Query         gi|254780224|ref|YP_003064637.1| hypothetical protein CLIBASIA_00545 [Candidatus Liberibacter asiaticus str. psy62]
Match_columns 382
No_of_seqs    178 out of 252
Neff          6.5 
Searched_HMMs 39220
Date          Mon May 23 19:59:09 2011
Command       /home/congqian_1/programs/hhpred/hhsearch -i 254780224.hhm -d /home/congqian_1/database/cdd/Cdd.hhm 

 No Hit                             Prob E-value P-value  Score    SS Cols Query HMM  Template HMM
  1 COG5330 Uncharacterized protei 100.0       0       0  373.8  32.7  356    1-363     7-362 (364)
  2 pfam10098 DUF2336 Uncharacteri 100.0       0       0  373.6  28.5  238   86-323     1-239 (263)
  3 COG5330 Uncharacterized protei  98.6 6.1E-06 1.5E-10   54.5  15.7  236   40-305     6-284 (364)
  4 PRK09687 hypothetical protein;  96.7   0.042 1.1E-06   30.8  17.0   55    4-67     26-80  (280)
  5 pfam10098 DUF2336 Uncharacteri  96.6   0.047 1.2E-06   30.5  21.0  220   44-304    15-238 (263)
  6 KOG2025 consensus               91.2     0.9 2.3E-05   22.7   8.9   46  133-180   174-219 (892)
  7 pfam01816 LRV Leucine rich rep  80.8     1.1 2.8E-05   22.2   2.1   25   56-84      2-26  (26)
  8 PRK13800 putative oxidoreducta  67.8     7.2 0.00018   17.1  11.5   41   46-86    626-668 (894)
  9 TIGR02160 PA_CoA_Oxy5 phenylac  52.2     9.9 0.00025   16.2   2.0  132  101-246   112-243 (371)
 10 KOG2023 consensus               48.0      16  0.0004   15.0   8.7  117    2-127   175-292 (885)
 11 PRK05686 fliG flagellar motor   46.9      16 0.00042   14.9  21.2  257   45-340    27-319 (337)
 12 pfam09339 HTH_IclR IclR helix-  45.0      18 0.00045   14.7   2.7   34  253-286     8-41  (52)
 13 pfam09904 DUF2131 Uncharacteri  41.1      16  0.0004   15.0   1.6   22  293-314     2-23  (67)
 14 cd00020 ARM Armadillo/beta-cat  37.9      23 0.00058   14.0  13.5   97    2-115     8-109 (120)
 15 TIGR02812 fadR_gamma fatty aci  33.6      24 0.00062   13.8   1.6   32  258-289    90-121 (275)
 16 pfam01602 Adaptin_N Adaptin N   32.5      28 0.00071   13.5   7.1   62    1-67     79-140 (534)
 17 KOG1240 consensus               28.7      32 0.00082   13.1   5.1   68    2-69    463-536 (1431)
 18 TIGR01691 enolase-ppase 2,3-di  26.3      34 0.00086   13.0   1.3   86  274-373    91-179 (240)
 19 TIGR02944 suf_reg_Xantho FeS a  24.2      39 0.00099   12.6   3.1   34  253-286    15-48  (130)
 20 cd01392 HTH_LacI Helix-turn-he  24.0      39   0.001   12.6   5.5   43  268-324     2-44  (52)
 21 smart00346 HTH_ICLR helix_turn  23.8      39   0.001   12.5   2.7   39  283-321    14-52  (91)
 22 TIGR02431 pcaR_pcaU beta-ketoa  23.5      40   0.001   12.5   2.2   19  318-336    50-68  (252)
 23 pfam02985 HEAT HEAT repeat. Th  23.3      40   0.001   12.5   2.9   22   45-66      4-25  (31)
 24 COG1414 IclR Transcriptional r  22.4      42  0.0011   12.4   2.8   59  261-325   127-187 (246)
 25 PRK09834 DNA-binding transcrip  21.4      44  0.0011   12.2   2.7   53  266-323   142-194 (264)

No 1  
>COG5330 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=100.00  E-value=0  Score=373.76  Aligned_cols=356  Identities=26%  Similarity=0.328  Sum_probs=337.6

Q ss_pred             CHHHHHHHHHCCCCHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHCCCCCCCHHHHHHHC
Q ss_conf             95899999841799789999999999996357899899999999999985196989999999982148789889999870
Q gi|254780224|r    1 MSVQSFIKWAKNAKLQERISIARILGRTWCMEELLDQEKDSLVLAMMHLLDDPSSRVRLSLARAIALSDTAPKHVVLALS   80 (382)
Q Consensus         1 miv~~fl~~~~~a~~~~Ra~~a~~l~r~~~~~~l~~~er~~a~~iL~~L~~d~~~~vR~alA~~La~~~~aP~~vi~~LA   80 (382)
                      |+++.|++|.+++++++|..+++.+++.+++++++-.|+..++++++.|++|+++.||+.+|+.|++|+.+|+.|+.+|+
T Consensus         7 ~~~~~~i~~~~~a~~~eR~~~A~~l~~~~~~~~~sr~d~~~~~~l~~~Ll~d~s~~vrr~lA~aL~~~~~~Pr~l~~~La   86 (364)
T COG5330           7 STDQDLIRLLEEASSGERALAARVLAFASLQRPLSREDMRQFEDLARPLLDDSSEEVRRELAAALAQCETAPRALARALA   86 (364)
T ss_pred             HHHHHHHHHHCCCCHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHCCCCCHHHHHHHH
T ss_conf             46999999844798368999999988888537521778999999999986086588999999998718767799999884


Q ss_pred             CCCHHHHHHHHHHCCCCCHHHHHHHHHCCCHHHHHHHHCCCCCCHHHHHHHHHCCCHHHHHHHHHCCCCCCCHHHHHHHH
Q ss_conf             89778999999738589989999999549999999986299999899999984398999999860899846946799999
Q gi|254780224|r   81 EDHPDVSGTIILHSPVLKDNDLVDLIGRGNKLTSIFVASRHKLSHVVVENLIETGCVDNIVALLGNKSVFLSNSLLMQIV  160 (382)
Q Consensus        81 ~D~~~vA~pvL~~Sp~L~d~dLv~ia~~~~~~~~~AIA~R~~ls~~V~~aLae~gd~~v~~~Ll~N~~A~is~~~l~~lv  160 (382)
                      +|+++|+.|+|.+||+|+|+||++|++++|+.|+.+||+|+++|+.|+++|++.|+.+++..++.|++|.+++.++..+.
T Consensus        87 ~d~~~IAapll~rSpal~d~dLv~i~~~~G~~h~raIarR~~ls~~v~~~Lv~~g~~~~~~~~~~n~~A~~~~~al~~~~  166 (364)
T COG5330          87 EDPISIAAPLLIRSPALTDDDLVDIARRQGPAHARAIARRPSLSPLVIDALVERGDEEEVLVLLENDAAPLSPYALQRVA  166 (364)
T ss_pred             CCCHHHHHHHHHCCCCCCHHHHHHHHHHCCHHHHHHHHHCCCCCHHHHHHHHHCCCCHHHHCCCCCCCCCCCHHHHHHHH
T ss_conf             59766767899718677837899999964889999998456888689999998077123310233545766788998876


Q ss_pred             HHHCCCHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHH
Q ss_conf             98178989999986246899899999999867999997852158998999999998888786432015677346999999
Q gi|254780224|r  161 ERFCHDASIRNLLSLRTDLSLKARYLLMKSVCNVLSQSKIVQKSITFRRTQILFEESMRVGILEMISHVRDVQALRELVD  240 (382)
Q Consensus       161 ~ra~~~~~l~~~L~~R~dLp~~~~~~L~~~vs~~lr~~l~~r~~l~~~~~~~~~~~a~~~a~~~~~~~~~~~~~~~~lv~  240 (382)
                      ++++.++.++..++.|..+|.+.+..++.++++.+++.++....+++.+...+...++++.+........+..+. .++.
T Consensus       167 d~~a~~~~~~~~~~~r~~lp~~~~~~~~~~~~~~~~~~~l~~~~~~~~r~~~l~~~a~~~~a~~~~aa~ad~~~~-~~~~  245 (364)
T COG5330         167 DRAAAEPALRQAAVDREALPLRARIELAARVGERLRDSILVKAQISEARAAELVRFARERAAILFAAALADALDI-RFVA  245 (364)
T ss_pred             HHHCCCHHHHHHHHCHHHCCHHHHHHHHHHHHHHHHCCCHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHCCCCCH-HHHH
T ss_conf             420147667786203342452579999999887763365044135777799999987322578877750673124-7899


Q ss_pred             HHHHCCCCCHHHHHHHHHCCCHHHHHHHHHHHHCCCHHHHHHHHHCCCCHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHC
Q ss_conf             99865899989999989819947999999998299989999997179917999999962999889999999999998402
Q gi|254780224|r  241 LLHDDGQLTPALLIYAIMIGAIDFVSVILANIAEYSTDRVYSILSTGGFHVICALYELVGLSPEISEIFVEATMIWRELA  320 (382)
Q Consensus       241 ~L~~~g~Lt~~lllral~~G~~~~f~~aLA~lsgi~~~~v~~ll~d~~~~~l~aL~~aaGLp~~~~~af~~A~~~~r~~~  320 (382)
                      +++..++++|+++..++|+|.+.||++++..++|+|...++.|+.+.+.+++..+|+.+|++++++-.|.+++.     +
T Consensus       246 ~~r~~~~~s~~~L~~aL~~~~~~~~~aalv~~ag~p~~~~r~i~~~~r~~al~~i~~~~~l~~rV~~~f~a~~~-----~  320 (364)
T COG5330         246 ALRIMLSLSPALLAAALRSLGLSFFEAALVDLAGLPSHRVRRIGRGGRPHALRAILRTAALDERVRSWFRADAL-----E  320 (364)
T ss_pred             HHHHHHCCCHHHHHHHHHCCCCCCHHHHHHHHCCCCCHHHHHHHCCCCHHHHHHHHHHCCCCHHHHHHHHHHHH-----H
T ss_conf             99997247889999999738987148999986278721279986033179999987522540789999997634-----3


Q ss_pred             CCCCCCCHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHH
Q ss_conf             6676531788999999999973025788200899999853168
Q gi|254780224|r  321 VGSTVMEPGIIAEKLLERMRKRNISGLPAGELLEMVERIYLDV  363 (382)
Q Consensus       321 ~~~~~~~~~~~~~~~~er~~~~~~~~~~~~~l~~ll~r~~~~~  363 (382)
                      +++..+.+..+...++.++.+.. ...+..+.-+..++.....
T Consensus       321 ~~~~~~~r~s~~a~~~~r~~r~s-~~aa~~~~~~~~r~~~~a~  362 (364)
T COG5330         321 LRDHAMARASALAEALARFPRDS-DEAAVDELSAPVRKLDLAA  362 (364)
T ss_pred             CCCCHHHHHHHHHHHHHHCCCCC-HHHHHHHHHHHHHHHHHHH
T ss_conf             14424444654458886046762-5778998997767765542


No 2  
>pfam10098 DUF2336 Uncharacterized protein conserved in bacteria (DUF2336). Members of this family of hypothetical bacterial proteins have no known function.
Probab=100.00  E-value=0  Score=373.58  Aligned_cols=238  Identities=28%  Similarity=0.406  Sum_probs=232.8

Q ss_pred             HHHHHHHHCCCCCHHHHHHHHHCCCHHHHHHHHCCCCCCHHHHHHHHHCCCHHHHHHHHHCCCCCCCHHHHHHHHHHHCC
Q ss_conf             99999973858998999999954999999998629999989999998439899999986089984694679999998178
Q gi|254780224|r   86 VSGTIILHSPVLKDNDLVDLIGRGNKLTSIFVASRHKLSHVVVENLIETGCVDNIVALLGNKSVFLSNSLLMQIVERFCH  165 (382)
Q Consensus        86 vA~pvL~~Sp~L~d~dLv~ia~~~~~~~~~AIA~R~~ls~~V~~aLae~gd~~v~~~Ll~N~~A~is~~~l~~lv~ra~~  165 (382)
                      ||+|||++||+|+|+||++|+++++++|+++||+|++||+.|+|+|+++||.+|+..|+.|+||.||+.+|+++++|+++
T Consensus         1 VA~PvL~~S~~Lsd~DLi~ia~~~~~~h~~AIA~R~~ls~~VtdaLve~gd~~vv~~Ll~N~gA~is~~~~~~lv~ra~~   80 (263)
T pfam10098         1 VAGPVLERSPVLSDADLIEIARTGGQEHLLAIARRPDLSEAVTDALVERGDREVVRRLLRNPGARFSEAGLERLVERAAD   80 (263)
T ss_pred             CCHHHHHCCCCCCHHHHHHHHHHCCHHHHHHHHCCCCCCHHHHHHHHHCCCHHHHHHHHCCCCCCCCHHHHHHHHHHHCC
T ss_conf             97677724999998999999996899999997778989989999999728889999987299981786789999998765


Q ss_pred             CHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHHCCC-CCHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHH
Q ss_conf             989999986246899899999999867999997852158-9989999999988887864320156773469999999986
Q gi|254780224|r  166 DASIRNLLSLRTDLSLKARYLLMKSVCNVLSQSKIVQKS-ITFRRTQILFEESMRVGILEMISHVRDVQALRELVDLLHD  244 (382)
Q Consensus       166 ~~~l~~~L~~R~dLp~~~~~~L~~~vs~~lr~~l~~r~~-l~~~~~~~~~~~a~~~a~~~~~~~~~~~~~~~~lv~~L~~  244 (382)
                      ++.++.+|+.|+|||++++++|++++++.++++++.+++ ++++.++.+..+++++++...+....++++++.+|++|+.
T Consensus        81 ~~~l~~~L~~R~dLp~~~~~~L~~~vs~~lr~~l~~~~~~~~~~~~~~~~~~a~~~a~~~~~~~~~~~~~~~~~v~~l~~  160 (263)
T pfam10098        81 DAALREALGARPDLPADVRRRLLAKVSEALRAKLLARAAPLSAERIQRAVREAAERAAADLAADSRDFAEAKRLVRHLRA  160 (263)
T ss_pred             CHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHH
T ss_conf             68899988556469999999999996799999999834556899999999999998750001234325679999999987


Q ss_pred             CCCCCHHHHHHHHHCCCHHHHHHHHHHHHCCCHHHHHHHHHCCCCHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHCCCC
Q ss_conf             5899989999989819947999999998299989999997179917999999962999889999999999998402667
Q gi|254780224|r  245 DGQLTPALLIYAIMIGAIDFVSVILANIAEYSTDRVYSILSTGGFHVICALYELVGLSPEISEIFVEATMIWRELAVGS  323 (382)
Q Consensus       245 ~g~Lt~~lllral~~G~~~~f~~aLA~lsgi~~~~v~~ll~d~~~~~l~aL~~aaGLp~~~~~af~~A~~~~r~~~~~~  323 (382)
                      +|+||+++|++++|+|+++||.++|+.|+|+|+.+|++||+++++++|.++||++|||+.+|++|+.++..|+++..+.
T Consensus       161 ~g~L~~~~l~r~l~~g~~~~~~~ala~l~gi~~~~v~~il~~~~~~~l~~l~kaaGL~~~~~~~~~~a~~~~~~~~~~~  239 (263)
T pfam10098       161 RGRLTEALLLRAALSGRLEEFAAALAELSGLPVETVRRLLHDGRGEGLAALCKAAGLSWATFAALLAARDGWRRIAPSD  239 (263)
T ss_pred             CCCCCHHHHHHHHHCCCHHHHHHHHHHHHCCCHHHHHHHHHCCCCHHHHHHHHHCCCCHHHHHHHHHHHHHHCCCCHHH
T ss_conf             5899999999999859978999999988693999999998379956999999985989999999999866322498778


No 3  
>COG5330 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=98.62  E-value=6.1e-06  Score=54.52  Aligned_cols=236  Identities=16%  Similarity=0.114  Sum_probs=121.4

Q ss_pred             HHHHHHHHHHHCCCCHHHHHHHHHHHCCCCCCCHHHHHHHCCCCHHHHHHHHHHCCCCCHHHHHHHHHCCCHHHHHHHHC
Q ss_conf             99999999985196989999999982148789889999870897789999997385899899999995499999999862
Q gi|254780224|r   40 DSLVLAMMHLLDDPSSRVRLSLARAIALSDTAPKHVVLALSEDHPDVSGTIILHSPVLKDNDLVDLIGRGNKLTSIFVAS  119 (382)
Q Consensus        40 ~~a~~iL~~L~~d~~~~vR~alA~~La~~~~aP~~vi~~LA~D~~~vA~pvL~~Sp~L~d~dLv~ia~~~~~~~~~AIA~  119 (382)
                      +...+-+..++.+++..-|.-+|..++.+...++ +-+..-++..++..|.+..+......++..........++..+..
T Consensus         6 ~~~~~~~i~~~~~a~~~eR~~~A~~l~~~~~~~~-~sr~d~~~~~~l~~~Ll~d~s~~vrr~lA~aL~~~~~~Pr~l~~~   84 (364)
T COG5330           6 QSTDQDLIRLLEEASSGERALAARVLAFASLQRP-LSREDMRQFEDLARPLLDDSSEEVRRELAAALAQCETAPRALARA   84 (364)
T ss_pred             HHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHCCC-CCHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHCCCCCHHHHHH
T ss_conf             6469999998447983689999999888885375-217789999999999860865889999999987187677999998


Q ss_pred             CCCCCHHHHHHHHHCCCHHHHHHHHHCCCCCCCHHHHHHHHHHHCCCHHHHHHHHHCCCCCHHHHHHHHHH---------
Q ss_conf             99999899999984398999999860899846946799999981789899999862468998999999998---------
Q gi|254780224|r  120 RHKLSHVVVENLIETGCVDNIVALLGNKSVFLSNSLLMQIVERFCHDASIRNLLSLRTDLSLKARYLLMKS---------  190 (382)
Q Consensus       120 R~~ls~~V~~aLae~gd~~v~~~Ll~N~~A~is~~~l~~lv~ra~~~~~l~~~L~~R~dLp~~~~~~L~~~---------  190 (382)
                      ....|..|++.|..            |. -.+++.-+-.++.+  +.+.-...++.|+++++.+...|...         
T Consensus        85 La~d~~~IAapll~------------rS-pal~d~dLv~i~~~--~G~~h~raIarR~~ls~~v~~~Lv~~g~~~~~~~~  149 (364)
T COG5330          85 LAEDPISIAAPLLI------------RS-PALTDDDLVDIARR--QGPAHARAIARRPSLSPLVIDALVERGDEEEVLVL  149 (364)
T ss_pred             HHCCCHHHHHHHHH------------CC-CCCCHHHHHHHHHH--CCHHHHHHHHHCCCCCHHHHHHHHHCCCCHHHHCC
T ss_conf             84597667678997------------18-67783789999996--48899999984568886899999980771233102


Q ss_pred             ----------------HH-----HHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHCCCCC
Q ss_conf             ----------------67-----999997852158998999999998888786432015677346999999998658999
Q gi|254780224|r  191 ----------------VC-----NVLSQSKIVQKSITFRRTQILFEESMRVGILEMISHVRDVQALRELVDLLHDDGQLT  249 (382)
Q Consensus       191 ----------------vs-----~~lr~~l~~r~~l~~~~~~~~~~~a~~~a~~~~~~~~~~~~~~~~lv~~L~~~g~Lt  249 (382)
                                      ..     ..+++....++.++............++..-.....              +.-+..+
T Consensus       150 ~~n~~A~~~~~al~~~~d~~a~~~~~~~~~~~r~~lp~~~~~~~~~~~~~~~~~~~l~~--------------~~~~~~r  215 (364)
T COG5330         150 LENDAAPLSPYALQRVADRAAAEPALRQAAVDREALPLRARIELAARVGERLRDSILVK--------------AQISEAR  215 (364)
T ss_pred             CCCCCCCCCHHHHHHHHHHHCCCHHHHHHHHCHHHCCHHHHHHHHHHHHHHHHCCCHHH--------------HCCCHHH
T ss_conf             33545766788998876420147667786203342452579999999887763365044--------------1357777


Q ss_pred             HHHHHHHHHCCCHHHHHHHHHHHHCCCHHHH-------------HHHHHCCCCHHHHHHHHHCCCCHHH
Q ss_conf             8999998981994799999999829998999-------------9997179917999999962999889
Q gi|254780224|r  250 PALLIYAIMIGAIDFVSVILANIAEYSTDRV-------------YSILSTGGFHVICALYELVGLSPEI  305 (382)
Q Consensus       250 ~~lllral~~G~~~~f~~aLA~lsgi~~~~v-------------~~ll~d~~~~~l~aL~~aaGLp~~~  305 (382)
                      ...++++.+.++..+|.++++.-.+......             ..+-+.+.+....++|+-+|+|...
T Consensus       216 ~~~l~~~a~~~~a~~~~aa~ad~~~~~~~~~~r~~~~~s~~~L~~aL~~~~~~~~~aalv~~ag~p~~~  284 (364)
T COG5330         216 AAELVRFARERAAILFAAALADALDIRFVAALRIMLSLSPALLAAALRSLGLSFFEAALVDLAGLPSHR  284 (364)
T ss_pred             HHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHCCCHHHHHHHHHCCCCCCHHHHHHHHCCCCCHH
T ss_conf             999999873225788777506731247899999972478899999997389871489999862787212


No 4  
>PRK09687 hypothetical protein; Provisional
Probab=96.65  E-value=0.042  Score=30.85  Aligned_cols=55  Identities=16%  Similarity=0.056  Sum_probs=23.7

Q ss_pred             HHHHHHHCCCCHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHCC
Q ss_conf             9999984179978999999999999635789989999999999998519698999999998214
Q gi|254780224|r    4 QSFIKWAKNAKLQERISIARILGRTWCMEELLDQEKDSLVLAMMHLLDDPSSRVRLSLARAIAL   67 (382)
Q Consensus         4 ~~fl~~~~~a~~~~Ra~~a~~l~r~~~~~~l~~~er~~a~~iL~~L~~d~~~~vR~alA~~La~   67 (382)
                      .+++++.+...+..|-.++..|..  ..+       ..+-..+..|+.|.++.||..-+..|.+
T Consensus        26 ~~Li~lL~D~n~~VR~~AA~aLg~--ig~-------~~a~~~li~llkd~n~~VR~~Aa~ALGq   80 (280)
T PRK09687         26 NELFRLLDDHNSLKRISSARVLQL--RGG-------QEAFRLAVELCSSKNYIERDLGAFILSQ   80 (280)
T ss_pred             HHHHHHHHCCCHHHHHHHHHHHHC--CCC-------HHHHHHHHHHHHCCCHHHHHHHHHHHHH
T ss_conf             889998726988889999999880--484-------6699999998737878899999999984


No 5  
>pfam10098 DUF2336 Uncharacterized protein conserved in bacteria (DUF2336). Members of this family of hypothetical bacterial proteins have no known function.
Probab=96.58  E-value=0.047  Score=30.55  Aligned_cols=220  Identities=15%  Similarity=0.072  Sum_probs=133.6

Q ss_pred             HHHHHHHCCCCHHHHHHHHHHHCCCCCCCHHHHHHHCCCCHH-HHHHHHH-HCCCCCHHHHHHHHH--CCCHHHHHHHHC
Q ss_conf             999998519698999999998214878988999987089778-9999997-385899899999995--499999999862
Q gi|254780224|r   44 LAMMHLLDDPSSRVRLSLARAIALSDTAPKHVVLALSEDHPD-VSGTIIL-HSPVLKDNDLVDLIG--RGNKLTSIFVAS  119 (382)
Q Consensus        44 ~iL~~L~~d~~~~vR~alA~~La~~~~aP~~vi~~LA~D~~~-vA~pvL~-~Sp~L~d~dLv~ia~--~~~~~~~~AIA~  119 (382)
                      +-|..++...++.-+.++|.+    ++.+..|...|+.--+. +...++. ..-.|++.-+..++.  ..++..+..+..
T Consensus        15 ~DLi~ia~~~~~~h~~AIA~R----~~ls~~VtdaLve~gd~~vv~~Ll~N~gA~is~~~~~~lv~ra~~~~~l~~~L~~   90 (263)
T pfam10098        15 ADLIEIARTGGQEHLLAIARR----PDLSEAVTDALVERGDREVVRRLLRNPGARFSEAGLERLVERAADDAALREALGA   90 (263)
T ss_pred             HHHHHHHHHCCHHHHHHHHCC----CCCCHHHHHHHHHCCCHHHHHHHHCCCCCCCCHHHHHHHHHHHCCCHHHHHHHHC
T ss_conf             999999996899999997778----9899899999997288899999872999817867899999987656889998855


Q ss_pred             CCCCCHHHHHHHHHCCCHHHHHHHHHCCCCCCCHHHHHHHHHHHCCCHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHH
Q ss_conf             99999899999984398999999860899846946799999981789899999862468998999999998679999978
Q gi|254780224|r  120 RHKLSHVVVENLIETGCVDNIVALLGNKSVFLSNSLLMQIVERFCHDASIRNLLSLRTDLSLKARYLLMKSVCNVLSQSK  199 (382)
Q Consensus       120 R~~ls~~V~~aLae~gd~~v~~~Ll~N~~A~is~~~l~~lv~ra~~~~~l~~~L~~R~dLp~~~~~~L~~~vs~~lr~~l  199 (382)
                      |+++|+.+...|...-...+...++. ....+.......++............     ..+.+      ..-...+...+
T Consensus        91 R~dLp~~~~~~L~~~vs~~lr~~l~~-~~~~~~~~~~~~~~~~a~~~a~~~~~-----~~~~~------~~~~~~~v~~l  158 (263)
T pfam10098        91 RPDLPADVRRRLLAKVSEALRAKLLA-RAAPLSAERIQRAVREAAERAAADLA-----ADSRD------FAEAKRLVRHL  158 (263)
T ss_pred             CCCCCHHHHHHHHHHHHHHHHHHHHH-HCCCCCHHHHHHHHHHHHHHHHHHHC-----CCCCC------HHHHHHHHHHH
T ss_conf             64699999999999967999999998-34556899999999999998750001-----23432------56799999999


Q ss_pred             HHCCCCCHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHCCCCCHHHHHHHHHCCCHHHHHHHHHHHHCCCHHH
Q ss_conf             52158998999999998888786432015677346999999998658999899999898199479999999982999899
Q gi|254780224|r  200 IVQKSITFRRTQILFEESMRVGILEMISHVRDVQALRELVDLLHDDGQLTPALLIYAIMIGAIDFVSVILANIAEYSTDR  279 (382)
Q Consensus       200 ~~r~~l~~~~~~~~~~~a~~~a~~~~~~~~~~~~~~~~lv~~L~~~g~Lt~~lllral~~G~~~~f~~aLA~lsgi~~~~  279 (382)
                      ..+..+++..+.+.+..             +.   ...+...+-.-..+....+-+.+.++... -...+..-+|+|...
T Consensus       159 ~~~g~L~~~~l~r~l~~-------------g~---~~~~~~ala~l~gi~~~~v~~il~~~~~~-~l~~l~kaaGL~~~~  221 (263)
T pfam10098       159 RARGRLTEALLLRAALS-------------GR---LEEFAAALAELSGLPVETVRRLLHDGRGE-GLAALCKAAGLSWAT  221 (263)
T ss_pred             HHCCCCCHHHHHHHHHC-------------CC---HHHHHHHHHHHHCCCHHHHHHHHHCCCCH-HHHHHHHHCCCCHHH
T ss_conf             87589999999999985-------------99---78999999988693999999998379956-999999985989999


Q ss_pred             HHHHHHCCCCHHHHHHHHHCCCCHH
Q ss_conf             9999717991799999996299988
Q gi|254780224|r  280 VYSILSTGGFHVICALYELVGLSPE  304 (382)
Q Consensus       280 v~~ll~d~~~~~l~aL~~aaGLp~~  304 (382)
                      ...++.        +.+..-+++..
T Consensus       222 ~~~~~~--------a~~~~~~~~~~  238 (263)
T pfam10098       222 FAALLA--------ARDGWRRIAPS  238 (263)
T ss_pred             HHHHHH--------HHHHHCCCCHH
T ss_conf             999999--------86632249877


No 6  
>KOG2025 consensus
Probab=91.22  E-value=0.9  Score=22.68  Aligned_cols=46  Identities=26%  Similarity=0.114  Sum_probs=26.9

Q ss_pred             HCCCHHHHHHHHHCCCCCCCHHHHHHHHHHHCCCHHHHHHHHHCCCCC
Q ss_conf             439899999986089984694679999998178989999986246899
Q gi|254780224|r  133 ETGCVDNIVALLGNKSVFLSNSLLMQIVERFCHDASIRNLLSLRTDLS  180 (382)
Q Consensus       133 e~gd~~v~~~Ll~N~~A~is~~~l~~lv~ra~~~~~l~~~L~~R~dLp  180 (382)
                      -+..++|.++.+.|-  ..+..++..+++|+.|....-..|+.-.=||
T Consensus       174 nDps~EVRraaLsnI--~vdnsTlp~IveRarDV~~anRrlvY~r~lp  219 (892)
T KOG2025         174 NDPSDEVRRAALSNI--SVDNSTLPCIVERARDVSGANRRLVYERCLP  219 (892)
T ss_pred             CCCCHHHHHHHHHHC--CCCCCCCHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             399589999999860--7787755168887500679999999999876


No 7  
>pfam01816 LRV Leucine rich repeat variant. The function of this repeat is unknown. It has an unusual structure of two helices. One is an alpha helix, the other is the much rarer 3-10 helix.
Probab=80.84  E-value=1.1  Score=22.16  Aligned_cols=25  Identities=28%  Similarity=0.389  Sum_probs=18.4

Q ss_pred             HHHHHHHHHHCCCCCCCHHHHHHHCCCCH
Q ss_conf             99999999821487898899998708977
Q gi|254780224|r   56 RVRLSLARAIALSDTAPKHVVLALSEDHP   84 (382)
Q Consensus        56 ~vR~alA~~La~~~~aP~~vi~~LA~D~~   84 (382)
                      .||..+|.+    |++|.+.+..|+.|++
T Consensus         2 ~VR~~vA~r----p~lp~~~L~~L~~Dpd   26 (26)
T pfam01816         2 EVRAAVARR----PDLPPEALERLAHDPD   26 (26)
T ss_pred             HHHHHHHCC----CCCCHHHHHHHCCCCC
T ss_conf             177776528----9999899998513989


No 8  
>PRK13800 putative oxidoreductase/HEAT repeat-containing protein; Provisional
Probab=67.84  E-value=7.2  Score=17.10  Aligned_cols=41  Identities=24%  Similarity=0.325  Sum_probs=17.8

Q ss_pred             HHHHHCCCCHHHHHHHHHHHCCC--CCCCHHHHHHHCCCCHHH
Q ss_conf             99985196989999999982148--789889999870897789
Q gi|254780224|r   46 MMHLLDDPSSRVRLSLARAIALS--DTAPKHVVLALSEDHPDV   86 (382)
Q Consensus        46 L~~L~~d~~~~vR~alA~~La~~--~~aP~~vi~~LA~D~~~v   86 (382)
                      |.-.++||+|.||+.....|...  |.+-+.++..|+....+|
T Consensus       626 ~~~~L~Dpdp~VRr~Av~~Lte~~pp~~~p~l~~al~D~~~~V  668 (894)
T PRK13800        626 LAPYLADPDPGVRRTAVAVLTEHTPDGYAPALLDALGDDAAAV  668 (894)
T ss_pred             HHHHCCCCCHHHHHHHHHHHHCCCCCCCHHHHHHHHCCCCHHH
T ss_conf             6554269974788999999860489861679999853998789


No 9  
>TIGR02160 PA_CoA_Oxy5 phenylacetate-CoA oxygenase/reductase, PaaK subunit; InterPro: IPR011884 Phenylacetate-CoA oxygenase is comprised of a five gene complex responsible for the hydroxylation of phenylacetate-CoA (PA-CoA) as the second catabolic step in phenylacetic acid (PA) degradation , . Although the exact function of this enzyme has not been determined, it has been shown to be required for phenylacetic acid degradation and has been proposed to function in a multicomponent oxygenase acting on phenylacetate-CoA .    .
Probab=52.22  E-value=9.9  Score=16.24  Aligned_cols=132  Identities=11%  Similarity=0.086  Sum_probs=101.9

Q ss_pred             HHHHHHHCCCHHHHHHHHCCCCCCHHHHHHHHHCCCHHHHHHHHHCCCCCCCHHHHHHHHHHHCCCHHHHHHHHHCCCCC
Q ss_conf             99999954999999998629999989999998439899999986089984694679999998178989999986246899
Q gi|254780224|r  101 DLVDLIGRGNKLTSIFVASRHKLSHVVVENLIETGCVDNIVALLGNKSVFLSNSLLMQIVERFCHDASIRNLLSLRTDLS  180 (382)
Q Consensus       101 dLv~ia~~~~~~~~~AIA~R~~ls~~V~~aLae~gd~~v~~~Ll~N~~A~is~~~l~~lv~ra~~~~~l~~~L~~R~dLp  180 (382)
                      |-..|+...++.|..|||.-..+.|-++-+         ...|+.||.+.|.-    --..|-.++--+++.|..-.|.=
T Consensus       112 daetiaqeaG~~hyvavAAGSGITP~lai~---------~tvLa~~p~S~ftL----vY~Nr~~~~vMFa~~L~DLKd~y  178 (371)
T TIGR02160       112 DAETIAQEAGAGHYVAVAAGSGITPILAIA---------KTVLAAEPKSTFTL----VYGNRRSASVMFAEELADLKDKY  178 (371)
T ss_pred             HHHHHHHHHCCCCEEEEEECCCCHHHHHHH---------HHHHCCCCCCEEEE----EECCCCCCCHHHHHHHHHHHCCH
T ss_conf             256888860689689998178705899999---------98740699520899----96178887277899898763120


Q ss_pred             HHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHCC
Q ss_conf             899999999867999997852158998999999998888786432015677346999999998658
Q gi|254780224|r  181 LKARYLLMKSVCNVLSQSKIVQKSITFRRTQILFEESMRVGILEMISHVRDVQALRELVDLLHDDG  246 (382)
Q Consensus       181 ~~~~~~L~~~vs~~lr~~l~~r~~l~~~~~~~~~~~a~~~a~~~~~~~~~~~~~~~~lv~~L~~~g  246 (382)
                      +. |-.|+...|..-+...+-+.-|+.+++..+.......-..+.|--.+..+-+..--..|...|
T Consensus       179 p~-Rf~l~~vlSrE~~~~~ll~GRlD~ekl~~L~~~li~~~~~deaFlCGP~~mv~~~~~~L~a~G  243 (371)
T TIGR02160       179 PQ-RFALLHVLSREEREAPLLSGRLDGEKLRALLDSLIDVDEVDEAFLCGPAAMVDDAEDALKALG  243 (371)
T ss_pred             HH-HHHHHHHHCCCCCCCCCCCCCCCHHHHHHHHHHHCCHHHCCEEEECCCHHHHHHHHHHHHHCC
T ss_conf             45-789986631211136410242278999988532002100240011185899999999997268


No 10 
>KOG2023 consensus
Probab=47.97  E-value=16  Score=15.00  Aligned_cols=117  Identities=15%  Similarity=0.159  Sum_probs=71.8

Q ss_pred             HHHHHHHHHCCCCHHHHHHHHHHHHHHH-HCCCCCHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHCCCCCCCHHHHHHHC
Q ss_conf             5899999841799789999999999996-357899899999999999985196989999999982148789889999870
Q gi|254780224|r    2 SVQSFIKWAKNAKLQERISIARILGRTW-CMEELLDQEKDSLVLAMMHLLDDPSSRVRLSLARAIALSDTAPKHVVLALS   80 (382)
Q Consensus         2 iv~~fl~~~~~a~~~~Ra~~a~~l~r~~-~~~~l~~~er~~a~~iL~~L~~d~~~~vR~alA~~La~~~~aP~~vi~~LA   80 (382)
                      ++-.|+...++.+|--|..+..-+-.-. ....--......+-+.+..|+.|.++.||+-+-..|.-.-+.-   .-+|.
T Consensus       175 mipkfl~f~~h~spkiRs~A~~cvNq~i~~~~qal~~~iD~Fle~lFalanD~~~eVRk~vC~alv~Llevr---~dkl~  251 (885)
T KOG2023         175 MIPKFLQFFKHPSPKIRSHAVGCVNQFIIIQTQALYVHIDKFLEILFALANDEDPEVRKNVCRALVFLLEVR---PDKLV  251 (885)
T ss_pred             HHHHHHHHHHCCCHHHHHHHHHHHHHEEECCCHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHC---HHHCC
T ss_conf             679999987289836789987202220233728899999999999999806998889999999999999836---77413


Q ss_pred             CCCHHHHHHHHHHCCCCCHHHHHHHHHCCCHHHHHHHHCCCCCCHHH
Q ss_conf             89778999999738589989999999549999999986299999899
Q gi|254780224|r   81 EDHPDVSGTIILHSPVLKDNDLVDLIGRGNKLTSIFVASRHKLSHVV  127 (382)
Q Consensus        81 ~D~~~vA~pvL~~Sp~L~d~dLv~ia~~~~~~~~~AIA~R~~ls~~V  127 (382)
                      -.-..|..-+|.+...-.+.  |.+-   .-+-+.++|..| ++..|
T Consensus       252 phl~~IveyML~~tqd~dE~--VALE---ACEFwla~aeqp-i~~~~  292 (885)
T KOG2023         252 PHLDNIVEYMLQRTQDVDEN--VALE---ACEFWLALAEQP-ICKEV  292 (885)
T ss_pred             CCHHHHHHHHHHHCCCCCHH--HHHH---HHHHHHHHHCCC-CCHHH
T ss_conf             22578999999970586545--7899---999999985076-73888


No 11 
>PRK05686 fliG flagellar motor switch protein G; Validated
Probab=46.92  E-value=16  Score=14.90  Aligned_cols=257  Identities=12%  Similarity=0.120  Sum_probs=132.5

Q ss_pred             HHHHHHCCCCHHHHHHHHHHHCCCCCCCHHHHHHHCCCCHH--------------HHHHHHHHCCCCCHHHHHHHHH---
Q ss_conf             99998519698999999998214878988999987089778--------------9999997385899899999995---
Q gi|254780224|r   45 AMMHLLDDPSSRVRLSLARAIALSDTAPKHVVLALSEDHPD--------------VSGTIILHSPVLKDNDLVDLIG---  107 (382)
Q Consensus        45 iL~~L~~d~~~~vR~alA~~La~~~~aP~~vi~~LA~D~~~--------------vA~pvL~~Sp~L~d~dLv~ia~---  107 (382)
                      .-..++..-++.--+.++...+.....|++.+.....+-..              .+.-+|.  ..|+++-.-.|..   
T Consensus        27 ~Aa~vlk~L~~~Ei~~i~~~m~~l~~i~~~~~~~Vl~EF~~~~~~~~~~~~g~~~~~~~~L~--~alg~~~a~~il~~i~  104 (337)
T PRK05686         27 AAAKVLKHLTPDEVQKLSAAMANLRNVSPEQVEAVLEEFEDEFEAGAYILMGGIDYARRLLE--KALGEEKANSILERIL  104 (337)
T ss_pred             HHHHHHHCCCHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHH--HHCCHHHHHHHHHHHC
T ss_conf             79999863999999999999975699899999999999999998247767773899999999--8359899999998621


Q ss_pred             -CCCHHHHHHHHCCCCCCHHHHHHHHHCCCHHHHHHHHHCCCCCCCHHHHHHHHHHHCCCHHHHHHHHHCCCCCHHHHHH
Q ss_conf             -4999999998629999989999998439899999986089984694679999998178989999986246899899999
Q gi|254780224|r  108 -RGNKLTSIFVASRHKLSHVVVENLIETGCVDNIVALLGNKSVFLSNSLLMQIVERFCHDASIRNLLSLRTDLSLKARYL  186 (382)
Q Consensus       108 -~~~~~~~~AIA~R~~ls~~V~~aLae~gd~~v~~~Ll~N~~A~is~~~l~~lv~ra~~~~~l~~~L~~R~dLp~~~~~~  186 (382)
                       ......   ...=.++++.+...+...-.+.++..++.+                                ||++.+-.
T Consensus       105 ~~~~~~~---~~~L~~~dp~~La~~L~~EhPQtiAlILs~--------------------------------L~~~~AA~  149 (337)
T PRK05686        105 ESLQTSG---FDFLRKMDPQQLANFIRNEHPQTIALILSY--------------------------------LDPDQAAE  149 (337)
T ss_pred             CCCCCCH---HHHHHCCCHHHHHHHHHCCCHHHHHHHHHH--------------------------------CCHHHHHH
T ss_conf             5665876---899865999999999872485899999980--------------------------------99999999


Q ss_pred             HHHHHHHHHHHHHHHC----CCCCHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHCCCCCHHHHHHHHHCCCH
Q ss_conf             9998679999978521----589989999999988887864320156773469999999986589998999998981994
Q gi|254780224|r  187 LMKSVCNVLSQSKIVQ----KSITFRRTQILFEESMRVGILEMISHVRDVQALRELVDLLHDDGQLTPALLIYAIMIGAI  262 (382)
Q Consensus       187 L~~~vs~~lr~~l~~r----~~l~~~~~~~~~~~a~~~a~~~~~~~~~~~~~~~~lv~~L~~~g~Lt~~lllral~~G~~  262 (382)
                      ++...++.++..++.|    ..++++....+..--.....................+.-|+...+-+..-++..+...+-
T Consensus       150 VL~~Lp~~~~~eVi~RiA~l~~v~p~~v~~ie~~L~~~~~~~~~~~~~~~~G~~~vA~ILN~~~~~~~~~il~~L~~~dp  229 (337)
T PRK05686        150 ILSLLPEELRADVMMRIATLEGVQPEALKELEEVLEKKLSSMANADRTKMGGVKTVAEILNNLDRQTEKTIMESLEEEDP  229 (337)
T ss_pred             HHHHCCHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHCCCCCCCCCCCCHHHHHHHHHHCCHHHHHHHHHHHHHHCH
T ss_conf             99869999999999998677899999999999999999743554223445539999999874764689999999987589


Q ss_pred             HHHHH------HHHHHHCCCHHHHHHHHHCCCCHHHHHHHHHCCCCHHHHHHHHHHHHHH------HHHCCCCCC--CCH
Q ss_conf             79999------9999829998999999717991799999996299988999999999999------840266765--317
Q gi|254780224|r  263 DFVSV------ILANIAEYSTDRVYSILSTGGFHVICALYELVGLSPEISEIFVEATMIW------RELAVGSTV--MEP  328 (382)
Q Consensus       263 ~~f~~------aLA~lsgi~~~~v~~ll~d~~~~~l~aL~~aaGLp~~~~~af~~A~~~~------r~~~~~~~~--~~~  328 (382)
                      ++...      .+-.+..++...+..++..-...-+...+|  |-+..+-..|+..++-+      .++++.|..  .+.
T Consensus       230 ~la~~Ir~~mF~Fedi~~l~~~~l~~ll~~v~~~~l~~ALK--ga~~~~~~~il~nmS~R~a~~l~eel~~~gpv~~~dv  307 (337)
T PRK05686        230 ELAEKIKDLMFVFEDLVDLDDRAIQRLLREVDNDDLALALK--GADEELREKFLSNMSKRAAEMLREDLEALGPVRLSDV  307 (337)
T ss_pred             HHHHHHHHHHEEHHHHHCCCHHHHHHHHHHCCHHHHHHHHC--CCCHHHHHHHHHHCCHHHHHHHHHHHHHCCCCCHHHH
T ss_conf             99999998812299774779999999998489999999877--8989999999986289999999999986399878999


Q ss_pred             HHHHHHHHHHHH
Q ss_conf             889999999999
Q gi|254780224|r  329 GIIAEKLLERMR  340 (382)
Q Consensus       329 ~~~~~~~~er~~  340 (382)
                      ..-++..+..+.
T Consensus       308 e~Aq~~Iv~~~r  319 (337)
T PRK05686        308 EEAQKKIVQIAR  319 (337)
T ss_pred             HHHHHHHHHHHH
T ss_conf             999999999999


No 12 
>pfam09339 HTH_IclR IclR helix-turn-helix domain.
Probab=45.05  E-value=18  Score=14.72  Aligned_cols=34  Identities=12%  Similarity=0.083  Sum_probs=16.8

Q ss_pred             HHHHHHCCCHHHHHHHHHHHHCCCHHHHHHHHHC
Q ss_conf             9998981994799999999829998999999717
Q gi|254780224|r  253 LIYAIMIGAIDFVSVILANIAEYSTDRVYSILST  286 (382)
Q Consensus       253 llral~~G~~~~f~~aLA~lsgi~~~~v~~ll~d  286 (382)
                      |+.++...+-..-...|+..+|+|..++.+++..
T Consensus         8 iL~~~~~~~~~~~l~eia~~~gl~kstv~RlL~t   41 (52)
T pfam09339         8 ILEALAEAPGGLSLTEIARRTGLPKSTAHRLLQT   41 (52)
T ss_pred             HHHHHHHCCCCCCHHHHHHHHCCCHHHHHHHHHH
T ss_conf             9999862899989999999989199999999999


No 13 
>pfam09904 DUF2131 Uncharacterized protein conserved in bacteria (DUF2131). This domain, found in various hypothetical prokaryotic proteins, has no known function.
Probab=41.11  E-value=16  Score=14.99  Aligned_cols=22  Identities=27%  Similarity=0.300  Sum_probs=18.6

Q ss_pred             HHHHHHCCCCHHHHHHHHHHHH
Q ss_conf             9999962999889999999999
Q gi|254780224|r  293 CALYELVGLSPEISEIFVEATM  314 (382)
Q Consensus       293 ~aL~~aaGLp~~~~~af~~A~~  314 (382)
                      ..|.+.+|+|++|.+.-.+|+.
T Consensus         2 P~L~~~TGmPRRT~QDti~AL~   23 (67)
T pfam09904         2 PALMELTGMPRRTAQDTIAALA   23 (67)
T ss_pred             CHHHHHHCCCHHHHHHHHHHHC
T ss_conf             1066531897337899998600


No 14 
>cd00020 ARM Armadillo/beta-catenin-like repeats. An approximately 40 amino acid long tandemly repeated sequence motif first identified in the Drosophila segment polarity gene armadillo; these repeats were also found in the mammalian armadillo homolog beta-catenin, the junctional plaque protein plakoglobin, the adenomatous polyposis coli (APC) tumor suppressor protein, and a number of other proteins. ARM has been implicated in mediating protein-protein interactions, but no common features among the target proteins recognized by the ARM repeats have been identified; related to the HEAT domain; three consecutive copies of the repeat are represented by this alignment model.
Probab=37.87  E-value=23  Score=14.03  Aligned_cols=97  Identities=13%  Similarity=0.102  Sum_probs=55.0

Q ss_pred             HHHHHHHHHCCCCHHHHHHHHHHHHHHHHCCCCCHHHHHHH-----HHHHHHHHCCCCHHHHHHHHHHHCCCCCCCHHHH
Q ss_conf             58999998417997899999999999963578998999999-----9999998519698999999998214878988999
Q gi|254780224|r    2 SVQSFIKWAKNAKLQERISIARILGRTWCMEELLDQEKDSL-----VLAMMHLLDDPSSRVRLSLARAIALSDTAPKHVV   76 (382)
Q Consensus         2 iv~~fl~~~~~a~~~~Ra~~a~~l~r~~~~~~l~~~er~~a-----~~iL~~L~~d~~~~vR~alA~~La~~~~aP~~vi   76 (382)
                      .|+.++++.++..++.+..++..|......   +++.+...     -..|..|+.+.++.++...+..           +
T Consensus         8 ~i~~Lv~lL~~~~~~~~~~A~~aL~~l~~~---~~~~~~~i~~~g~i~~Lv~lL~~~~~~v~~~a~~a-----------L   73 (120)
T cd00020           8 GLPALVSLLSSSDENVQREAAWALSNLSAG---NNDNIQAVVEAGGLPALVQLLKSEDEEVVKAALWA-----------L   73 (120)
T ss_pred             CHHHHHHHHCCCCHHHHHHHHHHHHHHHCC---CHHHHHHHHHCCCHHHHHHHHCCCCHHHHHHHHHH-----------H
T ss_conf             899999988599999999999999998328---99989999985869999998746980599999999-----------9


Q ss_pred             HHHCCCCHHHHHHHHHHCCCCCHHHHHHHHHCCCHHHHH
Q ss_conf             987089778999999738589989999999549999999
Q gi|254780224|r   77 LALSEDHPDVSGTIILHSPVLKDNDLVDLIGRGNKLTSI  115 (382)
Q Consensus        77 ~~LA~D~~~vA~pvL~~Sp~L~d~dLv~ia~~~~~~~~~  115 (382)
                      ..|+.+.+.....+... -.  -.-|+.+..++++..+.
T Consensus        74 ~nla~~~~~~~~~~~~~-g~--i~~Lv~ll~~~~~~v~~  109 (120)
T cd00020          74 RNLAAGPEDNKLIVLEA-GG--VPKLVNLLDSSNEDIQK  109 (120)
T ss_pred             HHHHCCCHHHHHHHHHC-CC--HHHHHHHHCCCCHHHHH
T ss_conf             99826989999999987-99--98999988589989999


No 15 
>TIGR02812 fadR_gamma fatty acid metabolism transcriptional regulator FadR; InterPro: IPR014178   Members of this entry are transcriptional regulators of fatty acid metabolism (FadR), including both biosynthesis and beta-oxidation reactions, which are found exclusively in a subset of Gammaproteobacteria with strictly one copy per genome. Proteins have an N-terminal DNA-binding domain and a less well conserved C-terminal long chain acyl-CoA-binding domain. FadR when expressed in Escherichia coli shows differences in regulatory response and fatty acid binding profiles. All members of this entry are expected to have the same function.; GO: 0000062 acyl-CoA binding, 0003677 DNA binding, 0003700 transcription factor activity, 0019217 regulation of fatty acid metabolic process.
Probab=33.65  E-value=24  Score=13.84  Aligned_cols=32  Identities=6%  Similarity=-0.019  Sum_probs=14.4

Q ss_pred             HCCCHHHHHHHHHHHHCCCHHHHHHHHHCCCC
Q ss_conf             81994799999999829998999999717991
Q gi|254780224|r  258 MIGAIDFVSVILANIAEYSTDRVYSILSTGGF  289 (382)
Q Consensus       258 ~~G~~~~f~~aLA~lsgi~~~~v~~ll~d~~~  289 (382)
                      .++-...+.-.||..|+|+.-.++..+-....
T Consensus        90 ~~~~P~l~dnLLSARTnIS~IYir~A~K~np~  121 (275)
T TIGR02812        90 GESVPSLIDNLLSARTNISAIYIRAAFKNNPE  121 (275)
T ss_pred             CCCCCHHHHHHHHHHHCCCHHHHHHHHHCCHH
T ss_conf             77770799999977641377889998622835


No 16 
>pfam01602 Adaptin_N Adaptin N terminal region. This family consists of the N terminal region of various alpha, beta and gamma subunits of the AP-1, AP-2 and AP-3 adaptor protein complexes. The adaptor protein (AP) complexes are involved in the formation of clathrin-coated pits and vesicles. The N-terminal region of the various adaptor proteins (APs) is constant by comparison to the C-terminal which is variable within members of the AP-2 family; and it has been proposed that this constant region interacts with another uniform component of the coated vesicles.
Probab=32.45  E-value=28  Score=13.49  Aligned_cols=62  Identities=23%  Similarity=0.162  Sum_probs=33.2

Q ss_pred             CHHHHHHHHHCCCCHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHCC
Q ss_conf             9589999984179978999999999999635789989999999999998519698999999998214
Q gi|254780224|r    1 MSVQSFIKWAKNAKLQERISIARILGRTWCMEELLDQEKDSLVLAMMHLLDDPSSRVRLSLARAIAL   67 (382)
Q Consensus         1 miv~~fl~~~~~a~~~~Ra~~a~~l~r~~~~~~l~~~er~~a~~iL~~L~~d~~~~vR~alA~~La~   67 (382)
                      |+|+.|.+=.++..+..|+-+.+.++..     .+++-.......+..++.|+++.||+..+-.+..
T Consensus        79 L~intl~kDl~s~n~~ir~lALr~ls~i-----~~~~l~~~l~~~i~~~l~d~~p~VRk~A~l~~~k  140 (534)
T pfam01602        79 LTTNTIKKDLQSPNPLIRGLALRTLSCI-----RVPELAEDLAPDIKKLLVDPNPYVRKKAALAILK  140 (534)
T ss_pred             HHHHHHHHHCCCCCHHHHHHHHHHHHCC-----CCHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHH
T ss_conf             9999999876999787899999998737-----9799999999999998679978999999999999


No 17 
>KOG1240 consensus
Probab=28.73  E-value=32  Score=13.10  Aligned_cols=68  Identities=16%  Similarity=0.253  Sum_probs=50.4

Q ss_pred             HHHHHHHHHCCCCHHHHHHHHHHHHHHH-HCCCCCHHHHHHHHH----HHHHHHCC-CCHHHHHHHHHHHCCCC
Q ss_conf             5899999841799789999999999996-357899899999999----99998519-69899999999821487
Q gi|254780224|r    2 SVQSFIKWAKNAKLQERISIARILGRTW-CMEELLDQEKDSLVL----AMMHLLDD-PSSRVRLSLARAIALSD   69 (382)
Q Consensus         2 iv~~fl~~~~~a~~~~Ra~~a~~l~r~~-~~~~l~~~er~~a~~----iL~~L~~d-~~~~vR~alA~~La~~~   69 (382)
                      |+-.|+.+.+...+..|+.+...|++.. ...+.++.+-.++-+    -|..|+.| ....||.+-|..|+...
T Consensus       463 VlPY~v~l~~Ds~a~Vra~Al~Tlt~~L~~Vr~~~~~daniF~eYlfP~L~~l~~d~~~~~vRiayAsnla~LA  536 (1431)
T KOG1240         463 VLPYFVHLLMDSEADVRATALETLTELLALVRDIPPSDANIFPEYLFPHLNHLLNDSSAQIVRIAYASNLAQLA  536 (1431)
T ss_pred             HHHHHHHHHCCCHHHHHHHHHHHHHHHHHHCCCCCCCCCHHHHHHHHHHHHHHHCCCCCCEEHHHHHHHHHHHH
T ss_conf             67778877528637889999999999986455788410413076650446764125763001366875599999


No 18 
>TIGR01691 enolase-ppase 2,3-diketo-5-methylthio-1-phosphopentane phosphatase; InterPro: IPR010041   This family of proteins are annotated as either enolase-phosphatases or putative enolase-phosphatases.    The methionine salvage pathway converts the methylthioribose moiety of 5'-(methylthio)-adenosine to methionine via a series of biochemical steps in a wide variety of organisms. One enzyme active in this pathway is a bifunctional enolase-phosphatase called E-1 that promotes oxidative cleavage of the synthetic substrate 2,3-diketo-1-phosphohexane to 2-keto-pentanoate; it has been purified from the Gram-negative bacterium Klebsiella pneumoniae . The unusual metabolite 2,3-diketo-5-methylthio-1-phosphopentane is oxidatively cleaved to yield formate (from C-1), 2-keto-4-methylthiobutyrate (the transamination product of methionine), and 3-methylthiopropionate by E-1. The native enzyme is a monomeric protein of M(r) 27,000 requiring magnesium ion as a cofactor . The cloning and analysis of E-1 from Klebsiella oxytoca has been reported . .
Probab=26.35  E-value=34  Score=12.96  Aligned_cols=86  Identities=20%  Similarity=0.243  Sum_probs=58.2

Q ss_pred             CCCHHHHHHHHHCCCCHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHCCCCCCCCHHHHH-HHHHHHHHHHHCCCCCCCHH
Q ss_conf             99989999997179917999999962999889999999999998402667653178899-99999999730257882008
Q gi|254780224|r  274 EYSTDRVYSILSTGGFHVICALYELVGLSPEISEIFVEATMIWRELAVGSTVMEPGIIA-EKLLERMRKRNISGLPAGEL  352 (382)
Q Consensus       274 gi~~~~v~~ll~d~~~~~l~aL~~aaGLp~~~~~af~~A~~~~r~~~~~~~~~~~~~~~-~~~~er~~~~~~~~~~~~~l  352 (382)
                      -.|..++.-+++..|       |..--|...+||....|+..|+..+..=..=-.+++. |.|+       ++++..|+|
T Consensus        91 ~tplK~lQG~iW~~G-------Y~~g~L~~hlYpDV~pAl~~w~~~Gl~~~vYSSGSvaAQKLl-------Fghs~~GdL  156 (240)
T TIGR01691        91 ATPLKTLQGLIWRQG-------YEDGELTAHLYPDVPPALEAWKKAGLRLYVYSSGSVAAQKLL-------FGHSDAGDL  156 (240)
T ss_pred             HHHHHHHHHHHHHHC-------CCCCCCCCCCCCCHHHHHHHHHHCCCEEEEECCCCHHHHHHH-------HHCCCCCCC
T ss_conf             125567634565400-------458850124465547899999874987998704417777766-------530533430


Q ss_pred             HHHHH-HHHHHH-HHHHHHHHHH
Q ss_conf             99999-853168-8999999999
Q gi|254780224|r  353 LEMVE-RIYLDV-NRRFVRSMAT  373 (382)
Q Consensus       353 ~~ll~-r~~~~~-~r~~ar~~a~  373 (382)
                      ..+++ .|++.. .++|+.+|-+
T Consensus       157 ~~lf~~YFDt~vG~K~e~~SY~~  179 (240)
T TIGR01691       157 TPLFSGYFDTLVGAKKEAQSYKK  179 (240)
T ss_pred             HHHHHHHHHCCCCCCHHHHHHHH
T ss_conf             45543231001477302256899


No 19 
>TIGR02944 suf_reg_Xantho FeS assembly SUF system regulator; InterPro: IPR014290   Iron-sulphur (FeS) clusters are important cofactors for numerous proteins involved in electron transfer, in redox and non-redox catalysis, in gene regulation, and as sensors of oxygen and iron. These functions depend on the various FeS cluster prosthetic groups, the most common being [2Fe-2S] and [4Fe-4S] . FeS cluster assembly is a complex process involving the mobilisation of Fe and S atoms from storage sources, their assembly into [Fe-S] form, their transport to specific cellular locations, and their transfer to recipient apoproteins. So far, three FeS assembly machineries have been identified, which are capable of synthesising all types of [Fe-S] clusters: ISC (iron-sulphur cluster), SUF (sulphur assimilation), and NIF (nitrogen fixation) systems.   The ISC system is conserved in eubacteria and eukaryotes (mitochondria), and has broad specificity, targeting general FeS proteins , . It is encoded by the isc operon (iscRSUA-hscBA-fdx-iscX). IscS is a cysteine desulphurase, which obtains S from cysteine (converting it to alanine) and serves as a S donor for FeS cluster assembly. IscU and IscA act as scaffolds to accept S and Fe atoms, assembling clusters and transfering them to recipient apoproteins. HscA is a molecular chaperone and HscB is a co-chaperone. Fdx is a [2Fe-2S]-type ferredoxin. IscR is a transcription factor that regulates expression of the isc operon. IscX (also known as YfhJ) appears to interact with IscS and may function as an Fe donor during cluster assembly .   The SUF system is an alternative pathway to the ISC system that operates under iron starvation and oxidative stress. It is found in eubacteria, archaea and eukaryotes (plastids). The SUF system is encoded by the suf operon (sufABCDSE), and the six encoded proteins are arranged into two complexes (SufSE and SufBCD) and one protein (SufA). SufS is a pyridoxal-phosphate (PLP) protein displaying cysteine desulphurase activity. SufE acts as a scaffold protein that accepts S from SufS and donates it to SufA . SufC is an ATPase with an unorthodox ATP-binding cassette (ABC)-like component. No specific functions have been assigned to SufB and SufD. SufA is homologous to IscA , acting as a scaffold protein in which Fe and S atoms are assembled into [FeS] cluster forms, which can then easily be transferred to apoproteins targets.   In the NIF system, NifS and NifU are required for the formation of metalloclusters of nitrogenase in Azotobacter vinelandii, and other organisms, as well as in the maturation of other FeS proteins. Nitrogenase catalyses the fixation of nitrogen. It contains a complex cluster, the FeMo cofactor, which contains molybdenum, Fe and S. NifS is a cysteine desulphurase. NifU binds one Fe atom at its N-terminal, assembling an FeS cluster that is transferred to nitrogenase apoproteins . Nif proteins involved in the formation of FeS clusters can also be found in organisms that do not fix nitrogen .   This entry represents proteins belonging to the Rtf2 family of transcriptional regulators and are found, typically, as the first gene of the SUF operon. They are found only in a subset of the genomes that encode the SUF system, including the genus Xanthomonas. The conserved location suggests an autoregulatory role..
Probab=24.21  E-value=39  Score=12.60  Aligned_cols=34  Identities=18%  Similarity=0.146  Sum_probs=25.8

Q ss_pred             HHHHHHCCCHHHHHHHHHHHHCCCHHHHHHHHHC
Q ss_conf             9998981994799999999829998999999717
Q gi|254780224|r  253 LIYAIMIGAIDFVSVILANIAEYSTDRVYSILST  286 (382)
Q Consensus       253 llral~~G~~~~f~~aLA~lsgi~~~~v~~ll~d  286 (382)
                      +...+..+.-.|-.+-||+.+|+..++|+++|..
T Consensus        15 l~~lA~~~~~~ySAA~lA~~tgL~~pTvsK~Lk~   48 (130)
T TIGR02944        15 LTVLAQADEQTYSAAELAEQTGLEAPTVSKILKA   48 (130)
T ss_pred             HHHHHCCCCCHHHHHHHHHHCCCCCCHHHHHHHH
T ss_conf             9998528997006888786459886047899887


No 20 
>cd01392 HTH_LacI Helix-turn-helix (HTH) DNA binding domain of the LacI family of transcriptional regulators. HTH-DNA binding domain of the LacI (lactose operon repressor) family of bacterial transcriptional regulators and their putative homologs found in plants. The LacI family has more than 500 members distributed among almost all bacterial species. The monomeric proteins of the LacI family contain common structural features that include a small DNA-binding domain with a helix-turn-helix motif in the N-terminus, a regulatory ligand-binding domain which exhibits the type I periplasmic binding protein fold in the C-terminus for oligomerization and for effector binding, and an approximately 18-amino acid linker connecting these two functional domains. In LacI-like transcriptional regulators, the ligands are monosaccharides including lactose, ribose, fructose, xylose, arabinose, galactose/glucose, and other sugars, with a few exceptions. When the C-terminal domain of the LacI family repre
Probab=23.95  E-value=39  Score=12.56  Aligned_cols=43  Identities=26%  Similarity=0.213  Sum_probs=31.9

Q ss_pred             HHHHHHCCCHHHHHHHHHCCCCHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHCCCCC
Q ss_conf             999982999899999971799179999999629998899999999999984026676
Q gi|254780224|r  268 ILANIAEYSTDRVYSILSTGGFHVICALYELVGLSPEISEIFVEATMIWRELAVGST  324 (382)
Q Consensus       268 aLA~lsgi~~~~v~~ll~d~~~~~l~aL~~aaGLp~~~~~af~~A~~~~r~~~~~~~  324 (382)
                      -+|..+|++..+|.+.|.+..           |+...+-..++.++   .+++|...
T Consensus         2 diA~~~gvS~~TVSr~ln~~~-----------~Vs~~tr~~I~~~~---~elgY~~~   44 (52)
T cd01392           2 DIARAAGVSVATVSRVLNGKP-----------RVSEETRERVLAAA---EELGYRPN   44 (52)
T ss_pred             HHHHHHCCCHHHHHHHHCCCC-----------CCCHHHHHHHHHHH---HHHCCCCC
T ss_conf             288887859999999987989-----------89999999999999---99888979


No 21 
>smart00346 HTH_ICLR helix_turn_helix isocitrate lyase regulation.
Probab=23.81  E-value=39  Score=12.55  Aligned_cols=39  Identities=15%  Similarity=0.130  Sum_probs=27.1

Q ss_pred             HHHCCCCHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHCC
Q ss_conf             971799179999999629998899999999999984026
Q gi|254780224|r  283 ILSTGGFHVICALYELVGLSPEISEIFVEATMIWRELAV  321 (382)
Q Consensus       283 ll~d~~~~~l~aL~~aaGLp~~~~~af~~A~~~~r~~~~  321 (382)
                      +-..+++..+.-+++..|+|..+.--++..+..+.=+..
T Consensus        14 l~~~~~~~sl~eia~~~~l~ksT~~RlL~tL~~~G~l~~   52 (91)
T smart00346       14 LAEEPGGLTLAELAERLGLSKSTAHRLLNTLQELGYVEQ   52 (91)
T ss_pred             HHHCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEE
T ss_conf             972899989999999989099999999999998899688


No 22 
>TIGR02431 pcaR_pcaU beta-ketoadipate pathway transcriptional regulators, PcaR/PcaU/PobR family; InterPro: IPR012794    Members of this family are IclR-type transcriptional regulators with similar DNA binding sites, able to bind at least three different metabolites related to protocatechuate metabolism. Beta-ketoadipate is the inducer for PcaR, p-hydroxybenzoate for PobR, and protocatechuate for PcaU.; GO: 0003677 DNA binding, 0016563 transcription activator activity, 0045941 positive regulation of transcription, 0046278 protocatechuate metabolic process.
Probab=23.47  E-value=40  Score=12.51  Aligned_cols=19  Identities=16%  Similarity=0.029  Sum_probs=6.3

Q ss_pred             HHCCCCCCCCHHHHHHHHH
Q ss_conf             4026676531788999999
Q gi|254780224|r  318 ELAVGSTVMEPGIIAEKLL  336 (382)
Q Consensus       318 ~~~~~~~~~~~~~~~~~~~  336 (382)
                      +++|...++....+.-|++
T Consensus        50 ~LGY~~~Dg~~F~LTPrvL   68 (252)
T TIGR02431        50 ELGYVESDGRLFWLTPRVL   68 (252)
T ss_pred             HHCCEECCCCCEECCHHHH
T ss_conf             6230421798331024677


No 23 
>pfam02985 HEAT HEAT repeat. The HEAT repeat family is related to armadillo/beta-catenin-like repeats (see pfam00514).
Probab=23.32  E-value=40  Score=12.49  Aligned_cols=22  Identities=36%  Similarity=0.641  Sum_probs=14.2

Q ss_pred             HHHHHHCCCCHHHHHHHHHHHC
Q ss_conf             9999851969899999999821
Q gi|254780224|r   45 AMMHLLDDPSSRVRLSLARAIA   66 (382)
Q Consensus        45 iL~~L~~d~~~~vR~alA~~La   66 (382)
                      .+..++.|+++.||.+.++.+.
T Consensus         4 ~l~~~~~d~~~~VR~~a~~~l~   25 (31)
T pfam02985         4 LLLELLNDPDPEVREAAAEALG   25 (31)
T ss_pred             HHHHHHCCCCHHHHHHHHHHHH
T ss_conf             9999965998799999999988


No 24 
>COG1414 IclR Transcriptional regulator [Transcription]
Probab=22.41  E-value=42  Score=12.38  Aligned_cols=59  Identities=10%  Similarity=0.000  Sum_probs=32.8

Q ss_pred             CHHHH--HHHHHHHHCCCHHHHHHHHHCCCCHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHCCCCCC
Q ss_conf             94799--999999829998999999717991799999996299988999999999999840266765
Q gi|254780224|r  261 AIDFV--SVILANIAEYSTDRVYSILSTGGFHVICALYELVGLSPEISEIFVEATMIWRELAVGSTV  325 (382)
Q Consensus       261 ~~~~f--~~aLA~lsgi~~~~v~~ll~d~~~~~l~aL~~aaGLp~~~~~af~~A~~~~r~~~~~~~~  325 (382)
                      +++.+  ....+.|+.+|...+..++......      ..+.-.....+.+...+...|+.+|.-..
T Consensus       127 rlPl~~tA~Gk~lLA~l~~~e~~~~~~~~~~~------~~t~~t~~~~~~l~~el~~iR~~Gya~~~  187 (246)
T COG1414         127 RLPLYATASGKALLAFLPEEEREALLEEEELR------PFTPRTITDPEALLEELAEIRARGYAVDD  187 (246)
T ss_pred             CCCCCCCHHHHHHHHCCCHHHHHHHHHHCCCC------CCCCCCCCCHHHHHHHHHHHHHCCEEEEC
T ss_conf             34687788999999369989999997511345------78998757999999999999955989764


No 25 
>PRK09834 DNA-binding transcriptional activator MhpR; Provisional
Probab=21.39  E-value=44  Score=12.25  Aligned_cols=53  Identities=9%  Similarity=-0.156  Sum_probs=26.6

Q ss_pred             HHHHHHHHCCCHHHHHHHHHCCCCHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHCCCC
Q ss_conf             9999998299989999997179917999999962999889999999999998402667
Q gi|254780224|r  266 SVILANIAEYSTDRVYSILSTGGFHVICALYELVGLSPEISEIFVEATMIWRELAVGS  323 (382)
Q Consensus       266 ~~aLA~lsgi~~~~v~~ll~d~~~~~l~aL~~aaGLp~~~~~af~~A~~~~r~~~~~~  323 (382)
                      ...-+.|+.+|+.....++........     ...-+...-..+...+...|+.+|.-
T Consensus       142 A~GkalLA~l~~~~~~~~l~~~~~~~~-----~~~~~~~~~~~l~~~L~~iR~~GyA~  194 (264)
T PRK09834        142 AAGRAYLAFCPEEEREALLELLRRRPG-----DEDQLARDPARLQAMLARTRKRGYGQ  194 (264)
T ss_pred             HHHHHHHHCCCHHHHHHHHHHHHCCCC-----CCCCCCCCHHHHHHHHHHHHHCCEEE
T ss_conf             679999836999999999986541678-----88876688999999999999678999


Done!