarity=0.373  Sum_probs=17.5

Q ss_pred             CCCCEEEEECCEECCHHHHHHH
Q ss_conf             3482699988678688999999
Q gi|254780396|r   38 MSSRIRTTINGEVITDGDISKR   59 (317)
Q Consensus        38 ~~~~vvA~Vng~~It~~e~~~~   59 (317)
                      ....+++.|||+++++++..+.
T Consensus        30 ~~~~vav~vNg~iVpr~~~~~~   51 (68)
T COG2104          30 NPEGVAVAVNGEIVPRSQWADT   51 (68)
T ss_pred             CCCEEEEEECCEECCCHHHHHC
T ss_conf             9855999988998250463201


No 33 
>pfam02669 KdpC K+-transporting ATPase, c chain. This family consists of K+-transporting ATPase, c chain, KdpC. KdpC forms strong interactions with the KdpA subunit, serving to assemble and stabilize the Kdp complex. It has been suggested that KdpC could be one of the connecting links between the energy providing subunit KdpB and the K+-transporting subunit KdpA. The K+ transport system actively transports K+ ions via ATP hydrolysis.
Probab=23.38  E-value=45  Score=12.95  Aligned_cols=53  Identities=13%  Similarity=-0.001  Sum_probs=29.8

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCEEEEECCEECCHHHH
Q ss_conf             99999999999999999999999999840232113482699988678688999
Q gi|254780396|r    4 KVFTSLSDFIKLLTTYFVLIIFCIVPIVSYKSWAMSSRIRTTINGEVITDGDI   56 (317)
Q Consensus         4 ~~~~~~~~fi~~~~~~~~~~~~~~~~~~~~~~~~~~~~vvA~Vng~~It~~e~   56 (317)
                      .++.++..++-++.+.-++..++.+++.-..-+..+++-+.++||+.|-..-+
T Consensus         3 ~l~~al~~~~~~~vl~G~~YPl~vtgiaq~~fp~qAnGSli~~~g~vvGS~LI   55 (188)
T pfam02669         3 NLVPALRSTALLWIITGLVYPLIVTVIGQLVFPYQANGSLITDSGQVVGSALI   55 (188)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCEEEECCEEEEEHHC
T ss_conf             58999999999999999999999999997756355886768389999654322


No 34 
>pfam02682 AHS1 Allophanate hydrolase subunit 1. This family is the first subunit of allophanate hydrolase.
Probab=22.88  E-value=28  Score=14.24  Aligned_cols=19  Identities=21%  Similarity=0.284  Sum_probs=13.6

Q ss_pred             CCCCC--CEEECCEEEEEEEE
Q ss_conf             88012--37638948999982
Q gi|254780396|r  255 NNTTN--PYVTQKGVEYIAIC  273 (317)
Q Consensus       255 G~is~--pv~t~~G~hiikv~  273 (317)
                      |.-++  |..+++|||||=-+
T Consensus       167 g~qt~IYP~~sPGGW~iIGrT  187 (202)
T pfam02682       167 GRQTGIYPLESPGGWQIIGRT  187 (202)
T ss_pred             CCEEEEECCCCCCCCCEEEEC
T ss_conf             552689858999713053223


Done!