Query         gi|254780376|ref|YP_003064789.1| flagellar basal body P-ring protein [Candidatus Liberibacter asiaticus str. psy62]
Match_columns 369
No_of_seqs    122 out of 669
Neff          4.9 
Searched_HMMs 39220
Date          Sun May 29 15:26:28 2011
Command       /home/congqian_1/programs/hhpred/hhsearch -i 254780376.hhm -d /home/congqian_1/database/cdd/Cdd.hhm 

 No Hit                             Prob E-value P-value  Score    SS Cols Query HMM  Template HMM
  1 PRK12789 flgI flagellar basal  100.0       0       0 1010.6  40.7  367    2-369     1-367 (367)
  2 PRK05303 flgI flagellar basal  100.0       0       0  980.5  41.2  361    2-369     4-368 (368)
  3 pfam02119 FlgI Flagellar P-rin 100.0       0       0  959.5  39.5  340   25-369     1-342 (342)
  4 COG1706 FlgI Flagellar basal-b 100.0       0       0  918.8  37.5  362    2-369     2-365 (365)
  5 PRK12706 flgI flagellar basal  100.0       0       0  733.9  30.3  310    1-369     1-327 (328)
  6 TIGR03177 pilus_cpaB Flp pilus  76.6     6.1 0.00016   19.7   5.9   88   95-199   126-218 (261)
  7 TIGR01172 cysE serine O-acetyl  69.7     6.4 0.00016   19.6   3.6   45  238-283    52-99  (163)
  8 cd05635 LbH_unknown Uncharacte  67.4     4.5 0.00011   20.6   2.4   56  257-316     2-57  (101)
  9 TIGR00014 arsC arsenate reduct  66.5     4.6 0.00012   20.5   2.3   36  325-366    31-67  (114)
 10 PTZ00298 mevalonate kinase; Pr  52.0      17 0.00044   16.6   3.2   36  331-366   241-280 (328)
 11 TIGR01676 GLDHase galactonolac  51.5      14 0.00037   17.1   2.7   38  315-352   117-154 (541)
 12 TIGR02324 CP_lyasePhnL phospho  50.1     5.7 0.00015   19.9   0.5   53  298-361   147-200 (224)
 13 pfam00207 A2M Alpha-2-macroglo  49.7      16  0.0004   16.8   2.7   25   89-113    55-79  (92)
 14 PRK04792 tolB translocation pr  49.4     9.9 0.00025   18.2   1.7   68    1-76      1-69  (450)
 15 PRK13861 type IV secretion sys  46.9      12 0.00032   17.6   1.8   21    2-22      1-21  (293)
 16 PRK09405 aceE pyruvate dehydro  45.4      19 0.00049   16.3   2.6   41   40-82    391-433 (886)
 17 pfam08784 RPA_C Replication pr  43.9      23 0.00059   15.7   4.1   36  327-364    63-98  (103)
 18 pfam00791 ZU5 ZU5 domain. Doma  43.1      24 0.00061   15.6   4.6   38   92-129    23-64  (103)
 19 PRK03629 tolB translocation pr  42.7      12  0.0003   17.8   1.1   67    2-76      1-68  (430)
 20 TIGR01990 bPGM beta-phosphoglu  41.8      22 0.00057   15.8   2.5   29  334-362   151-185 (190)
 21 TIGR00021 rpiA ribose 5-phosph  41.2      15 0.00038   17.1   1.5   63   44-111    16-81  (236)
 22 TIGR00549 mevalon_kin mevalona  39.3      27 0.00069   15.2   3.2   37  330-366   293-333 (345)
 23 PRK10431 N-acetylmuramoyl-l-al  38.7      28 0.00071   15.2   3.3   35    1-36      1-35  (444)
 24 cd02017 TPP_E1_EcPDC_like Thia  38.5      22 0.00056   15.9   2.0   10  131-140   145-154 (386)
 25 PRK11067 outer membrane protei  37.5      21 0.00054   15.9   1.8   30    1-30      1-30  (801)
 26 KOG4731 consensus               36.4      30 0.00076   14.9   2.4   95   45-146    59-170 (512)
 27 cd05791 S1_CSL4 S1_CSL4: CSL4,  32.8      33 0.00085   14.6   2.2   24   96-119    57-80  (92)
 28 KOG3930 consensus               32.5      34 0.00086   14.6   2.2   90  155-249   207-300 (389)
 29 pfam11543 UN_NPL4 Nuclear pore  32.3      35 0.00089   14.5   3.0   59  226-286    14-75  (80)
 30 COG4832 Uncharacterized conser  32.1      27 0.00069   15.2   1.6   23  187-209   100-122 (207)
 31 pfam12408 DUF3666 Ribose-5-pho  31.7      27  0.0007   15.2   1.6   15  344-358     2-16  (48)
 32 TIGR00064 ftsY signal recognit  31.3      35 0.00088   14.5   2.1   36   36-77     78-113 (284)
 33 TIGR03002 outer_YhbN cell enve  30.2      38 0.00096   14.2   3.7   28  257-289    16-43  (150)
 34 KOG2348 consensus               30.0      24 0.00061   15.6   1.1   12   38-49      7-18  (667)
 35 COG2373 Large extracellular al  29.4      39 0.00099   14.1   2.3   43   92-134   855-906 (1621)
 36 TIGR01139 cysK cysteine syntha  28.2      28 0.00072   15.1   1.2  119  102-237   163-304 (312)
 37 TIGR01136 cysKM cysteine synth  26.6      40   0.001   14.1   1.7   89  102-206   165-266 (315)
 38 COG1254 AcyP Acylphosphatases   25.7      43  0.0011   13.9   1.7   30  217-246    33-63  (92)
 39 cd05125 Mth938_2P1-like Mth938  25.6      41   0.001   14.0   1.6   26   50-78     60-85  (114)
 40 PRK11132 cysE serine acetyltra  25.4      45  0.0012   13.7   3.9   25  242-266   136-162 (273)
 41 PRK00178 tolB translocation pr  25.4      39 0.00099   14.1   1.5  115    1-126     1-134 (433)
 42 COG3164 Predicted membrane pro  25.3      17 0.00043   16.7  -0.4   60   84-146   604-665 (1271)
 43 COG1045 CysE Serine acetyltran  25.3      46  0.0012   13.7   3.7   43  240-283    60-105 (194)
 44 pfam07253 Gypsy Gypsy protein.  24.6      47  0.0012   13.6   5.2   49  251-300   314-365 (472)
 45 TIGR03431 PhnD phosphonate ABC  24.5      47  0.0012   13.6   2.8   24    1-24      1-24  (288)
 46 PRK10867 signal recognition pa  24.2      44  0.0011   13.8   1.6   25   43-72    102-126 (453)
 47 cd00248 Mth938-like Mth938-lik  24.2      28 0.00071   15.1   0.6   25   51-78     59-83  (109)
 48 pfam11685 DUF3281 Protein of u  24.1      48  0.0012   13.5   2.8   14  195-208   166-179 (269)
 49 pfam05872 DUF853 Bacterial pro  24.0      48  0.0012   13.5   2.8   77   43-132    23-124 (504)
 50 PRK11627 hypothetical protein;  23.3      50  0.0013   13.4   2.4   13  329-341   156-168 (192)
 51 pfam07499 RuvA_C RuvA, C-termi  23.0      50  0.0013   13.4   1.8   27  332-358     3-29  (47)
 52 TIGR00724 urea_amlyse_rel biot  22.8      33 0.00084   14.6   0.7   28  266-293   244-272 (334)
 53 COG0541 Ffh Signal recognition  22.1      52  0.0013   13.3   1.6   29   43-76    102-130 (451)
 54 cd03791 GT1_Glycogen_synthase_  22.1      52  0.0013   13.3   1.9   19  322-341   420-438 (476)
 55 pfam04430 DUF498 Protein of un  22.1      39 0.00099   14.1   1.0   25   51-78     60-84  (110)
 56 pfam05949 DUF881 Bacterial pro  22.0      53  0.0013   13.2   2.0   13   62-74     46-58  (150)
 57 KOG3432 consensus               21.3      34 0.00086   14.6   0.5   42  166-209    38-82  (121)
 58 pfam08817 YukD YukD. YukD is a  21.3      54  0.0014   13.1   4.0   59  224-286    12-75  (78)
 59 PRK13978 ribose-5-phosphate is  21.2      47  0.0012   13.6   1.2   66   41-113    19-87  (228)
 60 TIGR03220 catechol_dmpE 2-oxop  21.1      55  0.0014   13.1   5.6   15  331-345   203-217 (255)
 61 TIGR01356 aroA 3-phosphoshikim  20.8      44  0.0011   13.8   1.0   77  262-348   292-371 (444)
 62 TIGR02033 D-hydantoinase dihyd  20.2      57  0.0015   13.0   2.3   78  128-209   297-389 (466)
 63 PRK10894 hypothetical protein;  20.1      57  0.0015   13.0   3.6   14  256-269   139-152 (184)

No 1  
>PRK12789 flgI flagellar basal body P-ring protein; Reviewed
Probab=100.00  E-value=0  Score=1010.57  Aligned_cols=367  Identities=54%  Similarity=0.874  Sum_probs=354.7

Q ss_pred             HHHHHHHHHHHHHHHCCCCHHHHHHEEEEEEEECCCCCEEEEEEEECCCCCCCCCCCCHHHHHHHHHHHHHCCCCCCCCC
Q ss_conf             67899999999997425700100100013640001430267878876388999887746899999999998297457321
Q gi|254780376|r    2 IFRIAFLIFSLIGLHEISAQVVSRIKDVVSLQSGRDNQLIGYGLVVGLQGTGDSLRSSPFTEQSMRSLLQNLGISTPGGR   81 (369)
Q Consensus         2 ~~~~~~l~~~~~~~~~~~~~~a~rikDi~~i~GvR~NqL~GyGLVVGL~GTGD~~~~~~~t~qsl~nml~~~Gv~~~~~~   81 (369)
                      |||.+++++++.+++++.+++|+|||||++++|+|+|||+||||||||+||||+.++++||.|||+|||++||+++++.+
T Consensus         1 m~~~~~~~~~~~l~~~~~~~~a~RIkDi~~v~GvR~NqLiGYGLVVGL~GTGD~~~~~~fT~qsl~nmL~~~Gv~v~~~~   80 (367)
T PRK12789          1 MIRRLLLAVLLALLAGPAAAAATRIKDIATLQGVRDNQLVGYGLVTGLQGTGDTLRNSQFTEQSLQSMLDRMGINVRDTR   80 (367)
T ss_pred             CHHHHHHHHHHHHHHCCCHHHHHHHHHHEEEEEEEECCEEEEEEEEECCCCCCCCCCCCCHHHHHHHHHHHCCCCCCCCC
T ss_conf             90899999999998553066666564020040024435567789981388788877785289999999997696647888


Q ss_pred             CCCCCEEEEEEEEEECCCCCCCCEEEEEEECCCCCCCCCCCEEEEEECCCCCCCEEEEEECCEEECCCCCCCCCCCCCCC
Q ss_conf             46553269999997178775687689999568884544477799952147786189998161683343245676520047
Q gi|254780376|r   82 LGSKNVAAVMVTANLPPFASPGSRIDVSINSLGDASSLRGGILVMTSLLGADGNIYAVAQGSVVVSGLFVKGQSSSFMEG  161 (369)
Q Consensus        82 ~~~kNvAaVmVtA~lPpfa~~G~~iDv~VSSiGdAkSL~GG~LL~TpL~g~dg~vyAvAQG~i~vgg~~~~g~~~~~~~n  161 (369)
                      +++||+|||||||+||||+|+||||||+||||||||||+||+||||||||+||+|||+||||+++|||+++|.++++++|
T Consensus        81 ~~~kNvAAVmVTA~LPpfa~~G~~iDVtVSSiGDAkSL~GGtLL~TPL~g~DG~VYAvAQG~l~vgG~~~~g~g~~~~~n  160 (367)
T PRK12789         81 LRTRNVAAVMVTADLPPFIGPGSRIDVTVSSLGDATSLRGGTLLMTSLTGGDGQVYAVAQGALAVSGFSVQGQAESLTQG  160 (367)
T ss_pred             CCCCEEEEEEEEECCCCCCCCCCEEEEEEECCCCCCCCCCCEEEEEECCCCCCCEEEEEECCEEEECCCCCCCCCCCCCC
T ss_conf             77642689999811787568998478999766566567896789852137998789995076887033234677653347


Q ss_pred             CCCCEEEECCEEEEEECCCCCCCCCEEEEEEECCCHHHHHHHHHHHHHHHCCCCCCCCEEEECCCEEEEECCCCCCHHHH
Q ss_conf             65421741654887413543247764999950788789999999998752024565412451156368632887521213
Q gi|254780376|r  162 ISTGGKIVNGAIVERELPKKFKDSADLILQLRNPDFSTAIRIADQINSYSLNRFSRPIAEAYDSRTVKVSKPTNIDLTRL  241 (369)
Q Consensus       162 ~~t~GrIp~Ga~VErev~~~f~~~~~l~L~L~~pdfttA~~ia~aIN~~~~~~~g~~~A~a~d~~~I~v~~P~~~~~v~f  241 (369)
                      |||+||||+||+||||++++|.+.++++|+|++|||+||.||+++||+++.++||+++|+|.|+++|++++|++++.++|
T Consensus       161 ~pT~GrIp~Ga~VEr~v~~~~~~~~~l~l~L~~pDFtTA~ria~aIN~~~~~~~g~~~A~a~d~~tV~v~~P~~~~~v~f  240 (367)
T PRK12789        161 VPTAGRIPNGALIEREVPGTLRDLPELVLELKNPDFKTATQISDAINAYSLGRYGRRVASERDQRTVVLSRPRQIGPTRF  240 (367)
T ss_pred             CCCEEEECCCEEEEECCCCCCCCCCEEEEEECCCCHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCEEEEECCCCCCHHHH
T ss_conf             86704844860899725777678872999945977799999999986551123685756746896379817999788999


Q ss_pred             HHHHHCCCCCCCCCCEEEEECCCCEEEECCCEEEEEEEEECCCEEEEECCCCCCCCCCCCCCCCCEEECCCCEEEECCCC
Q ss_conf             22322012687898359994476349945973998999841707999637766657765456873442366414560467
Q gi|254780376|r  242 MSEVEMLTVETDTPARVIINERTGTIVIGDNVRISKVVVSYGNLTVQITENEQVVQPNAFSSNGSTVTQNNTDLKVSDNK  321 (369)
Q Consensus       242 la~ie~l~V~~~~~akVVINerTGTIV~g~~V~I~pvaVsHGnLtI~I~~~~~vsqp~~~~~~g~t~~~~~t~i~v~e~~  321 (369)
                      +|.+|+++|+|+.+|||||||||||||||+||||+|||||||||+|+|+++++||||+|| ++|+|+++++++++++|++
T Consensus       241 la~ie~l~V~p~~~ArVVINeRTGTIV~G~~VrIspvaVsHGnLtV~I~~~~~vsqP~pf-~~G~T~v~~~t~i~v~e~~  319 (367)
T PRK12789        241 IAEIGDLTIEPDTPARVVIDQRTGTVVIGRNVQISTVAVTHGNLTVRVTEAPEVSQPAPF-SNGQTVVVPRTEIDANEEG  319 (367)
T ss_pred             HHHHHCCCCCCCCCCEEEEECCCCEEEECCCEEEEEEEEEECCEEEEECCCCCCCCCCCC-CCCCEEECCCCEEEEECCC
T ss_conf             999756846789887799968853299689669978899508689998567534688866-8981362367445641277


Q ss_pred             CEEEECCCCCHHHHHHHHHHCCCCHHHHHHHHHHHHHCCCCCCEEEEC
Q ss_conf             358973898899999999847998789999999998716856258969
Q gi|254780376|r  322 GSFSLIDAPDLNSLISGMNSIGLKTDGIISILQGIKAAGALQSEIIIQ  369 (369)
Q Consensus       322 ~~~~~~~~~tl~~lV~ALN~lG~tp~DlIsILqalk~aGAL~AELiI~  369 (369)
                      +++.+.++++|+|||+|||++|+||+|||+|||+||+|||||||||||
T Consensus       320 ~~~~~~~g~tl~~lV~ALN~lGatp~DlIaILqalK~aGAL~AeLvIq  367 (367)
T PRK12789        320 GKLAILRGSDLQTLVRGLNQIGLKPSDIIAILQAIKTAGALQAELVVQ  367 (367)
T ss_pred             CEEEEECCCCHHHHHHHHHHCCCCHHHHHHHHHHHHHCCCCCEEEEEC
T ss_conf             346620799899999999866998799999999998768870799959


No 2  
>PRK05303 flgI flagellar basal body P-ring protein; Provisional
Probab=100.00  E-value=0  Score=980.45  Aligned_cols=361  Identities=51%  Similarity=0.793  Sum_probs=340.6

Q ss_pred             HHHHHHHHHHHHHHHCCCCHHHHHHEEEEEEEECCCCCEEEEEEEECCCCCCCCCCCCHHHHHHHHHHHHHCCCCCCCCC
Q ss_conf             67899999999997425700100100013640001430267878876388999887746899999999998297457321
Q gi|254780376|r    2 IFRIAFLIFSLIGLHEISAQVVSRIKDVVSLQSGRDNQLIGYGLVVGLQGTGDSLRSSPFTEQSMRSLLQNLGISTPGGR   81 (369)
Q Consensus         2 ~~~~~~l~~~~~~~~~~~~~~a~rikDi~~i~GvR~NqL~GyGLVVGL~GTGD~~~~~~~t~qsl~nml~~~Gv~~~~~~   81 (369)
                      +++.+++++++++++++++.+++|||||++++|+|+|||+||||||||+||||+.++++||.|||+|||++|||++|+ +
T Consensus         4 ~~~~~~~~~~~~~~~~~~~~~a~RIKDia~i~GvR~NqLiGYGLVVGL~GTGD~~~~~~fT~qsl~nmL~~~Gv~v~~-~   82 (368)
T PRK05303          4 MLMLLLLLLLLLLLLLAAPAQAERIKDLASIQGVRDNQLIGYGLVVGLDGTGDQTTQTPFTTQSLANMLEQLGVNVPP-N   82 (368)
T ss_pred             HHHHHHHHHHHHHHHHCCHHHHHHHHHHEEEEEEEECCEEEEEEEEECCCCCCCCCCCCCHHHHHHHHHHHCCCCCCC-C
T ss_conf             899999999999998443566655542210410355354778899822877888777632799999999974987898-7


Q ss_pred             CCCCCEEEEEEEEEECCCCCCCCEEEEEEECCCCCCCCCCCEEEEEECCCCCCCEEEEEECCEEECCCCCCC-CCCCCCC
Q ss_conf             465532699999971787756876899995688845444777999521477861899981616833432456-7652004
Q gi|254780376|r   82 LGSKNVAAVMVTANLPPFASPGSRIDVSINSLGDASSLRGGILVMTSLLGADGNIYAVAQGSVVVSGLFVKG-QSSSFME  160 (369)
Q Consensus        82 ~~~kNvAaVmVtA~lPpfa~~G~~iDv~VSSiGdAkSL~GG~LL~TpL~g~dg~vyAvAQG~i~vgg~~~~g-~~~~~~~  160 (369)
                      +++||+|||||||+||||+|+||||||+||||||||||+||+||||||||+||+|||+||||+++||++++| +++++++
T Consensus        83 ~~~kNvAAVmVTA~LPpFa~~G~~iDVtVSSiGDAkSL~GGtLL~TPL~gaDg~vYAvAQG~v~vgG~~a~g~~g~~~~~  162 (368)
T PRK05303         83 PKLKNVAAVMVTATLPPFAKPGQRIDVTVSSIGDAKSLRGGTLLMTPLKGADGQVYAVAQGNLVVGGFGAEGADGSSVTV  162 (368)
T ss_pred             CCCCEEEEEEEEEECCCCCCCCCEEEEEEECCCCCCCCCCCEEEECCCCCCCCCEEEEEECCEEECCCCCCCCCCCCEEE
T ss_conf             66551689999950588778997588999766676567897788602458998689994076676154234577752222


Q ss_pred             CCCCCEEEECCEEEEEECCCCCCCCCEEEEEEECCCHHHHHHHHHHHHHHHCCCCCCCCEEEECCCEEEEECCCCC-CHH
Q ss_conf             7654217416548874135432477649999507887899999999987520245654124511563686328875-212
Q gi|254780376|r  161 GISTGGKIVNGAIVERELPKKFKDSADLILQLRNPDFSTAIRIADQINSYSLNRFSRPIAEAYDSRTVKVSKPTNI-DLT  239 (369)
Q Consensus       161 n~~t~GrIp~Ga~VErev~~~f~~~~~l~L~L~~pdfttA~~ia~aIN~~~~~~~g~~~A~a~d~~~I~v~~P~~~-~~v  239 (369)
                      ||||+||||+||+||||+|++|.+.++++|+||+|||+||.||+++||+.    ||+++|+|+|+++|+|++|++. +++
T Consensus       163 n~pt~GrIp~GA~VErev~~~~~~~~~i~L~L~~pDFtTA~ri~~aIN~~----~g~~~A~a~D~~tV~v~~P~~~~~~v  238 (368)
T PRK05303        163 NVPTVGRIPNGAIVEREVPSDFGQGDSLTLNLRNPDFTTAQRIADAINRL----FGPGVATALDARTVQVRAPADPSQRV  238 (368)
T ss_pred             CCCCEEEECCCEEEEECCCCCCCCCCEEEEEECCCCHHHHHHHHHHHHHH----CCCCCEEEECCCEEEEECCCCCCCHH
T ss_conf             67543685287189972677767887499995686658999999999986----18896497379889996688877578


Q ss_pred             HHHHHHHCCCCCC-CCCCEEEEECCCCEEEECCCEEEEEEEEECCCEEEEECCCCCCCCCCCCCCCCCEEECCCCEEEEC
Q ss_conf             1322322012687-898359994476349945973998999841707999637766657765456873442366414560
Q gi|254780376|r  240 RLMSEVEMLTVET-DTPARVIINERTGTIVIGDNVRISKVVVSYGNLTVQITENEQVVQPNAFSSNGSTVTQNNTDLKVS  318 (369)
Q Consensus       240 ~fla~ie~l~V~~-~~~akVVINerTGTIV~g~~V~I~pvaVsHGnLtI~I~~~~~vsqp~~~~~~g~t~~~~~t~i~v~  318 (369)
                      +|+|.+|+++|+| +.+|||||||||||||||+||||+|||||||||+|+|+++++||||+|| + |+|+++++++++++
T Consensus       239 ~fla~ie~l~V~~~~~~arVVINeRTGTIV~g~~Vri~~vaVshGnLtv~I~~~~~vsQP~pf-~-G~t~v~~~t~i~v~  316 (368)
T PRK05303        239 AFLARIENLEVEPGDAPAKVVINERTGTIVMGQDVRVSPVAVSHGNLTVTITEQPQVSQPNPF-G-GQTVVTPQTQIEVE  316 (368)
T ss_pred             HHHHHHHCCCCCCCCCCCEEEEECCCCEEEECCCEEEEEEEEEECCEEEEECCCCCCCCCCCC-C-CCEEECCCCEEEEE
T ss_conf             999998577332587775699947854299679669967899608679998068632378887-8-85265368614774


Q ss_pred             CCCCE-EEECCCCCHHHHHHHHHHCCCCHHHHHHHHHHHHHCCCCCCEEEEC
Q ss_conf             46735-8973898899999999847998789999999998716856258969
Q gi|254780376|r  319 DNKGS-FSLIDAPDLNSLISGMNSIGLKTDGIISILQGIKAAGALQSEIIIQ  369 (369)
Q Consensus       319 e~~~~-~~~~~~~tl~~lV~ALN~lG~tp~DlIsILqalk~aGAL~AELiI~  369 (369)
                      |+++. +.++++++|+|||+|||++|++|+|||+||||||+||||||||+|.
T Consensus       317 e~~~~~~~~~~g~tl~~lV~aLN~lGatp~DlIaILqalk~aGAL~AeL~ii  368 (368)
T PRK05303        317 QEGGRLFVVPAGATLADLVRALNALGATPRDLIAILQALKAAGALHAELEVI  368 (368)
T ss_pred             ECCCEEEECCCCCCHHHHHHHHHHCCCCHHHHHHHHHHHHHCCCCEEEEEEC
T ss_conf             0576069718999599999999866998799999999998768870789979


No 3  
>pfam02119 FlgI Flagellar P-ring protein.
Probab=100.00  E-value=0  Score=959.51  Aligned_cols=340  Identities=56%  Similarity=0.857  Sum_probs=331.9

Q ss_pred             HHEEEEEEEECCCCCEEEEEEEECCCCCCCCCCCCHHHHHHHHHHHHHCCCCCCCCCCCCCCEEEEEEEEEECCCCCCCC
Q ss_conf             10001364000143026787887638899988774689999999999829745732146553269999997178775687
Q gi|254780376|r   25 RIKDVVSLQSGRDNQLIGYGLVVGLQGTGDSLRSSPFTEQSMRSLLQNLGISTPGGRLGSKNVAAVMVTANLPPFASPGS  104 (369)
Q Consensus        25 rikDi~~i~GvR~NqL~GyGLVVGL~GTGD~~~~~~~t~qsl~nml~~~Gv~~~~~~~~~kNvAaVmVtA~lPpfa~~G~  104 (369)
                      |||||++++|+|+|||+||||||||+||||+.++++||.|||+|||++||++++++++++||+|||||||+||||+|+||
T Consensus         1 RikDi~~v~GvR~NqLiGYGLVVGL~GTGD~~~~~~fT~qsl~nmL~~~Gv~v~~~~i~~kNvAaVmVTA~lPpfa~~G~   80 (342)
T pfam02119         1 RIKDIASIEGVRDNQLVGYGLVVGLNGTGDSLTQSPFTEQSLANMLERLGVNIPPNNIKSKNVAAVMVTATLPPFAKPGQ   80 (342)
T ss_pred             CCCCCCEEEEEEECCEEEEEEEEECCCCCCCCCCCCHHHHHHHHHHHHCCCCCCCCCCCCCEEEEEEEEEECCCCCCCCC
T ss_conf             94110005213554457789998238878887677308999999999759776866676542699999987277568998


Q ss_pred             EEEEEEECCCCCCCCCCCEEEEEECCCCCCCEEEEEECCEEECCCCCCCCCCCCCCCCCCCEEEECCEEEEEECCCCCCC
Q ss_conf             68999956888454447779995214778618999816168334324567652004765421741654887413543247
Q gi|254780376|r  105 RIDVSINSLGDASSLRGGILVMTSLLGADGNIYAVAQGSVVVSGLFVKGQSSSFMEGISTGGKIVNGAIVERELPKKFKD  184 (369)
Q Consensus       105 ~iDv~VSSiGdAkSL~GG~LL~TpL~g~dg~vyAvAQG~i~vgg~~~~g~~~~~~~n~~t~GrIp~Ga~VErev~~~f~~  184 (369)
                      ||||+||||||||||+||+||||||||+||+|||+||||+++|||+++++++++++||||+||||+||+||||++++|.+
T Consensus        81 ~iDVtVSSiGdAkSL~GGtLL~TPL~gadg~vYAvAQG~v~vgg~~~~~~g~~~~~n~pt~GrIp~GA~VErev~~~~~~  160 (342)
T pfam02119        81 RIDVTVSSIGDAKSLRGGTLLMTPLKGADGEVYAVAQGNLVVGGFGAEGAGSSVTVNVPTVGRIPNGAIVEREVPFDFGQ  160 (342)
T ss_pred             EEEEEEECCCCCCCCCCCEEEEEECCCCCCCEEEEECCCEEECCCCCCCCCCCEECCCCCCEEECCCEEEEECCCCCCCC
T ss_conf             48899976657656789778985224899878999407678724113577751110577603865862999715777677


Q ss_pred             CCEEEEEEECCCHHHHHHHHHHHHHHHCCCCCCCCEEEECCCEEEEECCCCC-CHHHHHHHHHCCCCCCCCCCEEEEECC
Q ss_conf             7649999507887899999999987520245654124511563686328875-212132232201268789835999447
Q gi|254780376|r  185 SADLILQLRNPDFSTAIRIADQINSYSLNRFSRPIAEAYDSRTVKVSKPTNI-DLTRLMSEVEMLTVETDTPARVIINER  263 (369)
Q Consensus       185 ~~~l~L~L~~pdfttA~~ia~aIN~~~~~~~g~~~A~a~d~~~I~v~~P~~~-~~v~fla~ie~l~V~~~~~akVVINer  263 (369)
                      .++++|+||+|||+||.||+++||+.    ||+++|+|+|+++|+|++|++| +.++|+|.+|+++|+|+++||||||||
T Consensus       161 ~~~l~l~L~~pdFtTA~ria~aIN~~----~g~~~A~a~D~~tV~v~~P~~~~~~v~fla~ie~l~V~p~~~arVVINeR  236 (342)
T pfam02119       161 GDSLTLNLRNPDFTTANRIADAINAR----FGPGVARALDARTIEVRAPRDYSQRVSFLAEIENLEVEPDAPAKVVINER  236 (342)
T ss_pred             CCEEEEEECCCCHHHHHHHHHHHHHH----HCCCCEEEECCCEEEEECCCCCCCHHHHHHHHHCCCCCCCCCCEEEEECC
T ss_conf             97289996698769999999999886----18895498579889996688854178999998538466788876999578


Q ss_pred             CCEEEECCCEEEEEEEEECCCEEEEECCCCCCCCCCCCCCCCCEEECCCCEEEECCCCCE-EEECCCCCHHHHHHHHHHC
Q ss_conf             634994597399899984170799963776665776545687344236641456046735-8973898899999999847
Q gi|254780376|r  264 TGTIVIGDNVRISKVVVSYGNLTVQITENEQVVQPNAFSSNGSTVTQNNTDLKVSDNKGS-FSLIDAPDLNSLISGMNSI  342 (369)
Q Consensus       264 TGTIV~g~~V~I~pvaVsHGnLtI~I~~~~~vsqp~~~~~~g~t~~~~~t~i~v~e~~~~-~~~~~~~tl~~lV~ALN~l  342 (369)
                      |||||||+||||+|||||||||+|+|+++++||||+|| ++|+|+++++|+++++|++++ +.++++++|+|||+|||++
T Consensus       237 TGTIV~g~~V~I~~vaVshGnLtv~I~~~~~vsQP~pf-~~g~tvv~~~t~i~v~e~~~~~~~~~~~~tl~~lV~aLN~l  315 (342)
T pfam02119       237 TGTIVIGQNVRISPVAVSHGNLTVTITETPQVSQPNPF-SGGQTVVVPRTDIDVEEEGGRLFVLPPGASLADLVRALNAL  315 (342)
T ss_pred             CCEEEECCCEEEEEEEEECCCEEEEECCCCCCCCCCCC-CCCCEEECCCCEEEEEECCCEEEECCCCCCHHHHHHHHHHC
T ss_conf             54199679669968899508679996267522478877-89831653786026640676069708999599999999866


Q ss_pred             CCCHHHHHHHHHHHHHCCCCCCEEEEC
Q ss_conf             998789999999998716856258969
Q gi|254780376|r  343 GLKTDGIISILQGIKAAGALQSEIIIQ  369 (369)
Q Consensus       343 G~tp~DlIsILqalk~aGAL~AELiI~  369 (369)
                      |++|+|||+||||||+||||||||||.
T Consensus       316 Gatp~DlIaILqalK~aGAL~AeL~ii  342 (342)
T pfam02119       316 GATPRDLIAILQALKAAGALHAELEVI  342 (342)
T ss_pred             CCCHHHHHHHHHHHHHCCCCEEEEEEC
T ss_conf             998799999999998778870789969


No 4  
>COG1706 FlgI Flagellar basal-body P-ring protein [Cell motility and secretion]
Probab=100.00  E-value=0  Score=918.84  Aligned_cols=362  Identities=55%  Similarity=0.832  Sum_probs=343.0

Q ss_pred             HHHHHHHHHHHHHHHCCCCHHHHHHEEEEEEEECCCCCEEEEEEEECCCCCCCCCCCCHHHHHHHHHHHHHCCCCCCCCC
Q ss_conf             67899999999997425700100100013640001430267878876388999887746899999999998297457321
Q gi|254780376|r    2 IFRIAFLIFSLIGLHEISAQVVSRIKDVVSLQSGRDNQLIGYGLVVGLQGTGDSLRSSPFTEQSMRSLLQNLGISTPGGR   81 (369)
Q Consensus         2 ~~~~~~l~~~~~~~~~~~~~~a~rikDi~~i~GvR~NqL~GyGLVVGL~GTGD~~~~~~~t~qsl~nml~~~Gv~~~~~~   81 (369)
                      |+++.+ ++.++++...++.+++|||||++++|+|+|||+||||||||+||||+.+++|||.||+.|||++|||.+|++.
T Consensus         2 ~~~~~~-~~~~~l~~~~~~~~a~rIKDiasiqgvRdNqLiGYGLVVGL~GtGD~~~~spfT~QSi~nML~~~gI~v~~~~   80 (365)
T COG1706           2 MLKLIT-LALLLLLTTAKAAQAERIKDIASIQGVRDNQLIGYGLVVGLDGTGDQLTQSPFTKQSINNMLEQLGIKVPPGD   80 (365)
T ss_pred             CEEHHH-HHHHHHHHHCCHHHHHHHHCCEEEECCCCCCEEEEEEEEECCCCCCCCCCCCCHHHHHHHHHHHCCCCCCCCC
T ss_conf             220489-9999998733056554330110450234562577779996156677655786539999999998697579998


Q ss_pred             -CCCCCEEEEEEEEEECCCCCCCCEEEEEEECCCCCCCCCCCEEEEEECCCCCCCEEEEEECCEEECCCCCCCCCCCCCC
Q ss_conf             -4655326999999717877568768999956888454447779995214778618999816168334324567652004
Q gi|254780376|r   82 -LGSKNVAAVMVTANLPPFASPGSRIDVSINSLGDASSLRGGILVMTSLLGADGNIYAVAQGSVVVSGLFVKGQSSSFME  160 (369)
Q Consensus        82 -~~~kNvAaVmVtA~lPpfa~~G~~iDv~VSSiGdAkSL~GG~LL~TpL~g~dg~vyAvAQG~i~vgg~~~~g~~~~~~~  160 (369)
                       +++||+|||||||+||||+++|+||||+||||||||||+|||||||||||+|||+||+|||++.+||+++.|.++++++
T Consensus        81 n~~sKNvAAVmVTA~LPpfa~~G~kiDv~VSSiGdAKSL~GGtLLmTpLkG~DGqiYAvAQG~vivgg~~a~g~~s~~~~  160 (365)
T COG1706          81 NIKSKNVAAVMVTASLPPFARQGSKIDVTVSSIGDAKSLRGGTLLMTPLKGADGQIYAVAQGNVIVGGFSAAGGGSSVTV  160 (365)
T ss_pred             CCCCCEEEEEEEECCCCCCCCCCCEEEEEEECCCCCCCCCCCEEEEEECCCCCCCEEEEEECCEEECCCCCCCCCCCEEC
T ss_conf             74400368999974689767899757899953555433569668861046888738999734587656445676642002


Q ss_pred             CCCCCEEEECCEEEEEECCCCCCCCCEEEEEEECCCHHHHHHHHHHHHHHHCCCCCCCCEEEECCCEEEEECCCCCCHHH
Q ss_conf             76542174165488741354324776499995078878999999999875202456541245115636863288752121
Q gi|254780376|r  161 GISTGGKIVNGAIVERELPKKFKDSADLILQLRNPDFSTAIRIADQINSYSLNRFSRPIAEAYDSRTVKVSKPTNIDLTR  240 (369)
Q Consensus       161 n~~t~GrIp~Ga~VErev~~~f~~~~~l~L~L~~pdfttA~~ia~aIN~~~~~~~g~~~A~a~d~~~I~v~~P~~~~~v~  240 (369)
                      |+||+||||+||+||||+|++|.+.+.++|+|++|||+||.||+++||.    .||.++|.|+|+.+|+++.|++++.++
T Consensus       161 ~~~t~Gri~nGAiIERevp~~f~~~~~~~l~L~~pdFttA~riad~iN~----~fg~~~A~aids~ti~v~~P~~~s~v~  236 (365)
T COG1706         161 NVPTSGRIPNGAIIEREVPSNFGDGNTLNLQLKNPDFTTAQRIADAINR----VFGKGIATAIDSRTIQVRVPKGASRVR  236 (365)
T ss_pred             CCCCCEECCCCCEEEECCCCCCCCCCEEEEEECCCCCHHHHHHHHHHHH----HHCCCCCCCCCCCCEEEECCCCCCHHH
T ss_conf             6644136058726873078776778559999679981789999999986----526343433477726885688863778


Q ss_pred             HHHHHHCCCCCCCCCCEEEEECCCCEEEECCCEEEEEEEEECCCEEEEECCCCCCCCCCCCCCCCCEEECCCCEEEECCC
Q ss_conf             32232201268789835999447634994597399899984170799963776665776545687344236641456046
Q gi|254780376|r  241 LMSEVEMLTVETDTPARVIINERTGTIVIGDNVRISKVVVSYGNLTVQITENEQVVQPNAFSSNGSTVTQNNTDLKVSDN  320 (369)
Q Consensus       241 fla~ie~l~V~~~~~akVVINerTGTIV~g~~V~I~pvaVsHGnLtI~I~~~~~vsqp~~~~~~g~t~~~~~t~i~v~e~  320 (369)
                      |||.+|+++|++|.+|||||||||||||+|+||+|+||||||||||++|.|.|.|+||+|| ++|+|+++|+|+|+++++
T Consensus       237 fla~ieni~I~~~~~aKVVIn~RTGtIV~g~~V~i~~~avs~g~ltv~I~e~p~v~qp~pf-~~gqt~v~p~t~I~v~~~  315 (365)
T COG1706         237 FLAEIENIEIETDTPAKVVINERTGTIVIGEDVKISPVAVSHGNLTVTITEQPNVSQPAPF-SGGQTVVVPKTTIEVNQE  315 (365)
T ss_pred             HHHHHHCCCCCCCCCCEEEEECCCCEEEECCCEEEEEEEEEECCEEEEEEECCCCCCCCCC-CCCCEEECCCCEEEEECC
T ss_conf             9988627521489986499957845699788548867889707678999816655788877-788334246760377437


Q ss_pred             CCE-EEECCCCCHHHHHHHHHHCCCCHHHHHHHHHHHHHCCCCCCEEEEC
Q ss_conf             735-8973898899999999847998789999999998716856258969
Q gi|254780376|r  321 KGS-FSLIDAPDLNSLISGMNSIGLKTDGIISILQGIKAAGALQSEIIIQ  369 (369)
Q Consensus       321 ~~~-~~~~~~~tl~~lV~ALN~lG~tp~DlIsILqalk~aGAL~AELiI~  369 (369)
                      ++. +.+..+++|+++|++||++|++|+|||+|||+||+||||+|||||+
T Consensus       316 ~~~~~~~~~~~tl~~lV~aLn~iGa~P~diiaILQalk~AGal~A~L~i~  365 (365)
T COG1706         316 KGKLFILKGGTTLNNLVRALNAIGATPQDIIAILQALKSAGALQAELEII  365 (365)
T ss_pred             CCEEEECCCCCCHHHHHHHHHHHCCCHHHHHHHHHHHHHCCCCCCCEEEC
T ss_conf             87378517888689999999984589789999999998758344344769


No 5  
>PRK12706 flgI flagellar basal body P-ring protein; Provisional
Probab=100.00  E-value=0  Score=733.89  Aligned_cols=310  Identities=27%  Similarity=0.424  Sum_probs=261.2

Q ss_pred             CHHHHHHHHHHHHHHHCC----------------CCHHHHHHEEEEEEEECCCCCEEEEEEEECCCCCCCCCCCCHHHHH
Q ss_conf             967899999999997425----------------7001001000136400014302678788763889998877468999
Q gi|254780376|r    1 MIFRIAFLIFSLIGLHEI----------------SAQVVSRIKDVVSLQSGRDNQLIGYGLVVGLQGTGDSLRSSPFTEQ   64 (369)
Q Consensus         1 m~~~~~~l~~~~~~~~~~----------------~~~~a~rikDi~~i~GvR~NqL~GyGLVVGL~GTGD~~~~~~~t~q   64 (369)
                      ||+++.+++++-+.+|..                +-..|+|||||++++|+|+|||+||||||||+||||+.+    +.|
T Consensus         1 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~aVRIKDia~v~GvR~NQLiGYGLVVGL~GTGD~~~----~~~   76 (328)
T PRK12706          1 MMKKLIMLIILNLSLFAQENQASKNFKNENSFNNQISESVKLKNIAEICPTNSNFLTGIGIVAGLADKGDSLK----QKD   76 (328)
T ss_pred             CCHHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHCCCCCEEEEEEEEEECCCCCCEEEEEEEEECCCCCCCCC----CHH
T ss_conf             9137688999851366552532323101211233255244551123340221264378889980488787765----369


Q ss_pred             HHHHHHHHCCCC-CCCCCCCCCCEEEEEEEEEECCCCCCCCEEEEEEECCCCCCCCCCCEEEEEECCCCCCCEEEEEECC
Q ss_conf             999999982974-5732146553269999997178775687689999568884544477799952147786189998161
Q gi|254780376|r   65 SMRSLLQNLGIS-TPGGRLGSKNVAAVMVTANLPPFASPGSRIDVSINSLGDASSLRGGILVMTSLLGADGNIYAVAQGS  143 (369)
Q Consensus        65 sl~nml~~~Gv~-~~~~~~~~kNvAaVmVtA~lPpfa~~G~~iDv~VSSiGdAkSL~GG~LL~TpL~g~dg~vyAvAQG~  143 (369)
                      ++.|||++|||+ .++.++++||+|||||||+||||+||||+||||||||||||||+||+||||||||+||+|||+||||
T Consensus        77 sl~nmL~~~GV~~~~~~~~~~kNvAAVmVTA~LPpFAk~Gq~iDVtVSSiGDAkSL~GGtLLmTPLkGaDG~VYAvAQG~  156 (328)
T PRK12706         77 ILNKILNEIGINEIDLTNIGSKNIALVNVSLQINGNMIKGSKHNVYIASMLDSKDLTNGILLKTELKDKEGKILATASGP  156 (328)
T ss_pred             HHHHHHHHCCCCCCCCCCCCCCEEEEEEEECCCCCCCCCCCEEEEEEECCCCCCCCCCCEEEEEECCCCCCCEEEEEECC
T ss_conf             99999997599878866777533699999725787668997067999746575567897788742368998689998557


Q ss_pred             EEECCCCCCCCCCCCCCCCCCCEEEECCEEEEEECCCCCCCCCEEEEEEECCCHHHHHHHHHHHHHHHCCCCCCCCEEEE
Q ss_conf             68334324567652004765421741654887413543247764999950788789999999998752024565412451
Q gi|254780376|r  144 VVVSGLFVKGQSSSFMEGISTGGKIVNGAIVERELPKKFKDSADLILQLRNPDFSTAIRIADQINSYSLNRFSRPIAEAY  223 (369)
Q Consensus       144 i~vgg~~~~g~~~~~~~n~~t~GrIp~Ga~VErev~~~f~~~~~l~L~L~~pdfttA~~ia~aIN~~~~~~~g~~~A~a~  223 (369)
                      +++||+.            +.+||||+||+|||+.+.+     +++|+|++|||+||.||+++||..    ++...+.+ 
T Consensus       157 l~vgg~~------------~g~G~I~nGA~VEr~~~~~-----~~~l~L~~pDFtTA~ria~ain~~----~~~~~~~~-  214 (328)
T PRK12706        157 IITNNKS------------KGTGYILNGATIHENQNYT-----HYNIILKKGDYTLINRISKILTSK----NIKNNIKS-  214 (328)
T ss_pred             EEECCCC------------CCCCCCCCCCEEEEECCCC-----EEEEEECCCCCHHHHHHHHHHHHH----HHCCCCCC-
T ss_conf             8867846------------6653626875677506886-----068996699916999999998531----00001468-


Q ss_pred             CCCEEEEECCCCCCHHHHHHHHHCCCCCCCCCCEEEEECCCCEEEECCCEEEEEEEEECCCEEEEECCCCCCCCCCCCCC
Q ss_conf             15636863288752121322322012687898359994476349945973998999841707999637766657765456
Q gi|254780376|r  224 DSRTVKVSKPTNIDLTRLMSEVEMLTVETDTPARVIINERTGTIVIGDNVRISKVVVSYGNLTVQITENEQVVQPNAFSS  303 (369)
Q Consensus       224 d~~~I~v~~P~~~~~v~fla~ie~l~V~~~~~akVVINerTGTIV~g~~V~I~pvaVsHGnLtI~I~~~~~vsqp~~~~~  303 (369)
                       ...+++++    +.+.|+|.+|+++|+  .+|||||||||||||||+||||       |+|+|+|++++    +++|.+
T Consensus       215 -~~~v~v~~----~~v~fla~iEnl~V~--~~ArVVVNeRTGTIV~G~~VrI-------g~ltVsI~e~~----~~v~~~  276 (328)
T PRK12706        215 -GNIIEIEV----KNIGLLEEIENIEIE--TMPKVLIDEQNKIILASTNAEI-------GPLTFSIERDD----QNLFNN  276 (328)
T ss_pred             -CCCEEEEC----CHHHHHHHHHCCCCC--CCCEEEEECCCCEEEECCCEEE-------ECEEEEEEECC----CCCCCC
T ss_conf             -87268853----230598886377778--8984999799672998899599-------06699998579----630158


Q ss_pred             CCCEEECCCCEEEECCCCCEEEECCCCCHHHHHHHHHHCCCCHHHHHHHHHHHHHCCCCCCEEEEC
Q ss_conf             873442366414560467358973898899999999847998789999999998716856258969
Q gi|254780376|r  304 NGSTVTQNNTDLKVSDNKGSFSLIDAPDLNSLISGMNSIGLKTDGIISILQGIKAAGALQSEIIIQ  369 (369)
Q Consensus       304 ~g~t~~~~~t~i~v~e~~~~~~~~~~~tl~~lV~ALN~lG~tp~DlIsILqalk~aGAL~AELiI~  369 (369)
                      +.        ...+      ....+..+++++|.+ |++|++|+|||+||||||+||||||||+||
T Consensus       277 ~~--------~~~~------~v~~~~~~l~~~V~~-N~~G~sprDlIaILQAlK~AGAL~AELVVQ  327 (328)
T PRK12706        277 KN--------NKTI------KIQIQKMKLNEFISK-NSNNLSNKELIQIIKAAKKINKLNGELILE  327 (328)
T ss_pred             CC--------CEEE------EEECCCCCHHHHEEC-CCCCCCHHHHHHHHHHHHHCCCCCEEEEEC
T ss_conf             98--------5479------996266656650003-658998689999999998738641699850


No 6  
>TIGR03177 pilus_cpaB Flp pilus assembly protein CpaB. Members of this protein family are the CpaB protein of Flp-type pilus assembly. Similar proteins include the FlgA protein of bacterial flagellum biosynthesis.
Probab=76.56  E-value=6.1  Score=19.69  Aligned_cols=88  Identities=24%  Similarity=0.291  Sum_probs=45.2

Q ss_pred             EECCCCCCCCEEEEEEECCCCCCCCCCCEEEEEECCCCCCCEEEEEECCEEECCCCCCCCCCCCCCCCCCCEEEECCEEE
Q ss_conf             71787756876899995688845444777999521477861899981616833432456765200476542174165488
Q gi|254780376|r   95 NLPPFASPGSRIDVSINSLGDASSLRGGILVMTSLLGADGNIYAVAQGSVVVSGLFVKGQSSSFMEGISTGGKIVNGAIV  174 (369)
Q Consensus        95 ~lPpfa~~G~~iDv~VSSiGdAkSL~GG~LL~TpL~g~dg~vyAvAQG~i~vgg~~~~g~~~~~~~n~~t~GrIp~Ga~V  174 (369)
                      -.-.|.+|||++||.++.-.+...=..+.  .|..-=.|-+|.|+.|-.-       .+..        ...+.++-.++
T Consensus       126 gv~Gfi~PGD~VDVl~t~~~~~~~~~~~~--~t~tiL~~v~VLAv~q~~~-------~~~~--------~~~~~~~tVTL  188 (261)
T TIGR03177       126 GVGGFILPGDRVDVLLTRRDDESRPNDRA--TSETVLQNIRVLAVDQTAQ-------EGED--------TKPKVVRTVTL  188 (261)
T ss_pred             CCCCCCCCCCEEEEEEEECCCCCCCCCCE--EHHHHHHCCEEEEECCCCC-------CCCC--------CCCCCCEEEEE
T ss_conf             55664689997899998505788776641--2120222867999536445-------6667--------88866248999


Q ss_pred             EEECCC----C-CCCCCEEEEEEECCCHHH
Q ss_conf             741354----3-247764999950788789
Q gi|254780376|r  175 ERELPK----K-FKDSADLILQLRNPDFST  199 (369)
Q Consensus       175 Erev~~----~-f~~~~~l~L~L~~pdftt  199 (369)
                      |-...-    . -.+..+|.|.||+++=..
T Consensus       189 evtp~qa~~L~lA~~~G~L~LaLR~~~D~~  218 (261)
T TIGR03177       189 EVTPEQAEKLALARQVGTLSLALRNAADTD  218 (261)
T ss_pred             EECHHHHHHHHHHHHCCEEEEEEECCCCCC
T ss_conf             879999999999862685999951887677


No 7  
>TIGR01172 cysE serine O-acetyltransferase; InterPro: IPR005881    The biosynthesis of L-cysteine is the predominant way by which inorganic sulphur is incorporated into organic compounds. In this process, the most abundant utilizable source of sulphur, inorganic sulphate, is taken up and reduced to sulphide. Sulphide is used to produce L-cysteine, which serves for protein synthesis or the production of other sulphur-containing organic compounds. Two routes for cysteine biosynthesis in nature have been documented. Serine transacetylase (2.3.1.30 from EC) catalyzes steps in pathway I, the activation of L-serine by acetyl-coenzyme A, yielding O-acetyl-L-serine.; GO: 0009001 serine O-acetyltransferase activity, 0006535 cysteine biosynthetic process from serine, 0005737 cytoplasm.
Probab=69.73  E-value=6.4  Score=19.57  Aligned_cols=45  Identities=22%  Similarity=0.472  Sum_probs=36.0

Q ss_pred             HHHHHHHHHCCCCCCCCC--CEEEEECCCCEEEECCCEEEE-EEEEECC
Q ss_conf             121322322012687898--359994476349945973998-9998417
Q gi|254780376|r  238 LTRLMSEVEMLTVETDTP--ARVIINERTGTIVIGDNVRIS-KVVVSYG  283 (369)
Q Consensus       238 ~v~fla~ie~l~V~~~~~--akVVINerTGTIV~g~~V~I~-pvaVsHG  283 (369)
                      ...|++.+-.+||.|..+  .||.||=-+| ||+|+-..|. -|.|-||
T Consensus        52 ~~~~~r~~tgidIHPgA~IG~g~fIDHg~G-vVIGETa~iGddv~iyhG   99 (163)
T TIGR01172        52 ISNFIRVLTGIDIHPGARIGRGVFIDHGTG-VVIGETAEIGDDVTIYHG   99 (163)
T ss_pred             HHHHHHHHCCCCCCCCCCCCCEEEEECCCC-EEEEEEEEECCCEEEEEC
T ss_conf             987665530232176430077307775603-685003687388378632


No 8  
>cd05635 LbH_unknown Uncharacterized proteins, Left-handed parallel beta-Helix (LbH) domain: Members in this group are uncharacterized bacterial proteins containing a LbH domain with multiple turns, each containing three imperfect tandem repeats of a hexapeptide repeat motif (X-[STAV]-X-[LIV]-[GAED]-X). Proteins containing hexapeptide repeats are often enzymes showing acyltransferase activity.
Probab=67.39  E-value=4.5  Score=20.63  Aligned_cols=56  Identities=20%  Similarity=0.291  Sum_probs=37.6

Q ss_pred             EEEEECCCCEEEECCCEEEEEEEEECCCEEEEECCCCCCCCCCCCCCCCCEEECCCCEEE
Q ss_conf             599944763499459739989998417079996377666577654568734423664145
Q gi|254780376|r  257 RVIINERTGTIVIGDNVRISKVVVSYGNLTVQITENEQVVQPNAFSSNGSTVTQNNTDLK  316 (369)
Q Consensus       257 kVVINerTGTIV~g~~V~I~pvaVsHGnLtI~I~~~~~vsqp~~~~~~g~t~~~~~t~i~  316 (369)
                      -+++|++.|-|+++.+++|.|-++-.|+..|  .+.-.+ .|+.+.- +.+..-+...+.
T Consensus         2 ~~~~d~~~GpV~I~~~~~I~~~~~i~Gp~~I--G~~~~I-~p~a~Ir-~~t~Ig~~~~IG   57 (101)
T cd05635           2 GAVLDAEDGPIYIGKDAVIEPFAVIEGPVYI--GPGSRV-KMGARIY-GNTTIGPTCKIG   57 (101)
T ss_pred             CCEEECCCCCEEECCCCEECCCCEEECCEEE--CCCCEE-CCCCEEE-CCCEECCCCEEC
T ss_conf             7178789899998799999999999766699--999999-9997863-887999997761


No 9  
>TIGR00014 arsC arsenate reductase; InterPro: IPR006659   This entry describes a distinct clade, including ArsC itself, of the broader family of ArsC and related proteins. This clade is almost completely restricted to the proteobacteria. An anion-translocating ATPase has been identified as the product of the arsenical resistance operon of resistance plasmid R773 . When expressed in Escherichia coli this ATP-driven oxyanion pump catalyses extrusion of the oxyanions arsenite, antimonite and arsenate. The pump is composed of two polypeptides, the products of the arsA and arsB genes. The pump alone produces resistance to arsenite and antimonite. This protein, ArsC, catalyzes the reduction of arsenate to arsenite, and thus extends resistance to include arsenate. ; GO: 0008794 arsenate reductase (glutaredoxin) activity, 0006118 electron transport.
Probab=66.48  E-value=4.6  Score=20.53  Aligned_cols=36  Identities=19%  Similarity=0.375  Sum_probs=29.6

Q ss_pred             EECCCCCHHHHHHHHHHCCCCH-HHHHHHHHHHHHCCCCCCEE
Q ss_conf             9738988999999998479987-89999999998716856258
Q gi|254780376|r  325 SLIDAPDLNSLISGMNSIGLKT-DGIISILQGIKAAGALQSEI  366 (369)
Q Consensus       325 ~~~~~~tl~~lV~ALN~lG~tp-~DlIsILqalk~aGAL~AEL  366 (369)
                      +|++..|.++|=+.+|++|+|| ||+|      +.-++++.||
T Consensus        31 YL~~pp~~seL~~~~~~LG~~~ar~~~------R~ke~~y~eL   67 (114)
T TIGR00014        31 YLKNPPTKSELKALLAKLGISSAREMI------RTKEELYKEL   67 (114)
T ss_pred             CCCCCCCHHHHHHHHHHCCCCHHHHHC------CCCCCCCCCC
T ss_conf             458974868899999870897036301------1765210004


No 10 
>PTZ00298 mevalonate kinase; Provisional
Probab=52.05  E-value=17  Score=16.60  Aligned_cols=36  Identities=19%  Similarity=0.302  Sum_probs=29.4

Q ss_pred             CHHHHHH----HHHHCCCCHHHHHHHHHHHHHCCCCCCEE
Q ss_conf             8999999----99847998789999999998716856258
Q gi|254780376|r  331 DLNSLIS----GMNSIGLKTDGIISILQGIKAAGALQSEI  366 (369)
Q Consensus       331 tl~~lV~----ALN~lG~tp~DlIsILqalk~aGAL~AEL  366 (369)
                      .|.+|.+    -|+++|++...|=.+.+..++.|||.|.|
T Consensus       241 ~lG~Lm~~nh~lL~~lgVS~p~Ld~lv~~a~~~GAlGAKL  280 (328)
T PTZ00298        241 RVGELMNANHDLCQKLTVSCRELDSIVQTCRTYGALGAKM  280 (328)
T ss_pred             HHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHCCCCEEEE
T ss_conf             9999999999989746889789999999999769965575


No 11 
>TIGR01676 GLDHase galactonolactone dehydrogenase; InterPro: IPR010029   This entry identifies L-galactono-gamma-lactone dehydrogenase 1.3.2.3 from EC. This enzyme performs the final step in ascorbic acid biosynthesis in higher plants. The protein is homologous to ascorbic acid biosynthesis enzymes of other species: L-gulono-gamma-lactone oxidase in rat and L-galactono-gamma-lactone oxidase in yeast. All three covalently bind the cofactor FAD..
Probab=51.53  E-value=14  Score=17.12  Aligned_cols=38  Identities=21%  Similarity=0.354  Sum_probs=17.1

Q ss_pred             EEECCCCCEEEECCCCCHHHHHHHHHHCCCCHHHHHHH
Q ss_conf             45604673589738988999999998479987899999
Q gi|254780376|r  315 LKVSDNKGSFSLIDAPDLNSLISGMNSIGLKTDGIISI  352 (369)
Q Consensus       315 i~v~e~~~~~~~~~~~tl~~lV~ALN~lG~tp~DlIsI  352 (369)
                      ..+++++..+.++.|..+++||+++..-|.|-+..-+|
T Consensus       117 l~vd~ekk~v~vqaGirvqqlvd~ikeyG~tlqnfasi  154 (541)
T TIGR01676       117 LEVDKEKKRVRVQAGIRVQQLVDAIKEYGLTLQNFASI  154 (541)
T ss_pred             HHHHCCCCEEEEEECCHHHHHHHHHHHHCCHHHHHHHH
T ss_conf             75302345788840621668887788623035555554


No 12 
>TIGR02324 CP_lyasePhnL phosphonate C-P lyase system protein PhnL; InterPro: IPR012701    Members of this family are the PhnL protein of C-P lyase systems for utilization of phosphonates. These systems resemble phosphonatase-based systems in having a three-component ABC transporter, where IPR005769 from INTERPRO is the permease, IPR005770 from INTERPRO is the phosphonates binding protein, and IPR012693 from INTERPRO is the ATP-binding cassette (ABC) protein. They differ, however, in having, typically, ten or more additional genes, many of which are believed to form a membrane-associated C-P lyase complex. This protein (PhnL) and the adjacent-encoded PhnK (IPR012700 from INTERPRO) resemble transporter ATP-binding proteins but are suggested, based on mutagenesis studies, to be part of this C-P lyase complex rather than part of a transporter per se ..
Probab=50.11  E-value=5.7  Score=19.90  Aligned_cols=53  Identities=21%  Similarity=0.251  Sum_probs=30.7

Q ss_pred             CCCCCCCCCEEECCCCEEEECCCCCEEEECCCCCHHHHHHHHHHCCCCHHH-HHHHHHHHHHCCC
Q ss_conf             765456873442366414560467358973898899999999847998789-9999999987168
Q gi|254780376|r  298 PNAFSSNGSTVTQNNTDLKVSDNKGSFSLIDAPDLNSLISGMNSIGLKTDG-IISILQGIKAAGA  361 (369)
Q Consensus       298 p~~~~~~g~t~~~~~t~i~v~e~~~~~~~~~~~tl~~lV~ALN~lG~tp~D-lIsILqalk~aGA  361 (369)
                      |+-| +|||..=++=+.--+.+.+--+.+++++||++          +-|. +|..++.+|+.||
T Consensus       147 PaTF-SGGEqQRVNIARg~i~d~PiLLLdEPTASLd~----------~nr~vVvELi~e~K~~G~  200 (224)
T TIGR02324       147 PATF-SGGEQQRVNIARGFIADYPILLLDEPTASLDA----------TNRKVVVELIAEAKARGA  200 (224)
T ss_pred             CCCC-CCCHHHHHHHHHHHHCCCCCCCCCCCCCCCCC----------CCHHHHHHHHHHHHHCCC
T ss_conf             8865-66058999998765257740011355402411----------424889999999976597


No 13 
>pfam00207 A2M Alpha-2-macroglobulin family. This family includes the C-terminal region of the alpha-2-macroglobulin family.
Probab=49.73  E-value=16  Score=16.83  Aligned_cols=25  Identities=20%  Similarity=0.410  Sum_probs=16.3

Q ss_pred             EEEEEEEECCCCCCCCEEEEEEECC
Q ss_conf             9999997178775687689999568
Q gi|254780376|r   89 AVMVTANLPPFASPGSRIDVSINSL  113 (369)
Q Consensus        89 aVmVtA~lPpfa~~G~~iDv~VSSi  113 (369)
                      -.++.-+||.|.++|+++.+.|+-.
T Consensus        55 p~~i~~~lP~~~~~Gd~~~i~v~v~   79 (92)
T pfam00207        55 PFFVDLNLPYSVRRGEQVEIKATVF   79 (92)
T ss_pred             CEEEEECCCCEEECCCEEEEEEEEE
T ss_conf             6899826996797499999999999


No 14 
>PRK04792 tolB translocation protein TolB; Provisional
Probab=49.39  E-value=9.9  Score=18.23  Aligned_cols=68  Identities=19%  Similarity=0.195  Sum_probs=34.6

Q ss_pred             CHHHHHHHHHHHHHHHCCCCHHHHHHEEEEEEEECCCCCE-EEEEEEECCCCCCCCCCCCHHHHHHHHHHHHHCCCC
Q ss_conf             9678999999999974257001001000136400014302-678788763889998877468999999999982974
Q gi|254780376|r    1 MIFRIAFLIFSLIGLHEISAQVVSRIKDVVSLQSGRDNQL-IGYGLVVGLQGTGDSLRSSPFTEQSMRSLLQNLGIS   76 (369)
Q Consensus         1 m~~~~~~l~~~~~~~~~~~~~~a~rikDi~~i~GvR~NqL-~GyGLVVGL~GTGD~~~~~~~t~qsl~nml~~~Gv~   76 (369)
                      ||+++++.++++++++...+++..+| +|+  +|+ ++++ |-   |+=....|+..-... -.+-+.+-|++-|.=
T Consensus         1 M~k~~~~~l~lll~~~s~~A~A~L~I-eIt--~G~-~~~~PIA---V~pF~~~g~~~~~~~-i~~II~~DL~rSG~F   69 (450)
T PRK04792          1 MLKRLILGLFVLLLSFSQVANAALEL-VIT--DGI-DSARPIA---IVPFKWEGEGKLPTD-ISAVIASDLQRSGKF   69 (450)
T ss_pred             CCHHHHHHHHHHHHHHHHHHEEEEEE-EEE--CCC-CCCCCEE---EECCCCCCCCCHHHH-HHHHHHHHHHHCCCC
T ss_conf             93899999999999865752024999-995--477-7742549---937545687432579-999999887608785


No 15 
>PRK13861 type IV secretion system protein VirB9; Provisional
Probab=46.91  E-value=12  Score=17.58  Aligned_cols=21  Identities=19%  Similarity=0.316  Sum_probs=11.1

Q ss_pred             HHHHHHHHHHHHHHHCCCCHH
Q ss_conf             678999999999974257001
Q gi|254780376|r    2 IFRIAFLIFSLIGLHEISAQV   22 (369)
Q Consensus         2 ~~~~~~l~~~~~~~~~~~~~~   22 (369)
                      |||.++++++++++..+++++
T Consensus         1 mmk~l~~~~~~~l~~~~~a~A   21 (293)
T PRK13861          1 MIKKLFLTLACLLFAAIGALA   21 (293)
T ss_pred             CCHHHHHHHHHHHHHHHHHHH
T ss_conf             908999999999986126678


No 16 
>PRK09405 aceE pyruvate dehydrogenase subunit E1; Reviewed
Probab=45.38  E-value=19  Score=16.28  Aligned_cols=41  Identities=20%  Similarity=0.502  Sum_probs=29.8

Q ss_pred             EEEEEEEECCCCCCCCCC--CCHHHHHHHHHHHHHCCCCCCCCCC
Q ss_conf             267878876388999887--7468999999999982974573214
Q gi|254780376|r   40 LIGYGLVVGLQGTGDSLR--SSPFTEQSMRSLLQNLGISTPGGRL   82 (369)
Q Consensus        40 L~GyGLVVGL~GTGD~~~--~~~~t~qsl~nml~~~Gv~~~~~~~   82 (369)
                      .-||||  |..|-|+...  ...++...|...=.+||+.++..++
T Consensus       391 VKGyGl--g~ageg~N~aHQ~Kkl~~e~l~~fRdrf~iPisDe~~  433 (886)
T PRK09405        391 IKGYGM--GEAGEGKNIAHQVKKLDLDDLKHFRDRFNIPISDEQL  433 (886)
T ss_pred             EECCCC--CCCCCCCCHHHHCCCCCHHHHHHHHHHCCCCCCHHHC
T ss_conf             642666--7444454201100359999999999985999884551


No 17 
>pfam08784 RPA_C Replication protein A C terminal. This domain corresponds to the C terminal of the single stranded DNA binding protein RPA (replication protein A). RPA is involved in many DNA metabolic pathways including DNA replication, DNA repair, recombination, cell cycle and DNA damage checkpoints.
Probab=43.90  E-value=23  Score=15.69  Aligned_cols=36  Identities=19%  Similarity=0.332  Sum_probs=32.3

Q ss_pred             CCCCCHHHHHHHHHHCCCCHHHHHHHHHHHHHCCCCCC
Q ss_conf             38988999999998479987899999999987168562
Q gi|254780376|r  327 IDAPDLNSLISGMNSIGLKTDGIISILQGIKAAGALQS  364 (369)
Q Consensus       327 ~~~~tl~~lV~ALN~lG~tp~DlIsILqalk~aGAL~A  364 (369)
                      .+|..+++|.+.||  |.+..|+-.+++.|-..|.++-
T Consensus        63 ~eG~h~~~l~~~l~--~~~~~~i~~a~d~L~~eG~IYs   98 (103)
T pfam08784        63 EEGVHVDELAAQLN--GLPVNDIRQAVDFLSNEGHIYS   98 (103)
T ss_pred             CCCCCHHHHHHHHC--CCCHHHHHHHHHHHHHCCEEEE
T ss_conf             88727999999982--9999999999999984880664


No 18 
>pfam00791 ZU5 ZU5 domain. Domain present in ZO-1 and Unc5-like netrin receptors Domain of unknown function.
Probab=43.08  E-value=24  Score=15.60  Aligned_cols=38  Identities=24%  Similarity=0.425  Sum_probs=29.2

Q ss_pred             EEEEECCCC-CCCCEEEEEEECCCCCCC---CCCCEEEEEEC
Q ss_conf             999717877-568768999956888454---44777999521
Q gi|254780376|r   92 VTANLPPFA-SPGSRIDVSINSLGDASS---LRGGILVMTSL  129 (369)
Q Consensus        92 VtA~lPpfa-~~G~~iDv~VSSiGdAkS---L~GG~LL~TpL  129 (369)
                      |+-.+||.| .+|.++.|+..-.-|.++   |++|.-|++|.
T Consensus        23 vsL~IPpgAi~~~~~~~i~l~v~~~~~~~p~l~~gE~llSpv   64 (103)
T pfam00791        23 VSLLIPPGAIPQGTRYEIYLTVNQRESTPPPLEEGETLLSPV   64 (103)
T ss_pred             EEEEECCCCCCCCCEEEEEEEEECCCCCCCCCCCCCEEECCE
T ss_conf             599979986689988999999815889999788985888998


No 19 
>PRK03629 tolB translocation protein TolB; Provisional
Probab=42.73  E-value=12  Score=17.78  Aligned_cols=67  Identities=21%  Similarity=0.181  Sum_probs=39.7

Q ss_pred             HHHHHHHHHHHHHHHCCCCHHHHHHEEEEEEEECCCCCE-EEEEEEECCCCCCCCCCCCHHHHHHHHHHHHHCCCC
Q ss_conf             678999999999974257001001000136400014302-678788763889998877468999999999982974
Q gi|254780376|r    2 IFRIAFLIFSLIGLHEISAQVVSRIKDVVSLQSGRDNQL-IGYGLVVGLQGTGDSLRSSPFTEQSMRSLLQNLGIS   76 (369)
Q Consensus         2 ~~~~~~l~~~~~~~~~~~~~~a~rikDi~~i~GvR~NqL-~GyGLVVGL~GTGD~~~~~~~t~qsl~nml~~~Gv~   76 (369)
                      |+++++++|.|++++...++++.+|.   =-+| .++++ |.   |+=....|++..... -.+-+.+-|.+-|.=
T Consensus         1 mk~~~~~~f~~lll~~~~a~A~L~I~---It~G-~~~~~PIA---V~pF~~~g~~~~~~~-i~~II~~DL~rSG~F   68 (430)
T PRK03629          1 MKQALRVAFGFLILWASVLHAEVRIE---ITQG-VDSARPIG---VVPFKWAGPGAAPED-IGGIVAADLRNSGKF   68 (430)
T ss_pred             CCHHHHHHHHHHHHHHHHHCEEEEEE---EECC-CCCCCCEE---EECCCCCCCCCCHHH-HHHHHHHHHHHCCCC
T ss_conf             90148889989998754422379999---9346-67732569---928644788864678-999998768757781


No 20 
>TIGR01990 bPGM beta-phosphoglucomutase; InterPro: IPR010972   This model represents the beta-phosphoglucomutase enzyme which catalyses the interconversion of beta-D-glucose-1-phosphate and beta-D-glucose-6-phosphate. The 6-phosphate is capable of non-enzymatic anomerization (alpha to beta or vice versa) while the 1-phosphate is not. A separate enzyme is responsible for the isomerisation of the alpha anomers. Beta-D-glucose-1-phosphate results from the phosphorolysis of maltose (2.4.1.8 from EC), trehalose (2.4.1.64 from EC) or trehalose-6-phosphate (2.4.1.216 from EC). Alternatively, these reactions can be run in the synthetic direction to create the disaccharides. All sequenced genomes which contain a member of this family also appear to contain at least one putative maltose or trehalose phosphorylase. Three species, Lactococcus, Enterococcus and Neisseria appear to contain a pair of paralogous beta-PGM's.   Beta-phosphoglucomutase is a member of the haloacid dehalogenase superfamily of hydrolase enzymes. These enzymes are characterised by a series of three catalytic motifs positioned within an alpha-beta (Rossman) fold . Beta-PGM contains an inserted alpha helical domain in between the first and second conserved motifs and thus is a member of subfamily IA of the superfamily , . The third catalytic motif comes in three variants, the third of which, containing a conserved DD or ED, is the only one found here as well as in several other related enzymes.    The enzyme from Lactococcus lactis has been extensively characterised including a remarkable crystal structure which traps the pentacoordinate transition state . .
Probab=41.85  E-value=22  Score=15.79  Aligned_cols=29  Identities=28%  Similarity=0.583  Sum_probs=24.5

Q ss_pred             HHHHHHHHCCCCHHHHHHH------HHHHHHCCCC
Q ss_conf             9999998479987899999------9999871685
Q gi|254780376|r  334 SLISGMNSIGLKTDGIISI------LQGIKAAGAL  362 (369)
Q Consensus       334 ~lV~ALN~lG~tp~DlIsI------Lqalk~aGAL  362 (369)
                      =...|...||++|.+-|.|      ++|||+||..
T Consensus       151 IFL~AA~~LGv~P~~cigiEDA~AGI~ai~~aGm~  185 (190)
T TIGR01990       151 IFLAAAEGLGVSPEECIGIEDAQAGIEAIKAAGMF  185 (190)
T ss_pred             HHHHHHHHCCCCHHHHHHEECHHHHHHHHHHCCCE
T ss_conf             99999976389755701012258999999975953


No 21 
>TIGR00021 rpiA ribose 5-phosphate isomerase A; InterPro: IPR004788 Ribose 5-phosphate isomerase (5.3.1.6 from EC), also known as phosphoriboisomerase, catalyses the conversion of D-ribose 5-phosphate to D-ribulose 5-phosphate in the non-oxidative branch of the pentose phosphate pathway.; GO: 0004751 ribose-5-phosphate isomerase activity, 0009052 pentose-phosphate shunt non-oxidative branch.
Probab=41.15  E-value=15  Score=17.05  Aligned_cols=63  Identities=25%  Similarity=0.448  Sum_probs=41.3

Q ss_pred             EEEECCCCCCCCCCCCHHHHHHHHHHHHH-CCC-CCCCCCCCCCCEEEEEEEEEECCCC-CCCCEEEEEEE
Q ss_conf             78876388999887746899999999998-297-4573214655326999999717877-56876899995
Q gi|254780376|r   44 GLVVGLQGTGDSLRSSPFTEQSMRSLLQN-LGI-STPGGRLGSKNVAAVMVTANLPPFA-SPGSRIDVSIN  111 (369)
Q Consensus        44 GLVVGL~GTGD~~~~~~~t~qsl~nml~~-~Gv-~~~~~~~~~kNvAaVmVtA~lPpfa-~~G~~iDv~VS  111 (369)
                      |.+||| |||..   ..|..+.|..+.++ =+. ++- .-..|+-++.-....-||=.. -+=++||++|-
T Consensus        16 Gm~~Gl-GTGST---~~~~i~~LG~~v~~Ge~l~~i~-gVpTS~~t~~lA~~~GIpl~~l~~~~~lDltID   81 (236)
T TIGR00021        16 GMVVGL-GTGST---VAYFIEALGERVKQGEGLDNIV-GVPTSKQTAELARELGIPLSSLDEVPELDLTID   81 (236)
T ss_pred             CCEEEE-CCHHH---HHHHHHHHHHHHHCCCCCCCCE-EEECHHHHHHHHHHCCCEEECCCCCCEEEEEEE
T ss_conf             978982-45046---8999999998743677556435-884838999999982980402255772006860


No 22 
>TIGR00549 mevalon_kin mevalonate kinase; InterPro: IPR006205   Mevalonate kinase (2.7.1.36 from EC) is well-characterised among the Eukaryotes, where it plays a role in the synthesis of isopentanyl pyrophosphate, a common intermediate for a number of pathways including cholesterol biosynthesis. It is also involved in mevalonate catabolism. Close homologs are found in the Archaea. A bacterial example is found in the Lyme disease spirochete Borrelia burgdorferi, but is not necessarily the same biosynthetic enzyme.; GO: 0004496 mevalonate kinase activity, 0005524 ATP binding, 0008299 isoprenoid biosynthetic process, 0005737 cytoplasm.
Probab=39.28  E-value=27  Score=15.21  Aligned_cols=37  Identities=22%  Similarity=0.419  Sum_probs=30.1

Q ss_pred             CCHHHHHH----HHHHCCCCHHHHHHHHHHHHHCCCCCCEE
Q ss_conf             88999999----99847998789999999998716856258
Q gi|254780376|r  330 PDLNSLIS----GMNSIGLKTDGIISILQGIKAAGALQSEI  366 (369)
Q Consensus       330 ~tl~~lV~----ALN~lG~tp~DlIsILqalk~aGAL~AEL  366 (369)
                      .+|.+|-+    -|.+||++.+.|=.+....+++|||-|.|
T Consensus       293 ~~lg~lm~~nq~lL~~lGVS~~~ld~l~~~~~~~GAlGaKl  333 (345)
T TIGR00549       293 ESLGELMNINQGLLKALGVSTPKLDQLVELARKAGALGAKL  333 (345)
T ss_pred             HHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHCCCCEEEE
T ss_conf             99999999999888870798579999999998679746310


No 23 
>PRK10431 N-acetylmuramoyl-l-alanine amidase II; Provisional
Probab=38.67  E-value=28  Score=15.15  Aligned_cols=35  Identities=17%  Similarity=0.262  Sum_probs=21.5

Q ss_pred             CHHHHHHHHHHHHHHHCCCCHHHHHHEEEEEEEECC
Q ss_conf             967899999999997425700100100013640001
Q gi|254780376|r    1 MIFRIAFLIFSLIGLHEISAQVVSRIKDVVSLQSGR   36 (369)
Q Consensus         1 m~~~~~~l~~~~~~~~~~~~~~a~rikDi~~i~GvR   36 (369)
                      ||+++.++++++++++...+. |.-|+|+--...-.
T Consensus         1 ~~~~~r~~~~~~l~l~~~~a~-Aa~v~~vRvw~a~d   35 (444)
T PRK10431          1 MMYRIRNWLVATLLLLCAQAG-AATLSDIQVSNGNQ   35 (444)
T ss_pred             CHHHHHHHHHHHHHHHHHHHH-HHHHCEEEEECCCC
T ss_conf             917999999999999876766-51204289507998


No 24 
>cd02017 TPP_E1_EcPDC_like Thiamine pyrophosphate (TPP) family, E1 of E. coli PDC-like subfamily, TPP-binding module; composed of proteins similar to the E1 component of the Escherichia coli pyruvate dehydrogenase multienzyme complex (PDC). PDC catalyzes the oxidative decarboxylation of pyruvate and the subsequent acetylation of coenzyme A to acetyl-CoA. The E1 component of PDC catalyzes the first step of the multistep process, using TPP and a divalent cation as cofactors. E. coli PDC is a homodimeric enzyme.
Probab=38.47  E-value=22  Score=15.88  Aligned_cols=10  Identities=20%  Similarity=0.434  Sum_probs=6.7

Q ss_pred             CCCCCEEEEE
Q ss_conf             7786189998
Q gi|254780376|r  131 GADGNIYAVA  140 (369)
Q Consensus       131 g~dg~vyAvA  140 (369)
                      .++++|||+.
T Consensus       145 ~~~~rv~~~~  154 (386)
T cd02017         145 TSDQKVWAFL  154 (386)
T ss_pred             CCCCEEEEEE
T ss_conf             7777389996


No 25 
>PRK11067 outer membrane protein assembly factor YaeT; Provisional
Probab=37.55  E-value=21  Score=15.94  Aligned_cols=30  Identities=13%  Similarity=0.109  Sum_probs=15.3

Q ss_pred             CHHHHHHHHHHHHHHHCCCCHHHHHHEEEE
Q ss_conf             967899999999997425700100100013
Q gi|254780376|r    1 MIFRIAFLIFSLIGLHEISAQVVSRIKDVV   30 (369)
Q Consensus         1 m~~~~~~l~~~~~~~~~~~~~~a~rikDi~   30 (369)
                      ||||.+++.+.++....+.++..--|+||-
T Consensus         1 ~~~k~~~~~~~l~~~~~~~~a~~~~I~~I~   30 (801)
T PRK11067          1 MAMKKLLIASLLFSSATVYGAEGFVVKDIH   30 (801)
T ss_pred             CCHHHHHHHHHHHHHHHHHHCCCEEEEEEE
T ss_conf             975899999999999998755872997999


No 26 
>KOG4731 consensus
Probab=36.42  E-value=30  Score=14.93  Aligned_cols=95  Identities=21%  Similarity=0.218  Sum_probs=37.1

Q ss_pred             EEECCCCCCCCCCCCHHHHHHHHHHHHHCCCCCCCCC--------CCCCCEEEEEEEEEECCCCCCCCEEE-EEEECCCC
Q ss_conf             8876388999887746899999999998297457321--------46553269999997178775687689-99956888
Q gi|254780376|r   45 LVVGLQGTGDSLRSSPFTEQSMRSLLQNLGISTPGGR--------LGSKNVAAVMVTANLPPFASPGSRID-VSINSLGD  115 (369)
Q Consensus        45 LVVGL~GTGD~~~~~~~t~qsl~nml~~~Gv~~~~~~--------~~~kNvAaVmVtA~lPpfa~~G~~iD-v~VSSiGd  115 (369)
                      .+++++=+|-.  +.+|---++.|.-.++|+..-..+        ..-+|-   -++-.||-. +.++.|. ..|-..- 
T Consensus        59 qI~nF~~~~~~--~d~~fw~~~sn~psn~gi~~~~~e~G~t~~l~~~~~N~---~~~v~lp~~-~t~de~kw~sv~~l~-  131 (512)
T KOG4731          59 QIVNFNYDGGP--PDVFFWGGMSNRPSNEGIRHNDDEYGSTQSLNRTYKNK---DFTVRLPEN-KTIDEIKWFSVWDLP-  131 (512)
T ss_pred             EEEEECCCCCC--CCEEEEECCCCCCCCCCCCCCCCCCCCCCCCCEECCCC---CEEEECCCC-CEEEHEEEEEEEECC-
T ss_conf             99974047998--74279710477889754214663225430133311366---379975777-364021069999725-


Q ss_pred             CCCCCCCEEEEEECCCC--------CCCEEEEEECCEEE
Q ss_conf             45444777999521477--------86189998161683
Q gi|254780376|r  116 ASSLRGGILVMTSLLGA--------DGNIYAVAQGSVVV  146 (369)
Q Consensus       116 AkSL~GG~LL~TpL~g~--------dg~vyAvAQG~i~v  146 (369)
                      .-+=-|-.++-+.+..+        -+.+|.+-.+|+.+
T Consensus       132 ta~nfg~Vv~pee~d~P~~es~~~~s~~~~~v~Sdniev  170 (512)
T KOG4731         132 TASNFGDVVIPEESDTPKAESPPSFSNGVYGVSSDNIEV  170 (512)
T ss_pred             CCCCCCCEECCCCCCCCCCCCCCCCCCCCCCCCCCCEEE
T ss_conf             777641243367899853347721136745544687367


No 27 
>cd05791 S1_CSL4 S1_CSL4: CSL4, S1-like RNA-binding domain. S1-like RNA-binding domains are found in a wide variety of RNA-associated proteins. ScCSL4 protein is a subunit of the exosome complex. The exosome plays a central role in 3' to 5' RNA processing and degradation in eukarytes and archaea. Its functions include the removal of incorrectly processed RNA and the maintenance of proper levels of mRNA, rRNA and a number of small RNA species. In S. cerevisiae, the exosome includes nine core components, six of which are homologous to bacterial RNase PH. These form a hexameric ring structure. The other three subunits (RrP4, Rrp40, and Csl4) contain an S1 RNA binding domain and are part of the "S1 pore structure".
Probab=32.77  E-value=33  Score=14.62  Aligned_cols=24  Identities=38%  Similarity=0.497  Sum_probs=19.6

Q ss_pred             ECCCCCCCCEEEEEEECCCCCCCC
Q ss_conf             178775687689999568884544
Q gi|254780376|r   96 LPPFASPGSRIDVSINSLGDASSL  119 (369)
Q Consensus        96 lPpfa~~G~~iDv~VSSiGdAkSL  119 (369)
                      +--.-||||=+-..|-|+||++|.
T Consensus        57 m~~~FrpGDIVrA~Vislgd~~~y   80 (92)
T cd05791          57 MYKCFRPGDIVRAKVISLGDASSY   80 (92)
T ss_pred             HHHCCCCCCEEEEEEEECCCCCEE
T ss_conf             413549998999999974787249


No 28 
>KOG3930 consensus
Probab=32.48  E-value=34  Score=14.57  Aligned_cols=90  Identities=10%  Similarity=0.010  Sum_probs=40.9

Q ss_pred             CCCCCCCCCCCEEEECCEEEEEECCCCCCCCCEEEEEEECCCHHHHHHHHHHHHHHHCCCCCCCCEEEECCCEEEEECCC
Q ss_conf             65200476542174165488741354324776499995078878999999999875202456541245115636863288
Q gi|254780376|r  155 SSSFMEGISTGGKIVNGAIVERELPKKFKDSADLILQLRNPDFSTAIRIADQINSYSLNRFSRPIAEAYDSRTVKVSKPT  234 (369)
Q Consensus       155 ~~~~~~n~~t~GrIp~Ga~VErev~~~f~~~~~l~L~L~~pdfttA~~ia~aIN~~~~~~~g~~~A~a~d~~~I~v~~P~  234 (369)
                      |...+|+.++++-=++++.-. -........+.++-....-.-..+.++...    +.-.-|+.++.+..+..|....|.
T Consensus       207 g~~~tK~~~~~~~k~~~~~tq-Lga~P~~~~d~~~ds~~d~~ss~~~ymGvl----kk~Grg~kv~~~ass~~V~~i~~~  281 (389)
T KOG3930         207 GQSGTKKTISNRPKLNSRLTQ-LGASPAAATDSLRDSVGDNGSSKASYMGVL----KKDGRGQKVSTAASSSDVLLIDDN  281 (389)
T ss_pred             CCCCCCCCCCCCCCCCCHHHH-CCCCCCCCCCCHHCCCCCCCCHHHHHHHHH----HHCCCCCCCCCCCCCCCCEEECCC
T ss_conf             665434575567875204554-036865455401102586421088773033----323676431356764200122564


Q ss_pred             C-C---CHHHHHHHHHCCC
Q ss_conf             7-5---2121322322012
Q gi|254780376|r  235 N-I---DLTRLMSEVEMLT  249 (369)
Q Consensus       235 ~-~---~~v~fla~ie~l~  249 (369)
                      . |   +.+.|.-.++.-+
T Consensus       282 say~~~~~~~~~~~~~sr~  300 (389)
T KOG3930         282 SAYEDDEIVEEVVDYESRE  300 (389)
T ss_pred             CCCCCCHHHHHHHHHHHHC
T ss_conf             2222220468775323311


No 29 
>pfam11543 UN_NPL4 Nuclear pore localisation protein NPL4. Npl4 is part of the heterodimer UN along with Ufd1 which is involved in the recruitment of p97, an AAA ATPase, for tasks involving the ubiquitin pathway. Npl4 has a ubiquitin-like domain which has within its structure a beta-grasp fold with a helical insert.
Probab=32.33  E-value=35  Score=14.48  Aligned_cols=59  Identities=22%  Similarity=0.306  Sum_probs=42.9

Q ss_pred             CEEEEECCCCCCHHHHHHHH-HCCCCCCCCCCEEEEECC--CCEEEECCCEEEEEEEEECCCEE
Q ss_conf             63686328875212132232-201268789835999447--63499459739989998417079
Q gi|254780376|r  226 RTVKVSKPTNIDLTRLMSEV-EMLTVETDTPARVIINER--TGTIVIGDNVRISKVVVSYGNLT  286 (369)
Q Consensus       226 ~~I~v~~P~~~~~v~fla~i-e~l~V~~~~~akVVINer--TGTIV~g~~V~I~pvaVsHGnLt  286 (369)
                      |+-+|.+|+......|...+ |.+.++.+  .--+--+|  ++-++.+.++.++...+.||++-
T Consensus        14 GtkRIev~~~~t~~~l~~kV~~~f~~~~~--gf~Ly~~rn~~~el~as~s~tl~~~~lkHGDml   75 (80)
T pfam11543        14 GTKRIEISSTSTLSTLLSKVAEELGFPNN--GFSLYLERNKTTELVSSGSKSVSELGLKHGDML   75 (80)
T ss_pred             CCEEEEECCCCHHHHHHHHHHHHHCCCCC--CEEEEEECCCCCEEECCCCEEHHHCCCCCCCEE
T ss_conf             84677608701299999999999688976--535566336652051176357876287877689


No 30 
>COG4832 Uncharacterized conserved protein [Function unknown]
Probab=32.06  E-value=27  Score=15.24  Aligned_cols=23  Identities=22%  Similarity=0.335  Sum_probs=19.7

Q ss_pred             EEEEEEECCCHHHHHHHHHHHHH
Q ss_conf             49999507887899999999987
Q gi|254780376|r  187 DLILQLRNPDFSTAIRIADQINS  209 (369)
Q Consensus       187 ~l~L~L~~pdfttA~~ia~aIN~  209 (369)
                      ..++.+++|||-|..-+..|+..
T Consensus       100 ~wt~mirqPDFit~ei~e~A~ev  122 (207)
T COG4832         100 KWTIMIRQPDFITQEIFEKAKEV  122 (207)
T ss_pred             HHEEEECCCCHHHHHHHHHHHHH
T ss_conf             10012018642449999999999


No 31 
>pfam12408 DUF3666 Ribose-5-phosphate isomerase. This domain family is found in bacteria, and is approximately 50 amino acids in length. The family is found in association with pfam02502. There are two completely conserved residues (D and F) that may be functionally important.
Probab=31.67  E-value=27  Score=15.21  Aligned_cols=15  Identities=20%  Similarity=0.401  Sum_probs=12.1

Q ss_pred             CCHHHHHHHHHHHHH
Q ss_conf             987899999999987
Q gi|254780376|r  344 LKTDGIISILQGIKA  358 (369)
Q Consensus       344 ~tp~DlIsILqalk~  358 (369)
                      ++-+|+++||++|..
T Consensus         2 vt~kdll~iLk~iDq   16 (48)
T pfam12408         2 ATYKDLLDILKAIDQ   16 (48)
T ss_pred             CCHHHHHHHHHHHCH
T ss_conf             234569999999689


No 32 
>TIGR00064 ftsY signal recognition particle-docking protein FtsY; InterPro: IPR004390   ABC transporters belong to the ATP-Binding Cassette (ABC) superfamily, which uses the hydrolysis of ATP to energize diverse biological systems. ABC transporters are minimally constituted of two conserved regions: a highly conserved ATP binding cassette (ABC) and a less conserved transmembrane domain (TMD). These regions can be found on the same protein or on two different ones. Most ABC transporters function as a dimer and therefore are constituted of four domains, two ABC modules and two TMDs.   ABC transporters are involved in the export or import of a wide variety of substrates ranging from small ions to macromolecules. The major function of ABC import systems is to provide essential nutrients to bacteria. They are found only in prokaryotes and their four constitutive domains are usually encoded by independent polypeptides (two ABC proteins and two TMD proteins). Prokaryotic importers require additional extracytoplasmic binding proteins (one or more per systems) for function. In contrast, export systems are involved in the extrusion of noxious substances, the export of extracellular toxins and the targeting of membrane components. They are found in all living organisms and in general the TMD is fused to the ABC module in a variety of combinations. Some eukaryotic exporters encode the four domains on the same polypeptide chain .    The ABC module (approximately two hundred amino acid residues) is known to bind and hydrolyze ATP, thereby coupling transport to ATP hydrolysis in a large number of biological processes. The cassette is duplicated in several subfamilies. Its primary sequence is highly conserved, displaying a typical phosphate-binding loop: Walker A, and a magnesium binding site: Walker B. Besides these two regions, three other conserved motifs are present in the ABC cassette: the switch region which contains a histidine loop, postulated to polarize the attaching water molecule for hydrolysis, the signature conserved motif (LSGGQ) specific to the ABC transporter, and the Q-motif (between Walker A and the signature), which interacts with the gamma phosphate through a water bond. The Walker A, Walker B, Q-loop and switch region form the nucleotide binding site , , .   The 3D structure of a monomeric ABC module adopts a stubby L-shape with two distinct arms. ArmI (mainly beta-strand) contains Walker A and Walker B. The important residues for ATP hydrolysis and/or binding are located in the P-loop. The ATP-binding pocket is located at the extremity of armI. The perpendicular armII contains mostly the alpha helical subdomain with the signature motif. It only seems to be required for structural integrity of the ABC module. ArmII is in direct contact with the TMD. The hinge between armI and armII contains both the histidine loop and the Q-loop, making contact with the gamma phosphate of the ATP molecule. ATP hydrolysis leads to a conformational change that could facilitate ADP release. In the dimer the two ABC cassettes contact each other through hydrophobic interactions at the antiparallel beta-sheet of armI by a two-fold axis , , , , , .   Proteins known to belong to this family are classified in several functional subfamilies depending on the substrate used (for further information see http://www.tcdb.org/tcdb/index.php?tc=3.A.1).  This family includes the cell division ABC transporter and the periplasmic substrate-binding protein FtsY. There is a weak division between FtsY and SRP54; both are GTPases. In Escherichia coli, ftsY is an essential gene located in an operon with cell division genes ftsE and ftsX, but its apparent function is as the signal recognition particle docking protein.; GO: 0005525 GTP binding.
Probab=31.29  E-value=35  Score=14.50  Aligned_cols=36  Identities=25%  Similarity=0.326  Sum_probs=23.5

Q ss_pred             CCCCEEEEEEEECCCCCCCCCCCCHHHHHHHHHHHHHCCCCC
Q ss_conf             143026787887638899988774689999999999829745
Q gi|254780376|r   36 RDNQLIGYGLVVGLQGTGDSLRSSPFTEQSMRSLLQNLGIST   77 (369)
Q Consensus        36 R~NqL~GyGLVVGL~GTGD~~~~~~~t~qsl~nml~~~Gv~~   77 (369)
                      ++|.+.= =|+||-||+|=.+     |.==|++||.+-|-++
T Consensus        78 ~~~kp~V-il~VGVNG~GKTT-----TIaKLA~~l~~~Gk~V  113 (284)
T TIGR00064        78 EEKKPNV-ILFVGVNGVGKTT-----TIAKLANKLKKQGKSV  113 (284)
T ss_pred             CCCCCEE-EEEEEEECCCHHH-----HHHHHHHHHHHCCCEE
T ss_conf             4789779-9998440886010-----2889999998749908


No 33 
>TIGR03002 outer_YhbN cell envelope biogenesis protein YhbN; InterPro: IPR014340   Members of this entry include YhbN, which is an essential protein in Escherichia coli. It is implicated in cell envelope integrity, and has numerous homologues in other Proteobacteria in a conserved location near lipopolysaccharide inner core biosynthesis genes. This entry is distantly related to the organic solvent tolerance protein (OstA)..
Probab=30.20  E-value=38  Score=14.24  Aligned_cols=28  Identities=18%  Similarity=0.426  Sum_probs=22.5

Q ss_pred             EEEEECCCCEEEECCCEEEEEEEEECCCEEEEE
Q ss_conf             599944763499459739989998417079996
Q gi|254780376|r  257 RVIINERTGTIVIGDNVRISKVVVSYGNLTVQI  289 (369)
Q Consensus       257 kVVINerTGTIV~g~~V~I~pvaVsHGnLtI~I  289 (369)
                      +.-.|.++++++..|||.|     +||+|.|.=
T Consensus        16 ~~~~D~~~~~~~f~GnV~i-----tQG~~~I~A   43 (150)
T TIGR03002        16 SQTLDDKKNVVTFTGNVVI-----TQGTLKIRA   43 (150)
T ss_pred             EEEEECCCCEEEEECCEEE-----EECCEEEEC
T ss_conf             0665402883888656587-----829759852


No 34 
>KOG2348 consensus
Probab=30.05  E-value=24  Score=15.61  Aligned_cols=12  Identities=67%  Similarity=1.243  Sum_probs=9.5

Q ss_pred             CCEEEEEEEECC
Q ss_conf             302678788763
Q gi|254780376|r   38 NQLIGYGLVVGL   49 (369)
Q Consensus        38 NqL~GyGLVVGL   49 (369)
                      ||=+|||+|+||
T Consensus         7 ~Qg~GY~IVlGl   18 (667)
T KOG2348           7 NQGVGYGIVLGL   18 (667)
T ss_pred             CCCCCEEEEEEC
T ss_conf             677445888704


No 35 
>COG2373 Large extracellular alpha-helical protein [General function prediction only]
Probab=29.35  E-value=39  Score=14.15  Aligned_cols=43  Identities=23%  Similarity=0.401  Sum_probs=25.1

Q ss_pred             EEEEECCCCCCCCEEEEEEECCCCC-----C----CCCCCEEEEEECCCCCC
Q ss_conf             9997178775687689999568884-----5----44477799952147786
Q gi|254780376|r   92 VTANLPPFASPGSRIDVSINSLGDA-----S----SLRGGILVMTSLLGADG  134 (369)
Q Consensus        92 VtA~lPpfa~~G~~iDv~VSSiGdA-----k----SL~GG~LL~TpL~g~dg  134 (369)
                      |+-+-|.-.+||+.+.+.|++.+..     +    =..=|.|=+|+.+.||=
T Consensus       855 v~l~~p~k~~Pg~~l~i~l~~~~~~~~~~a~vtV~aVDegIl~lt~y~~Pdp  906 (1621)
T COG2373         855 VQLKTPKKVKPGEPLTIKLSVSGAGGPKSAYVTVAAVDEGILNLTGYEAPDP  906 (1621)
T ss_pred             EEECCCCCCCCCCEEEEEEEECCCCCCCCEEEEEEEEEEEHHHCCCCCCCCH
T ss_conf             8824766458998068899976788875428999995501112267779997


No 36 
>TIGR01139 cysK cysteine synthase A; InterPro: IPR005859    This model discriminates cysteine synthase A (CysK) and cysteine synthase B (CysM) from cystathionine beta-synthase, a protein found primarily in eukaryotes and carrying a C-terminal CBS domain lacking from this protein. Bacterial proteins lacking the CBS domain but otherwise showing resemblance to cystathionine beta-synthases and considerable phylogenetic distance from known cysteine synthases were excluded.    Cysteine synthase (O-acetylserine (thiol)-lyase, 2.5.1.47 from EC) is the enzyme responsible for the formation of cysteine from O-acetyl-serine and hydrogen sulphide with the concomitant release of acetic acid. In bacteria such two forms of the enzyme are known (genes cysK and cysM). CysK differs from CysM in that it can also use sulphide instead of thiosulphate, to produce cysteine instead of cysteine thiosulphonate. ; GO: 0004124 cysteine synthase activity, 0006535 cysteine biosynthetic process from serine.
Probab=28.20  E-value=28  Score=15.11  Aligned_cols=119  Identities=21%  Similarity=0.256  Sum_probs=63.7

Q ss_pred             CCC-EEEEEEECCCCCCCCCCCEEEEE--ECCCCCC-----CEEEE--EECCEEECCCCCCCCCCC-CCCCCCC----CE
Q ss_conf             687-68999956888454447779995--2147786-----18999--816168334324567652-0047654----21
Q gi|254780376|r  102 PGS-RIDVSINSLGDASSLRGGILVMT--SLLGADG-----NIYAV--AQGSVVVSGLFVKGQSSS-FMEGIST----GG  166 (369)
Q Consensus       102 ~G~-~iDv~VSSiGdAkSL~GG~LL~T--pL~g~dg-----~vyAv--AQG~i~vgg~~~~g~~~~-~~~n~~t----~G  166 (369)
                      -|+ ++|+.||..|     .|||+==+  -||..++     ++||+  +.=||.-||..    |.. .--.|+-    .|
T Consensus       163 dg~G~~D~FVaG~G-----TGGTITGvG~~LK~~~pkG~~~~~~AVEP~~SPVLSggLA----G~~ikpGpHKIQGiGAG  233 (312)
T TIGR01139       163 DGKGRLDAFVAGVG-----TGGTITGVGEVLKEKKPKGKDIKIVAVEPAESPVLSGGLA----GEEIKPGPHKIQGIGAG  233 (312)
T ss_pred             CCCCCEEEEEEEEC-----CCCHHHHHHHHHHCCCCCCCEEEEEEECCCCCHHHHHHHH----HHHCCCCCCCCCCCCCC
T ss_conf             78983117997323-----6851547899874007899558999872774313443330----01026694964127978


Q ss_pred             EEECCEEEEEECCCCCCCCCEEEEEEECCCHHHHHHHHHHHHHHHCCCCCC------CCEEEEC-CCEEEEE-CCCCCC
Q ss_conf             741654887413543247764999950788789999999998752024565------4124511-5636863-288752
Q gi|254780376|r  167 KIVNGAIVERELPKKFKDSADLILQLRNPDFSTAIRIADQINSYSLNRFSR------PIAEAYD-SRTVKVS-KPTNID  237 (369)
Q Consensus       167 rIp~Ga~VErev~~~f~~~~~l~L~L~~pdfttA~~ia~aIN~~~~~~~g~------~~A~a~d-~~~I~v~-~P~~~~  237 (369)
                      .||.  ++-+++.      |++.=.-++.-|.||+|+++.===+.+=+-|.      ++|+-.. ++..-|. +|+.-+
T Consensus       234 FIP~--~Ln~~v~------D~vi~V~~EeAi~~ARrLA~eEGiL~GISSGA~vaAAl~~Ak~~~n~dK~iV~i~Ps~GE  304 (312)
T TIGR01139       234 FIPK--VLNRSVI------DEVITVSDEEAIETARRLAKEEGILVGISSGAAVAAALKLAKRLENPDKLIVVILPSTGE  304 (312)
T ss_pred             CCCC--CCCCCCC------CEEEECCCHHHHHHHHHHHHHCCEEECCCHHHHHHHHHHHHHHHCCCCCEEEEEECCCCC
T ss_conf             7263--3684136------214740755689999999986780101557899999999987324889889998278984


No 37 
>TIGR01136 cysKM cysteine synthases; InterPro: IPR005856    This model discriminates cysteine synthases (both CysK and CysM) from cystathionine beta-synthase, a protein found primarily in eukaryotes and carrying a C-terminal CBS domain lacking from this protein. Bacterial proteins lacking the CBS domain but otherwise showing resemblance to cystathionine beta-synthases and considerable phylogenetic distance from known cysteine synthases were excluded.    Cysteine synthase (O-acetylserine (thiol)-lyase) is the enzyme responsible for the formation of cysteine from O-acetyl-serine and hydrogen sulphide with the concomitant release of acetic acid. In bacteria such two forms of the enzyme are known (genes cysK and cysM). CysM differs from CysK in that it can also use thiosulphate instead of sulphide, to produce cysteine thiosulphonate instead of cysteine. ; GO: 0004124 cysteine synthase activity, 0006535 cysteine biosynthetic process from serine.
Probab=26.58  E-value=40  Score=14.09  Aligned_cols=89  Identities=27%  Similarity=0.317  Sum_probs=52.2

Q ss_pred             CCCEEEEEEECCCCCCCCCCCEEEEE--ECCCCCC-----CEEEE--EECCEEECCCCCCCCCCCCCCCCCC----CEEE
Q ss_conf             68768999956888454447779995--2147786-----18999--8161683343245676520047654----2174
Q gi|254780376|r  102 PGSRIDVSINSLGDASSLRGGILVMT--SLLGADG-----NIYAV--AQGSVVVSGLFVKGQSSSFMEGIST----GGKI  168 (369)
Q Consensus       102 ~G~~iDv~VSSiGdAkSL~GG~LL~T--pL~g~dg-----~vyAv--AQG~i~vgg~~~~g~~~~~~~n~~t----~GrI  168 (369)
                      -+.+||+.||++|     .|||+.=+  -||..+.     +|+|+  +.+|+..+|.....   -.--.|+-    .|+|
T Consensus       165 t~G~id~FVaG~G-----TGGTItGvgr~LK~~~pkG~~i~i~avEP~~s~~Ls~GLAG~~---i~pGpHKIqgig~gFi  236 (315)
T TIGR01136       165 TDGRIDHFVAGVG-----TGGTITGVGRVLKEQNPKGKNIQIVAVEPAESPVLSGGLAGEE---IKPGPHKIQGIGAGFI  236 (315)
T ss_pred             CCCCEEEEEEECC-----CCCCHHHHHHHHHHHCCCCCEEEEEEEECCCCCHHHHHHCCCC---CCCCCCCCCCCCCCCC
T ss_conf             2892358997115-----6751116898986326899617999975687301001112222---3679287778885557


Q ss_pred             ECCEEEEEECCCCCCCCCEEEEEEECCCHHHHHHHHHH
Q ss_conf             16548874135432477649999507887899999999
Q gi|254780376|r  169 VNGAIVERELPKKFKDSADLILQLRNPDFSTAIRIADQ  206 (369)
Q Consensus       169 p~Ga~VErev~~~f~~~~~l~L~L~~pdfttA~~ia~a  206 (369)
                      |.  +..+++-      +.+.-.-.+-=|.||+|+|+.
T Consensus       237 P~--iLd~~~~------D~v~~V~~edA~~~ARrLA~~  266 (315)
T TIGR01136       237 PK--ILDRSLI------DEVITVSDEDAIETARRLARE  266 (315)
T ss_pred             CC--CCCCCCC------CEEEECCHHHHHHHHHHHHHH
T ss_conf             63--1371133------104641828999999999874


No 38 
>COG1254 AcyP Acylphosphatases [Energy production and conversion]
Probab=25.70  E-value=43  Score=13.88  Aligned_cols=30  Identities=7%  Similarity=0.111  Sum_probs=15.5

Q ss_pred             CCCEEEECCCEEEEECCCCC-CHHHHHHHHH
Q ss_conf             54124511563686328875-2121322322
Q gi|254780376|r  217 RPIAEAYDSRTVKVSKPTNI-DLTRLMSEVE  246 (369)
Q Consensus       217 ~~~A~a~d~~~I~v~~P~~~-~~v~fla~ie  246 (369)
                      .+.++-.+.++|++-+--.. +.-.|+..+.
T Consensus        33 ~G~V~N~~DGsVeiva~G~~~~v~~~~~~l~   63 (92)
T COG1254          33 TGWVKNLDDGSVEIVAEGPDEAVEKFIEWLR   63 (92)
T ss_pred             EEEEEECCCCEEEEEEECCHHHHHHHHHHHH
T ss_conf             7999978998299999769899999999997


No 39 
>cd05125 Mth938_2P1-like Mth938_2P1-like domain. This model contains sequences that are similar to 2P1, a partially characterized nuclear protein, which is homologous to E3-3 from rat and known to be alternatively spliced. Its function is unknown. This family is part of the Mth938 family, for which structures, but no functional data are available.
Probab=25.57  E-value=41  Score=14.01  Aligned_cols=26  Identities=31%  Similarity=0.493  Sum_probs=15.0

Q ss_pred             CCCCCCCCCCHHHHHHHHHHHHHCCCCCC
Q ss_conf             88999887746899999999998297457
Q gi|254780376|r   50 QGTGDSLRSSPFTEQSMRSLLQNLGISTP   78 (369)
Q Consensus        50 ~GTGD~~~~~~~t~qsl~nml~~~Gv~~~   78 (369)
                      =|||++.+   |-.+++...|++.||.+.
T Consensus        60 iGtG~~~~---~~~~~~~~~l~~~gI~vE   85 (114)
T cd05125          60 IGTGRKSR---PLSPELRKYFKKLGIAVE   85 (114)
T ss_pred             ECCCCCCC---CCCHHHHHHHHHCCCEEE
T ss_conf             86699877---899999999997599179


No 40 
>PRK11132 cysE serine acetyltransferase; Provisional
Probab=25.45  E-value=45  Score=13.69  Aligned_cols=25  Identities=12%  Similarity=0.274  Sum_probs=12.6

Q ss_pred             HHHHHCCCCCCCCC--CEEEEECCCCE
Q ss_conf             22322012687898--35999447634
Q gi|254780376|r  242 MSEVEMLTVETDTP--ARVIINERTGT  266 (369)
Q Consensus       242 la~ie~l~V~~~~~--akVVINerTGT  266 (369)
                      .+.+-.++|.|..+  .++.||--||.
T Consensus       136 ~s~~~gvdIHP~A~iG~gi~iDH~~Gv  162 (273)
T PRK11132        136 ISVAFQVDIHPAAKIGRGIMLDHATGI  162 (273)
T ss_pred             HHHHHCCCCCCCCEECCCEEEECCCCE
T ss_conf             999851252666511685688347635


No 41 
>PRK00178 tolB translocation protein TolB; Provisional
Probab=25.40  E-value=39  Score=14.15  Aligned_cols=115  Identities=21%  Similarity=0.242  Sum_probs=53.9

Q ss_pred             CHHHHHHHHHHHHHHHCCCCHHHHHHEEEEEEEECCCCCEEEEEEEECCCCCCCCCCCCHHHHHHHHHHHHHCCCC--CC
Q ss_conf             9678999999999974257001001000136400014302678788763889998877468999999999982974--57
Q gi|254780376|r    1 MIFRIAFLIFSLIGLHEISAQVVSRIKDVVSLQSGRDNQLIGYGLVVGLQGTGDSLRSSPFTEQSMRSLLQNLGIS--TP   78 (369)
Q Consensus         1 m~~~~~~l~~~~~~~~~~~~~~a~rikDi~~i~GvR~NqL~GyGLVVGL~GTGD~~~~~~~t~qsl~nml~~~Gv~--~~   78 (369)
                      ||+...++++++++++...+++..+|    +|-+-..+++- ..+ +=..+.|+..-... -.+-+.+-|++-|.=  ++
T Consensus         1 m~~l~~~~~l~~~l~~~~~a~A~l~I----~It~g~~~~ip-IAI-~pF~~~~~~~~~~~-i~~iI~~DL~~sG~F~~l~   73 (433)
T PRK00178          1 MIKLKRIALLVLCLLAGGAAAAELNI----EITSGSDRAIP-IAV-VPFGWQGGSVLPED-MAQIIGNDLRNSGYFEPIP   73 (433)
T ss_pred             CCCHHHHHHHHHHHHHHHHHCEEEEE----EEECCCCCEEE-EEE-CCCCCCCCCCHHHH-HHHHHHHHHHCCCCCEECC
T ss_conf             90179999999999876762203999----99347776040-698-57666687622489-9999998886288855248


Q ss_pred             CCC-CC--------------CCCEEEEEEEEEECCCCCCCCEEEEEE--ECCCCCCCCCCCEEEE
Q ss_conf             321-46--------------553269999997178775687689999--5688845444777999
Q gi|254780376|r   79 GGR-LG--------------SKNVAAVMVTANLPPFASPGSRIDVSI--NSLGDASSLRGGILVM  126 (369)
Q Consensus        79 ~~~-~~--------------~kNvAaVmVtA~lPpfa~~G~~iDv~V--SSiGdAkSL~GG~LL~  126 (369)
                      +.. +.              ..+ |-.+|++.+-+   .|.+++|..  --+-..+-|.|..+.-
T Consensus        74 ~~~~~~~p~~~~~i~f~~W~~lg-ad~Lv~G~i~~---~gg~~~v~~~L~DV~~~~~l~g~~~~~  134 (433)
T PRK00178         74 RQNMISLPSQASEVIFRDWKALG-AQYVMVGNIVP---AGGRLQVQYALFNVATEQQVLTGSVSG  134 (433)
T ss_pred             HHHCCCCCCCCCCCCHHHHHHCC-CCEEEEEEEEE---CCCEEEEEEEEEECCCCEEEECCEEEE
T ss_conf             35524688854575756877509-87899987994---599799999999714520760326995


No 42 
>COG3164 Predicted membrane protein [Function unknown]
Probab=25.30  E-value=17  Score=16.67  Aligned_cols=60  Identities=22%  Similarity=0.232  Sum_probs=39.6

Q ss_pred             CCCEEEEEEEEEECCCCCCCCEEEEEEECCCCCCCCCCCEEEEEECCCCCCCEEEE--EECCEEE
Q ss_conf             55326999999717877568768999956888454447779995214778618999--8161683
Q gi|254780376|r   84 SKNVAAVMVTANLPPFASPGSRIDVSINSLGDASSLRGGILVMTSLLGADGNIYAV--AQGSVVV  146 (369)
Q Consensus        84 ~kNvAaVmVtA~lPpfa~~G~~iDv~VSSiGdAkSL~GG~LL~TpL~g~dg~vyAv--AQG~i~v  146 (369)
                      .-+|-++-|||.||-|.+.-=-||-.|++  +.|.+ ++++..|||+--+|++.+-  ++||+..
T Consensus       604 L~gV~~s~lta~IPd~~k~~L~Ida~v~g--~~~~~-~~y~~atPl~ds~g~tl~e~q~~Gp~~~  665 (1271)
T COG3164         604 LGGVRASDLTAGIPDYSKEKLYIDADVDG--PGKAV-LPYFDATPLKDSVGATLDELQADGPVSG  665 (1271)
T ss_pred             ECCCCHHHEEECCCCCCCCCEEEEEECCC--CHHHH-HHHHHCCCCCHHHHHHHHHHCCCCCCEE
T ss_conf             65602454355167777651799876367--50345-6555518841457777676222786216


No 43 
>COG1045 CysE Serine acetyltransferase [Amino acid transport and metabolism]
Probab=25.26  E-value=46  Score=13.66  Aligned_cols=43  Identities=23%  Similarity=0.368  Sum_probs=23.7

Q ss_pred             HHHHHHHCCCCCCCCC--CEEEEECCCCEEEECCCEEEE-EEEEECC
Q ss_conf             1322322012687898--359994476349945973998-9998417
Q gi|254780376|r  240 RLMSEVEMLTVETDTP--ARVIINERTGTIVIGDNVRIS-KVVVSYG  283 (369)
Q Consensus       240 ~fla~ie~l~V~~~~~--akVVINerTGTIV~g~~V~I~-pvaVsHG  283 (369)
                      .+++.+-.+||.|...  .++.|+-.+| ||+|+..+|. -|.+.||
T Consensus        60 ~~~~~~~gieIhp~A~IG~g~fIdHg~G-vVIgeta~IGddv~I~~g  105 (194)
T COG1045          60 SLSRFLFGIEIHPGAKIGRGLFIDHGTG-VVIGETAVIGDDVTIYHG  105 (194)
T ss_pred             HHHHHHCCEEECCCCEECCCEEECCCCE-EEECCEEEECCCEEEEEC
T ss_conf             9888630313477772778568737755-897642498797289706


No 44 
>pfam07253 Gypsy Gypsy protein. This family consists of several Gypsy/Env proteins from Drosophila and Ceratitis fruit fly species. Gypsy is an endogenous retrovirus of Drosophila melanogaster. Phylogenetic studies suggest that occasional horizontal transfer events of gypsy occur between Drosophila species. gypsy possesses infective properties associated with the products of the envelope gene that might be at the origin of these interspecies transfers.
Probab=24.63  E-value=47  Score=13.58  Aligned_cols=49  Identities=20%  Similarity=0.351  Sum_probs=37.7

Q ss_pred             CCCCCCEEEEECCCCEEEECCCEEE---EEEEEECCCEEEEECCCCCCCCCCC
Q ss_conf             8789835999447634994597399---8999841707999637766657765
Q gi|254780376|r  251 ETDTPARVIINERTGTIVIGDNVRI---SKVVVSYGNLTVQITENEQVVQPNA  300 (369)
Q Consensus       251 ~~~~~akVVINerTGTIV~g~~V~I---~pvaVsHGnLtI~I~~~~~vsqp~~  300 (369)
                      .|=-+--|+||+++|+|.++++.++   .+--|+. +=++.|+++..+.+-.+
T Consensus       314 ~~VDdGiIiIND~~a~V~~d~~~E~~isGTYLItF-~~s~~INGt~FvN~~~~  365 (472)
T pfam07253       314 EPVDDGIIVINDAHAHVRTDDNIEIHINGTYLITF-ERSATINETEFVNLRKP  365 (472)
T ss_pred             EEECCCEEEEECCCCEEECCCCEEEEEEEEEEEEE-EEEEEECCEEEECCCCC
T ss_conf             14126579985687358628981799722499997-50589977888704453


No 45 
>TIGR03431 PhnD phosphonate ABC transporter, periplasmic phosphonate binding protein. Note that this model does not identify all phnD-subfamily genes with evident phosphonate context, but all sequences above the trusted context may be inferred to bind phosphonate compounds even in the absence of such context. Furthermore, there is ample evidence to suggest that many other members of the TIGR01098 subfamily have a different primary function.
Probab=24.48  E-value=47  Score=13.57  Aligned_cols=24  Identities=21%  Similarity=0.220  Sum_probs=13.9

Q ss_pred             CHHHHHHHHHHHHHHHCCCCHHHH
Q ss_conf             967899999999997425700100
Q gi|254780376|r    1 MIFRIAFLIFSLIGLHEISAQVVS   24 (369)
Q Consensus         1 m~~~~~~l~~~~~~~~~~~~~~a~   24 (369)
                      |+++.++++++++++..+.+.++.
T Consensus         1 m~~r~l~~~~~~~~~~~~~a~a~~   24 (288)
T TIGR03431         1 MLRRLILSLVAAFMLISSNAQAED   24 (288)
T ss_pred             CCHHHHHHHHHHHHHHCCHHHHCC
T ss_conf             908899999999999743224304


No 46 
>PRK10867 signal recognition particle protein; Provisional
Probab=24.23  E-value=44  Score=13.76  Aligned_cols=25  Identities=28%  Similarity=0.509  Sum_probs=17.9

Q ss_pred             EEEEECCCCCCCCCCCCHHHHHHHHHHHHH
Q ss_conf             878876388999887746899999999998
Q gi|254780376|r   43 YGLVVGLQGTGDSLRSSPFTEQSMRSLLQN   72 (369)
Q Consensus        43 yGLVVGL~GTGD~~~~~~~t~qsl~nml~~   72 (369)
                      .=+.|||+|+|-.+     |.--|++.+++
T Consensus       102 VIm~vGLqGsGKTT-----T~aKLA~~lk~  126 (453)
T PRK10867        102 VVLMAGLQGAGKTT-----SVGKLGKFLRE  126 (453)
T ss_pred             EEEEECCCCCCHHH-----HHHHHHHHHHH
T ss_conf             99997468885185-----89999999997


No 47 
>cd00248 Mth938-like Mth938-like domain. The members of this family include: Mth938, 2P1, Xcr35, Rpa2829, and several uncharacterized sequences. Mth938 is a hypothetical protein encoded by the Methanobacterium thermoautotrophicum (Mth) genome. This protein crystallizes as a dimer, although it is monomeric in solution, with one disulfide bond in each monomer.  2P1 is a partially characterized nuclear protein which is homologous to E3-3 from rat and known to be alternately spliced. Xcr35 and Rpa2829 are hypothetical proteins of unknown function from the Xanthomonas campestris and Rhodopseudomonas palustris genomes, respectively, for which the crystal structures have been determined.
Probab=24.15  E-value=28  Score=15.14  Aligned_cols=25  Identities=32%  Similarity=0.646  Sum_probs=12.3

Q ss_pred             CCCCCCCCCHHHHHHHHHHHHHCCCCCC
Q ss_conf             8999887746899999999998297457
Q gi|254780376|r   51 GTGDSLRSSPFTEQSMRSLLQNLGISTP   78 (369)
Q Consensus        51 GTGD~~~~~~~t~qsl~nml~~~Gv~~~   78 (369)
                      |||...   .|..+.+.+.|+++|+.+.
T Consensus        59 GtG~~~---~~~~~~~~~~l~~~gI~~E   83 (109)
T cd00248          59 GTGAEI---AFLPRALRAALRAAGIGVE   83 (109)
T ss_pred             CCCCCC---CCCCHHHHHHHHHCCCEEE
T ss_conf             658977---7899999999998799499


No 48 
>pfam11685 DUF3281 Protein of unknown function (DUF3281). This family of bacterial proteins has no known function.
Probab=24.07  E-value=48  Score=13.51  Aligned_cols=14  Identities=36%  Similarity=0.425  Sum_probs=6.1

Q ss_pred             CCHHHHHHHHHHHH
Q ss_conf             88789999999998
Q gi|254780376|r  195 PDFSTAIRIADQIN  208 (369)
Q Consensus       195 pdfttA~~ia~aIN  208 (369)
                      ||=-|-..+.++.|
T Consensus       166 p~gLTl~~LV~~LN  179 (269)
T pfam11685       166 PDGLTLQALVDALN  179 (269)
T ss_pred             CCCCCHHHHHHHHC
T ss_conf             99868999999851


No 49 
>pfam05872 DUF853 Bacterial protein of unknown function (DUF853). This family consists of several bacterial proteins of unknown function. One member from Brucella melitensis is thought to be an ATPase.
Probab=24.04  E-value=48  Score=13.51  Aligned_cols=77  Identities=22%  Similarity=0.367  Sum_probs=49.0

Q ss_pred             EEEEECCCCCCCCCCCCHHHHHHHHHHHHHCCCCCCCCCCCC----------------CCEEEEE---------EEEEEC
Q ss_conf             878876388999887746899999999998297457321465----------------5326999---------999717
Q gi|254780376|r   43 YGLVVGLQGTGDSLRSSPFTEQSMRSLLQNLGISTPGGRLGS----------------KNVAAVM---------VTANLP   97 (369)
Q Consensus        43 yGLVVGL~GTGD~~~~~~~t~qsl~nml~~~Gv~~~~~~~~~----------------kNvAaVm---------VtA~lP   97 (369)
                      -|||.|-.|||-.     .|.|-|+.-+++.||.+=-.+++.                +..+..=         =+--.-
T Consensus        23 HGLiaGATGTGKT-----vTLq~lAE~~S~~GVPvf~aDvKGDLsGia~~G~~~~kl~~R~~~~g~~~~~~~~~Pv~fwd   97 (504)
T pfam05872        23 HGLIAGATGTGKT-----VTLQVLAESFSDAGVPVFLADVKGDLSGIAAPGEPQDKLAARAASIGLDDYQPQAFPVIFWD   97 (504)
T ss_pred             CCEECCCCCCCHH-----HHHHHHHHHHHHCCCCEEEECCCCCHHHCCCCCCCCHHHHHHHHHCCCCCCCCCCCCEEEEE
T ss_conf             1662265778617-----89999999874549938871056614321688999757999999719988886779878886


Q ss_pred             CCCCCCCEEEEEEECCCCCCCCCCCEEEEEECCCC
Q ss_conf             87756876899995688845444777999521477
Q gi|254780376|r   98 PFASPGSRIDVSINSLGDASSLRGGILVMTSLLGA  132 (369)
Q Consensus        98 pfa~~G~~iDv~VSSiGdAkSL~GG~LL~TpL~g~  132 (369)
                      -|.+.|-.+-.|||.||.        ||+..|.+-
T Consensus        98 l~g~~G~pvR~Tise~GP--------lLLsr~L~L  124 (504)
T pfam05872        98 LFGEKGHPVRTTISEMGP--------LLLSRLLNL  124 (504)
T ss_pred             CCCCCCCEEEEEHHHCCH--------HHHHHHCCC
T ss_conf             578889737864543068--------999987178


No 50 
>PRK11627 hypothetical protein; Provisional
Probab=23.27  E-value=50  Score=13.41  Aligned_cols=13  Identities=15%  Similarity=0.256  Sum_probs=7.7

Q ss_pred             CCCHHHHHHHHHH
Q ss_conf             9889999999984
Q gi|254780376|r  329 APDLNSLISGMNS  341 (369)
Q Consensus       329 ~~tl~~lV~ALN~  341 (369)
                      +++..++-.+||+
T Consensus       156 sa~~~~Ie~~lN~  168 (192)
T PRK11627        156 QASNKNIADAVNS  168 (192)
T ss_pred             CCCHHHHHHHHHH
T ss_conf             8888999999999


No 51 
>pfam07499 RuvA_C RuvA, C-terminal domain. Homologous recombination is a crucial process in all living organisms. In bacteria, this process the RuvA, RuvB, and RuvC proteins are involved. More specifically the proteins process the Holliday junction DNA. RuvA is comprised of three distinct domains. The domain represents the C-terminal domain and plays a significant role in the ATP-dependent branch migration of the hetero-duplex through direct contact with RuvB. Within the Holliday junction, the C-terminal domain makes no interaction with DNA.
Probab=23.01  E-value=50  Score=13.38  Aligned_cols=27  Identities=15%  Similarity=0.250  Sum_probs=23.8

Q ss_pred             HHHHHHHHHHCCCCHHHHHHHHHHHHH
Q ss_conf             999999998479987899999999987
Q gi|254780376|r  332 LNSLISGMNSIGLKTDGIISILQGIKA  358 (369)
Q Consensus       332 l~~lV~ALN~lG~tp~DlIsILqalk~  358 (369)
                      ..|.+.||-.||-++++.-..++.+..
T Consensus         3 ~~da~~AL~~LGy~~~ea~~av~~v~~   29 (47)
T pfam07499         3 LEEAVSALLALGYKEKEAEKAVAKVLE   29 (47)
T ss_pred             HHHHHHHHHHCCCCHHHHHHHHHHHHC
T ss_conf             889999999939989999999999764


No 52 
>TIGR00724 urea_amlyse_rel biotin-dependent carboxylase uncharacterized domain; InterPro: IPR003778 This domain represents subunit 2 of allophanate hydrolase (AHS2)..
Probab=22.80  E-value=33  Score=14.64  Aligned_cols=28  Identities=4%  Similarity=0.148  Sum_probs=15.4

Q ss_pred             EEEECCCEEEEEEEEECCC-EEEEECCCC
Q ss_conf             4994597399899984170-799963776
Q gi|254780376|r  266 TIVIGDNVRISKVVVSYGN-LTVQITENE  293 (369)
Q Consensus       266 TIV~g~~V~I~pvaVsHGn-LtI~I~~~~  293 (369)
                      -=..++++..+.+.|-|.+ .=|-+..+.
T Consensus       244 ~~~~~h~~~~G~~QVP~nGD~Piil~~Da  272 (334)
T TIGR00724       244 RELLTHAIVLGSIQVPPNGDQPIILMADA  272 (334)
T ss_pred             CCCCCCCCCCCEEEECCCCCCCEEECCCC
T ss_conf             00033450114257888889787953788


No 53 
>COG0541 Ffh Signal recognition particle GTPase [Intracellular trafficking and secretion]
Probab=22.15  E-value=52  Score=13.31  Aligned_cols=29  Identities=34%  Similarity=0.532  Sum_probs=20.4

Q ss_pred             EEEEECCCCCCCCCCCCHHHHHHHHHHHHHCCCC
Q ss_conf             8788763889998877468999999999982974
Q gi|254780376|r   43 YGLVVGLQGTGDSLRSSPFTEQSMRSLLQNLGIS   76 (369)
Q Consensus        43 yGLVVGL~GTGD~~~~~~~t~qsl~nml~~~Gv~   76 (369)
                      .=|.|||+|+|-.    . |.--|++.|++.|-.
T Consensus       102 vImmvGLQGsGKT----T-t~~KLA~~lkk~~~k  130 (451)
T COG0541         102 VILMVGLQGSGKT----T-TAGKLAKYLKKKGKK  130 (451)
T ss_pred             EEEEEECCCCCHH----H-HHHHHHHHHHHCCCC
T ss_conf             8999815679748----6-899999999974994


No 54 
>cd03791 GT1_Glycogen_synthase_DULL1_like This family is most closely related to the GT1 family of glycosyltransferases. Glycogen synthase catalyzes the formation and elongation of the alpha-1,4-glucose backbone using ADP-glucose, the second and key step of glycogen biosynthesis. This family includes starch synthases of plants, such as DULL1 in Zea mays and glycogen synthases of various organisms.
Probab=22.12  E-value=52  Score=13.26  Aligned_cols=19  Identities=11%  Similarity=0.303  Sum_probs=11.6

Q ss_pred             CEEEECCCCCHHHHHHHHHH
Q ss_conf             35897389889999999984
Q gi|254780376|r  322 GSFSLIDAPDLNSLISGMNS  341 (369)
Q Consensus       322 ~~~~~~~~~tl~~lV~ALN~  341 (369)
                      +.|.+.+ .+..+|.+|++.
T Consensus       420 tGf~f~~-~~~~~l~~ai~~  438 (476)
T cd03791         420 TGFVFEG-YNADALLAALRR  438 (476)
T ss_pred             CEEEECC-CCHHHHHHHHHH
T ss_conf             4588679-999999999999


No 55 
>pfam04430 DUF498 Protein of unknown function (DUF498/DUF598). This is a large family of uncharacterized proteins found in all domains of life. The structure shows a novel fold with three beta sheets. A dimeric form is found in the crystal structure. It was suggested that the cleft in between the two monomers might bing nucleic acid.
Probab=22.11  E-value=39  Score=14.14  Aligned_cols=25  Identities=40%  Similarity=0.678  Sum_probs=12.0

Q ss_pred             CCCCCCCCCHHHHHHHHHHHHHCCCCCC
Q ss_conf             8999887746899999999998297457
Q gi|254780376|r   51 GTGDSLRSSPFTEQSMRSLLQNLGISTP   78 (369)
Q Consensus        51 GTGD~~~~~~~t~qsl~nml~~~Gv~~~   78 (369)
                      |||...   .|-.+.+.+.+++.|+.+.
T Consensus        60 GtG~~~---~~l~~~~~~~l~~~gI~vE   84 (110)
T pfam04430        60 GTGARL---RFLPPELREALRKLGIGVE   84 (110)
T ss_pred             ECCCCC---CCCCHHHHHHHHHCCCEEE
T ss_conf             559866---7899999999997599079


No 56 
>pfam05949 DUF881 Bacterial protein of unknown function (DUF881). This family consists of a series of hypothetical bacterial proteins. One of the family members from Bacillus subtilis is thought to be involved in cell division and sporulation.
Probab=22.01  E-value=53  Score=13.25  Aligned_cols=13  Identities=15%  Similarity=0.023  Sum_probs=6.4

Q ss_pred             HHHHHHHHHHHCC
Q ss_conf             9999999999829
Q gi|254780376|r   62 TEQSMRSLLQNLG   74 (369)
Q Consensus        62 t~qsl~nml~~~G   74 (369)
                      ..+.+.|-|...|
T Consensus        46 dl~~vvNeL~~aG   58 (150)
T pfam05949        46 DLLAVVNELWAAG   58 (150)
T ss_pred             HHHHHHHHHHHCC
T ss_conf             9999999998779


No 57 
>KOG3432 consensus
Probab=21.34  E-value=34  Score=14.57  Aligned_cols=42  Identities=21%  Similarity=0.283  Sum_probs=18.8

Q ss_pred             EEEECCEEEEEECCC---CCCCCCEEEEEEECCCHHHHHHHHHHHHH
Q ss_conf             174165488741354---32477649999507887899999999987
Q gi|254780376|r  166 GKIVNGAIVERELPK---KFKDSADLILQLRNPDFSTAIRIADQINS  209 (369)
Q Consensus       166 GrIp~Ga~VErev~~---~f~~~~~l~L~L~~pdfttA~~ia~aIN~  209 (369)
                      =.|..-.+-++++.-   .|..++.+-+.|-+.  --|.+|.+.|..
T Consensus        38 f~vv~~~Tt~~eiedaF~~f~~RdDIaIiLInq--~~Ae~iR~~vD~   82 (121)
T KOG3432          38 FLVVDSKTTVEEIEDAFKSFTARDDIAIILINQ--FIAEMIRDRVDA   82 (121)
T ss_pred             EEEEECCCCHHHHHHHHHHHCCCCCEEEEEEHH--HHHHHHHHHHHH
T ss_conf             899955689899999998633456758987738--899999999874


No 58 
>pfam08817 YukD YukD. YukD is a bacterial protein that adopts a ubiquitin-like fold. Ubiquitin covalently binds to protein and flags them for protein degradation, however conjugation assays have indicated that YukD lacks the capacity for covalent bond formation with other proteins.
Probab=21.25  E-value=54  Score=13.14  Aligned_cols=59  Identities=17%  Similarity=0.205  Sum_probs=40.5

Q ss_pred             CCCEEEEECCCCCCH---HHHHHHHHCCCCCCCC--CCEEEEECCCCEEEECCCEEEEEEEEECCCEE
Q ss_conf             156368632887521---2132232201268789--83599944763499459739989998417079
Q gi|254780376|r  224 DSRTVKVSKPTNIDL---TRLMSEVEMLTVETDT--PARVIINERTGTIVIGDNVRISKVVVSYGNLT  286 (369)
Q Consensus       224 d~~~I~v~~P~~~~~---v~fla~ie~l~V~~~~--~akVVINerTGTIV~g~~V~I~pvaVsHGnLt  286 (369)
                      +.++.++++|..+..   +..+.++++++.++-.  .-||+ |   --+|.+++=+++.+-|+-|.+-
T Consensus        12 ~~~~~DLRip~~~~vK~lI~~v~~~~~i~~~~~~~~~irV~-N---K~~vl~~~d~L~d~~It~GD~L   75 (78)
T pfam08817        12 NGSVYDLRIPDQLSVKKLIDNVWETLKIEVPRREGYWIRVV-N---KGIVLSGNDILADHGITDGDRL   75 (78)
T ss_pred             CCCEEEEECCCCHHHHHHHHHHHHHCCCCCCCCCCCEEEEE-E---CCEEECCCCEEEECCCCCCCEE
T ss_conf             89658886456020999999999870656578778789997-4---3577068878630796788789


No 59 
>PRK13978 ribose-5-phosphate isomerase A; Provisional
Probab=21.16  E-value=47  Score=13.61  Aligned_cols=66  Identities=18%  Similarity=0.241  Sum_probs=35.6

Q ss_pred             EEEEEEECCCCCCCCCCCCHHHHHHHHHHHHHCCCCCC--CCCCCCCCEEEEEEEEEECCC-CCCCCEEEEEEECC
Q ss_conf             67878876388999887746899999999998297457--321465532699999971787-75687689999568
Q gi|254780376|r   41 IGYGLVVGLQGTGDSLRSSPFTEQSMRSLLQNLGISTP--GGRLGSKNVAAVMVTANLPPF-ASPGSRIDVSINSL  113 (369)
Q Consensus        41 ~GyGLVVGL~GTGD~~~~~~~t~qsl~nml~~~Gv~~~--~~~~~~kNvAaVmVtA~lPpf-a~~G~~iDv~VSSi  113 (369)
                      +--|.|+|| |||..   ..|..+.|...++.-+.++-  +...+++..|   ...-||-. ....+++|+++--.
T Consensus        19 V~~gmviGL-GTGST---v~~~I~~L~~~~k~~~l~i~~V~tS~~T~~~a---~~~Gi~l~~l~~~~~iDl~iDGA   87 (228)
T PRK13978         19 INGDMTLGI-GTGST---MELLLPQMAQLIKERGYNITGVCTSNKIAFLA---KELGIKICEINDVDHIDLAIDGA   87 (228)
T ss_pred             CCCCCEEEE-CCHHH---HHHHHHHHHHHHHCCCCCEEEEECCHHHHHHH---HHCCCEEECCCCCCCCCEEEECC
T ss_conf             899999985-55799---99999999999860798489997999999999---98798076455687346798088


No 60 
>TIGR03220 catechol_dmpE 2-oxopent-4-enoate hydratase. Members of this protein family are 2-oxopent-4-enoate hydratase, which is also called 2-hydroxypent-2,4-dienoate hydratase. It is closely related to another gene found in the same operon, 4-oxalocrotonate decarboxylase, with which it interacts closely.
Probab=21.11  E-value=55  Score=13.12  Aligned_cols=15  Identities=13%  Similarity=0.346  Sum_probs=8.5

Q ss_pred             CHHHHHHHHHHCCCC
Q ss_conf             899999999847998
Q gi|254780376|r  331 DLNSLISGMNSIGLK  345 (369)
Q Consensus       331 tl~~lV~ALN~lG~t  345 (369)
                      .|.-|++-|.+.|.+
T Consensus       203 al~WL~n~l~~~g~~  217 (255)
T TIGR03220       203 AVAWLANTLGRLGIP  217 (255)
T ss_pred             HHHHHHHHHHHCCCC
T ss_conf             999999999875999


No 61 
>TIGR01356 aroA 3-phosphoshikimate 1-carboxyvinyltransferase; InterPro: IPR006264   These sequences represent 5-enolpyruvyl shikimate-3-phosphate synthase (EPSP_synthase) (3-phosphoshikimate-1-carboxyvinyltransferase,aroA), which catalyzes the sixth of seven steps in the shikimate pathway of the biosynthesis of chorimate. Chorismate is last common precursor of all three aromatic amino acids. ; GO: 0003866 3-phosphoshikimate 1-carboxyvinyltransferase activity.
Probab=20.79  E-value=44  Score=13.79  Aligned_cols=77  Identities=10%  Similarity=0.198  Sum_probs=45.0

Q ss_pred             CCCCEEEECC---CEEEEEEEEECCCEEEEECCCCCCCCCCCCCCCCCEEECCCCEEEECCCCCEEEECCCCCHHHHHHH
Q ss_conf             4763499459---7399899984170799963776665776545687344236641456046735897389889999999
Q gi|254780376|r  262 ERTGTIVIGD---NVRISKVVVSYGNLTVQITENEQVVQPNAFSSNGSTVTQNNTDLKVSDNKGSFSLIDAPDLNSLISG  338 (369)
Q Consensus       262 erTGTIV~g~---~V~I~pvaVsHGnLtI~I~~~~~vsqp~~~~~~g~t~~~~~t~i~v~e~~~~~~~~~~~tl~~lV~A  338 (369)
                      |.-++|.+-+   .-.++++-|.-=++.=-+.+-|.+.-=.+| ..|.|....         -..+.++|+-.++.++..
T Consensus       292 E~~~~~~V~~vr~~~~lkg~~v~~~d~~~~~D~~p~lA~la~f-A~G~t~i~~---------~~~lR~KEsDRi~A~~~~  361 (444)
T TIGR01356       292 EPVADVEVEGVRQASGLKGIKVPDIDMDDMIDLLPTLAVLAAF-AEGPTRITG---------AEELRVKESDRIAAIAEE  361 (444)
T ss_pred             CEEEEEEEEECCCCCCCCCEEECCCCCCCCHHHHHHHHHHHHH-CCCCEEEEC---------CCCCCCCCCHHHHHHHHH
T ss_conf             5057999841310788885123677766400089999999863-799539931---------110221233248999999


Q ss_pred             HHHCCCCHHH
Q ss_conf             9847998789
Q gi|254780376|r  339 MNSIGLKTDG  348 (369)
Q Consensus       339 LN~lG~tp~D  348 (369)
                      |+++|+.-++
T Consensus       362 L~klG~~~~E  371 (444)
T TIGR01356       362 LRKLGVEVEE  371 (444)
T ss_pred             HHHCCCEEEE
T ss_conf             9856937885


No 62 
>TIGR02033 D-hydantoinase dihydropyrimidinase; InterPro: IPR011778    This entry represents the D-hydantoinase (dihydropyrimidinase) which primarily converts 5,6-dihydrouracil to 3-ureidopropanoate but also acts on dihydrothymine and hydantoin. The enzyme is a metalloenzyme ..
Probab=20.20  E-value=57  Score=13.00  Aligned_cols=78  Identities=21%  Similarity=0.188  Sum_probs=37.3

Q ss_pred             ECC-CCCCC---EEEEEECCEEECC-----CCCCCCCCCCCCCCCCCEEEECCE-EEEEECCCCCC---CCCEEEEEEEC
Q ss_conf             214-77861---8999816168334-----324567652004765421741654-88741354324---77649999507
Q gi|254780376|r  128 SLL-GADGN---IYAVAQGSVVVSG-----LFVKGQSSSFMEGISTGGKIVNGA-IVERELPKKFK---DSADLILQLRN  194 (369)
Q Consensus       128 pL~-g~dg~---vyAvAQG~i~vgg-----~~~~g~~~~~~~n~~t~GrIp~Ga-~VErev~~~f~---~~~~l~L~L~~  194 (369)
                      ||| -..-|   =-|+..|.|.+-+     |+..+.|.......+.==+||||. -||..++.-|.   ....+++    
T Consensus       297 PLRP~~~~qd~Lw~~l~~G~Lq~v~sDHC~F~~~~~Gkl~~~G~dDF~~iPNG~PGvE~Rm~~lf~~gV~~Gri~~----  372 (466)
T TIGR02033       297 PLRPEKEDQDALWQALSSGALQTVSSDHCTFNFAQKGKLKAIGKDDFRKIPNGLPGVEERMELLFDEGVAKGRITL----  372 (466)
T ss_pred             CCCCCCCCHHHHHHHHHCCCCCEEEECCCCCCCCCCCHHHCCCCCCCCCCCCCCCCCCCCHHHHHHHCCCCCCCCH----
T ss_conf             0133876608999987618511033033663543561411288876450788458621114798873326587876----


Q ss_pred             CCHH--HHHHHHHHHHH
Q ss_conf             8878--99999999987
Q gi|254780376|r  195 PDFS--TAIRIADQINS  209 (369)
Q Consensus       195 pdft--tA~~ia~aIN~  209 (369)
                      ..|=  ||.++|+--|-
T Consensus       373 e~FV~~TSt~~AK~F~l  389 (466)
T TIGR02033       373 EKFVELTSTNPAKIFNL  389 (466)
T ss_pred             HHHHHHHHHHHHHHHCC
T ss_conf             67989988866887188


No 63 
>PRK10894 hypothetical protein; Provisional
Probab=20.14  E-value=57  Score=12.99  Aligned_cols=14  Identities=0%  Similarity=0.031  Sum_probs=6.4

Q ss_pred             CEEEEECCCCEEEE
Q ss_conf             35999447634994
Q gi|254780376|r  256 ARVIINERTGTIVI  269 (369)
Q Consensus       256 akVVINerTGTIV~  269 (369)
                      .+++.|-+++++.+
T Consensus       139 ~~I~Ydl~~~~~~a  152 (184)
T PRK10894        139 DKITYLVKEQKMQA  152 (184)
T ss_pred             CEEEEEECCCEEEE
T ss_conf             78999906679999


Done!