Query         T0523 3MQO, Burkholderia thailandensis, 120 residues
Match_columns 120
No_of_seqs    112 out of 16486
Neff          10.1
Searched_HMMs 11830
Date          Fri May 21 18:06:16 2010
Command       /home/syshi_2/2008/ferredoxin/manualcheck/update/HHsearch/bin/hhsearch -i /home/syshi_3/CASP9/HHsearch4Targetseq/pfamAsearch/hhm/T0523.hhm -d /home/syshi_2/2008/ferredoxin/manualcheck/update/HHsearch/database/pfamA_24_hhmdb -o /home/syshi_3/CASP9/HHsearch4Targetseq/pfamAsearch/hhm/T0523.hhr 

 No Hit                             Prob E-value P-value  Score    SS Cols Query HMM  Template HMM
  1 PF08448 PAS_4:  PAS fold;  Int  99.7 4.1E-18 3.4E-22  113.8   4.8  108    9-118     1-110 (110)
  2 PF00989 PAS:  PAS fold;  Inter  99.7 2.2E-17 1.9E-21  109.9   6.7  109    4-113     2-113 (113)
  3 PF08447 PAS_3:  PAS fold;  Int  99.1 1.1E-11 9.2E-16   79.6   4.1   85   24-110     1-91  (91)
  4 PF08670 MEKHLA:  MEKHLA domain  97.7 2.9E-05 2.4E-09   45.5   5.8  108    3-112    32-144 (148)
  5 PF08446 PAS_2:  PAS fold;  Int  92.4   0.029 2.5E-06   29.5   2.4   74   16-94     19-96  (108)
  6 PF07310 PAS_5:  PAS domain;  I  90.3     0.2 1.7E-05   25.0   5.0  101    6-110    31-136 (137)
  7 PF06785 UPF0242:  Uncharacteri  84.2   0.031 2.6E-06   29.3  -2.1   95    2-102   282-382 (401)
  8 PF08348 PAS_6:  YheO-like PAS   39.3     9.9 0.00084   16.1   5.0   45   73-119    67-112 (118)
  9 PF09547 Spore_IV_A:  Stage IV   11.2      34  0.0029   13.2   1.1   46    7-52    140-188 (492)
 10 PF01731 Arylesterase:  Arylest   8.4      38  0.0032   12.9   0.5   14   79-92     59-72  (86)

No 1  
>PF08448 PAS_4:  PAS fold;  InterPro: IPR013656   The PAS fold corresponds to the structural domain that has previously been defined as PAS and PAC motifs . The PAS fold appears in archaea, eubacteria and eukarya. ; PDB: 3fc7_A 3fg8_F 2r78_D 3bwl_D.
Probab=99.70  E-value=4.1e-18  Score=113.80  Aligned_cols=108  Identities=19%  Similarity=0.323  Sum_probs=89.9

Q ss_pred             HHHCCCCEEEEC-CCEEEEECHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCE
Q ss_conf             871897489965-9868760368886420133311100122344333322222222222222222222222222221101
Q T0523             9 FHLAPIGLVLSR-DRVIEDCNDELAAIFRCARADLIGRSFEVLYPSSDEFERIGERISPVMIAHGSYADDRIMKRAGGEL   87 (120)
Q Consensus         9 ~e~~p~gi~~~~-~g~i~~~N~~~~~~~G~~~~el~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~~dG~~   87 (120)
                      |+++|+++++.+ +|+|+++|+++++++|++.++++|+++.+++++. ....+...+...+..+.....+..+.. +|+.
T Consensus         1 l~~~~~~i~~~d~~g~i~~~N~~~~~~~g~~~~~~~g~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~-~g~~   78 (110)
T PF08448_consen    1 LDNIPDGIFILDPDGRIIYANRAFEDLFGYSPEELLGKPLWELFPPE-DREDFQAALRQALEGGKPVQFEEEIHR-DGEE   78 (110)
T ss_dssp             HHHSSSEEEEEETT-BEEEE-HHHHHHHT--HHHHTT-BGGGTSCCH-HHHHHHHHHHHHHHT-EEEEEEEEESS----E
T ss_pred             CCCCCHHHEEECCCCEEEEEHHHHHHHHCCCHHHHCCCCHHHHCCCH-HHHHHHHHHHHHHCCCCEEEEEEEEEC-CCCC
T ss_conf             99987152899898959977699998859298998599447847710-002368899998646980899999952-7871


Q ss_pred             EEEEEEEEEE-CCCCCEEEEEEEEEEHHHHHH
Q ss_conf             3433245676-379988899998884014733
Q T0523            88 FWCHVTGRAL-DRTAPLAAGVWTFEDLSATRR  118 (120)
Q Consensus        88 ~~v~~~~~~i-~~~~~~~~~v~~~~DITerkr  118 (120)
                      +|+.++..|+ +.+|...+++++++|||++||
T Consensus        79 ~~~~~~~~p~~d~~g~~~~~i~~~~DiTe~kr  110 (110)
T PF08448_consen   79 RWFEVTLSPVRDEDGEVQGVIVIARDITERKR  110 (110)
T ss_dssp             EEEEEEEEEC-CTTTTTCEEEEEEEEETT---
T ss_pred             EEEEEEEEEEECCCCCEEEEEEEEEECCHHHC
T ss_conf             99999999968799989799999997874319


No 2  
>PF00989 PAS:  PAS fold;  InterPro: IPR013767   PAS domains are involved in many signalling proteins where they are used as a signal sensor domain. PAS domains appear in archaea, bacteria and eukaryotes. Several PAS-domain proteins are known to detect their signal by way of an associated cofactor. Haeme, flavin, and a 4-hydroxycinnamyl chromophore are used in different proteins. The PAS domain was named after three proteins that it occurs in:  Per- period circadian protein Arnt- Ah receptor nuclear translocator protein Sim- single-minded protein.   PAS domains are often associated with PAC domains IPR001610 from INTERPRO. It appears that these domains are directly linked, and that together they form the conserved 3D PAS fold. The division between the PAS and PAC domains is caused by major differences in sequences in the region connecting these two motifs . In human PAS kinase, this region has been shown to be very flexible, and adopts different conformations depending on the bound ligand . Probably the most surprising identification of a PAS domain was that in EAG-like K^+-channels . ; GO: 0006355 regulation of transcription, DNA-dependent; PDB: 1ll8_A 1wa9_B 3gec_A 1v9z_B 1s67_U 1vb6_A 1s66_L 1v9y_B 3b33_A 2w0n_A ....
Probab=99.68  E-value=2.2e-17  Score=109.86  Aligned_cols=109  Identities=18%  Similarity=0.348  Sum_probs=87.7

Q ss_pred             HHHHHHHHCCCCEEEEC-CCEEEEECHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC-CCCCCCC
Q ss_conf             68899871897489965-986876036888642013331110012234433332222222222222222222-2222222
Q T0523             4 DYKTAFHLAPIGLVLSR-DRVIEDCNDELAAIFRCARADLIGRSFEVLYPSSDEFERIGERISPVMIAHGSY-ADDRIMK   81 (120)
Q Consensus         4 ~~~~i~e~~p~gi~~~~-~g~i~~~N~~~~~~~G~~~~el~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~e~~~~   81 (120)
                      +|+++++++|.|+++.+ +|+|+++|+++++|+||++++++|+++.+++++.+.. .....+...+..++.. ..+..+.
T Consensus         2 ~~~~ii~~~~~~i~v~d~~g~I~~~N~a~~~l~g~~~~~~~g~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~   80 (113)
T PF00989_consen    2 RFRAIIESSPDGIFVVDADGRILYVNSAAEELFGYSPEELIGKSIFDLFHPDDRE-EFRDQLSQLLQQGESSESFEVRFN   80 (113)
T ss_dssp             HHHHHHHTTSSEEEEEETTSBEEEETHHHHHHCTS-HHHHTTSBGGGGCSTTTHH-HHHHHHHHHHHHTC-BEEEEEEEE
T ss_pred             HHHHHHHCCCCEEEEECCCCCEEEECHHHHHHHCCCHHHHCCCCHHHHCCCHHHH-HHHHHHHHHHHHCCCCEEEEEEEE
T ss_conf             7899977384429999595989999889999879595884799699945852366-799999999983898346899999


Q ss_pred             CCCCCEEEEEEEEEEE-CCCCCEEEEEEEEEEH
Q ss_conf             2211013433245676-3799888999988840
Q T0523            82 RAGGELFWCHVTGRAL-DRTAPLAAGVWTFEDL  113 (120)
Q Consensus        82 ~~dG~~~~v~~~~~~i-~~~~~~~~~v~~~~DI  113 (120)
                      .++|+.+|+.++++|+ +.+|...+++++++||
T Consensus        81 ~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~DI  113 (113)
T PF00989_consen   81 LRDGSIIWIEVSASPIRDEDGEIIGIIGIFRDI  113 (113)
T ss_dssp             ESTSCEEEEEEEEEEEEETTEEEEEEEEEEEEC
T ss_pred             ECCCCEEEEEEEEEEEEECCCCEEEEEEEEECC
T ss_conf             449969999999999991999999999999919


No 3  
>PF08447 PAS_3:  PAS fold;  InterPro: IPR013655   The PAS fold corresponds to the structural domain that has previously been defined as PAS and PAC motifs . The PAS fold appears in archaea, eubacteria and eukarya. The PAS domain contains a sensory box, or S-box domain that occupies the central portion of the PAS domain but is more widely distributed. It is often tandemly repeated. Known prosthetic groups bound in the S-box domain include heme in the oxygen sensor FixL , FAD in the redox potential sensor NifL , and a 4-hydroxycinnamyl chromophore in photoactive yellow protein . Proteins containing the domain often contain other regulatory domains such as response regulator or sensor histidine kinase domains. Other S-box proteins include phytochromes and the aryl hydrocarbon receptor nuclear translocator.    This domain has been found in the gene product of the madA gene of the filamentous zygomycete fungus Phycomyces blakesleeanus. It has been shown that MadA encodes a blue-light photoreceptor for phototropism and other light responses. The gene is involved in the phototropic responses associated with sporangiophore growth; they exhibit phototropism by bending toward near-UV and blue wavelengths and away from far-UV wavelengths in a manner that is physiologically similar to plant phototropic responses . ; PDB: 3h9w_A 3eeh_A 2vlg_C 1g28_C 1jnu_D 1n9n_A 1n9l_A 1n9o_A 2a24_A 3f1o_A ....
Probab=99.14  E-value=1.1e-11  Score=79.64  Aligned_cols=85  Identities=20%  Similarity=0.310  Sum_probs=70.9

Q ss_pred             EEEECHHHHHHHHCCCCCCCCCC----CCCCCCCCCCCCCCCCCCCC-CCCCCCCCCCCCCCCCCCCCEEEEEEEEEEE-
Q ss_conf             87603688864201333111001----22344333322222222222-2222222222222222211013433245676-
Q T0523            24 IEDCNDELAAIFRCARADLIGRS----FEVLYPSSDEFERIGERISP-VMIAHGSYADDRIMKRAGGELFWCHVTGRAL-   97 (120)
Q Consensus        24 i~~~N~~~~~~~G~~~~el~g~~----~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~e~~~~~~dG~~~~v~~~~~~i-   97 (120)
                      |+++|+.+++++||+++++ +..    +..+. ++++...+.+.+.. ....+..++.|++++++||+.+|+..++.++ 
T Consensus         1 ~~~~s~~~~~i~Gy~~~e~-~~~~~~~~~~~i-hpeD~~~~~~~~~~~~~~~~~~~~~e~r~~~~~G~~~wv~~~~~~~~   78 (91)
T PF08447_consen    1 IVYVSDAFYEILGYSPEEL-GKSSPDTWFDLI-HPEDRERVRQAIERASLRNGEPFSFEYRIRTKDGSYRWVHSRGRPIR   78 (91)
T ss_dssp             EEEE-THHHHHHT--HHHH-TCB-HHHGGGGB-GHHHHHHHHHHHHHHHHHCTTCEEEEEEEEGTTSTEEEEEEEEEEEE
T ss_pred             CEEEEHHHHHHHCCCHHHH-CCCCHHHHHHEE-CCCCHHHHHHHHHHHHCCCCCCEEEEEEEECCCCCEEEEEEEEEEEE
T ss_conf             9998079999879998998-467777897627-91249999999875430345523599999979998999999999999


Q ss_pred             CCCCCEEEEEEEE
Q ss_conf             3799888999988
Q T0523            98 DRTAPLAAGVWTF  110 (120)
Q Consensus        98 ~~~~~~~~~v~~~  110 (120)
                      +.+|.+.+++++.
T Consensus        79 d~~g~~~~~~G~~   91 (91)
T PF08447_consen   79 DENGKPVRLVGVN   91 (91)
T ss_dssp             TTTTCEEEEEEEE
T ss_pred             CCCCCEEEEEEEC
T ss_conf             9999999999989


No 4  
>PF08670 MEKHLA:  MEKHLA domain;  InterPro: IPR013978    The MEKHLA domain shares similarity with the PAS domain and is found in the 3' end of plant HD-ZIP III homeobox genes, and bacterial proteins. 
Probab=97.69  E-value=2.9e-05  Score=45.49  Aligned_cols=108  Identities=16%  Similarity=0.094  Sum_probs=77.4

Q ss_pred             HHHHHHHHHCCCCEEEEC---CCEEEEECHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
Q ss_conf             268899871897489965---98687603688864201333111001223443333222222222222222222222222
Q T0523             3 IDYKTAFHLAPIGLVLSR---DRVIEDCNDELAAIFRCARADLIGRSFEVLYPSSDEFERIGERISPVMIAHGSYADDRI   79 (120)
Q Consensus         3 ~~~~~i~e~~p~gi~~~~---~g~i~~~N~~~~~~~G~~~~el~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~e~~   79 (120)
                      .-++.+++ +|.+|+--+   +=.++|+|++.++|++++-+++.+.+...... +..+......+....+.|-....--.
T Consensus        32 ~~~~~L~~-~p~ail~h~~~~dPvf~yaN~aaL~m~E~tw~~l~~lpsr~tae-~~~r~~r~~~l~~v~~qG~~~~y~GI  109 (148)
T PF08670_consen   32 ELAKALWH-APFAILCHSTKADPVFIYANQAALDMWETTWDELQDLPSRKTAE-EPERKERQSLLDQVMQQGYACLYSGI  109 (148)
T ss_pred             HHHHHHHC-CCCEEEECCCCCCCEEEECCHHHHHHHCCCHHHHHCCCHHHCCC-HHHHHHHHHHHHHHHHCCCCCCCCEE
T ss_conf             99999971-99779984788897687610899999718899984697765169-35089999889999981850078857


Q ss_pred             CCCCCCCEEEEEEEE-EE-ECCCCCEEEEEEEEEE
Q ss_conf             222211013433245-67-6379988899998884
Q T0523            80 MKRAGGELFWCHVTG-RA-LDRTAPLAAGVWTFED  112 (120)
Q Consensus        80 ~~~~dG~~~~v~~~~-~~-i~~~~~~~~~v~~~~D  112 (120)
                      .+.+.|+.++++-.. -. ++++|...|.-..|.+
T Consensus       110 Riss~Grrf~ie~A~~W~v~d~~g~~~gqAa~F~n  144 (148)
T PF08670_consen  110 RISSMGRRFSIEQAVAWKVLDEDGNYHGQAAMFSN  144 (148)
T ss_pred             EECCCCCEEEEEEEEEEEEECCCCCEEEEEEEEEE
T ss_conf             88289976898026998788578888999999611


No 5  
>PF08446 PAS_2:  PAS fold;  InterPro: IPR013654   The PAS fold corresponds to the structural domain that has previously been defined as PAS and PAC motifs . The PAS fold appears in archaea, eubacteria and eukarya. ; GO: 0008020 G-protein coupled photoreceptor activity, 0007600 sensory perception, 0018298 protein-chromophore linkage, 0045449 regulation of transcription; PDB: 1ztu_A 2o9b_A 2o9c_A 2ool_A 2vea_A 3c2w_F.
Probab=92.36  E-value=0.029  Score=29.50  Aligned_cols=74  Identities=22%  Similarity=0.328  Sum_probs=45.7

Q ss_pred             EEEEC-CCEEEEECHHHHHHHHCC-CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC-CCCCCC-CCCCCCEEEEE
Q ss_conf             89965-986876036888642013-331110012234433332222222222222222222-222222-22211013433
Q T0523            16 LVLSR-DRVIEDCNDELAAIFRCA-RADLIGRSFEVLYPSSDEFERIGERISPVMIAHGSY-ADDRIM-KRAGGELFWCH   91 (120)
Q Consensus        16 i~~~~-~g~i~~~N~~~~~~~G~~-~~el~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~e~~~-~~~dG~~~~v~   91 (120)
                      ++++. +++|+.++.-..+++|.+ .++++|+++.+++.... ...+...    +.....- .....+ .+.+|+.+++.
T Consensus        19 La~d~~~~~I~~~SeN~~~~lg~~~~~~llG~~l~~ll~~~~-~~~l~~~----~~~~~~~~~~~~~~~~~~~~~~f~~~   93 (108)
T PF08446_consen   19 LALDPPDLRIIQASENIADLLGIPPPEDLLGRPLSDLLSPES-AHRLREA----LQSESISDSNPIRIRLRIGGRPFDAI   93 (108)
T ss_dssp             EEEETTTTEEEEEETTHHHHHSS--HCCHTT-CHHHHSCCCC-HHHHHHH----C----HCCHCCEEEEEES-EEEEEEE
T ss_pred             EEEECCCCEEEEECCCHHHHHCCCCHHHHCCCCHHHHHCHHH-HHHHHHH----HHCCCCCCCCCEEEEECCCCEEEEEE
T ss_conf             999878988999866989985873206451898999859778-9999986----50378443586899952577359999


Q ss_pred             EEE
Q ss_conf             245
Q T0523            92 VTG   94 (120)
Q Consensus        92 ~~~   94 (120)
                      ++.
T Consensus        94 ~H~   96 (108)
T PF08446_consen   94 IHR   96 (108)
T ss_dssp             EEE
T ss_pred             EEE
T ss_conf             999


No 6  
>PF07310 PAS_5:  PAS domain;  InterPro: IPR009922   This family contains a number of hypothetical bacterial proteins of unknown function approximately 200 residues long.
Probab=90.29  E-value=0.2  Score=25.02  Aligned_cols=101  Identities=16%  Similarity=0.169  Sum_probs=71.0

Q ss_pred             HHHHHHCCCCEEE--ECCC--EEEEECHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
Q ss_conf             8998718974899--6598--68760368886420133311100122344333322222222222222222222222222
Q T0523             6 KTAFHLAPIGLVL--SRDR--VIEDCNDELAAIFRCARADLIGRSFEVLYPSSDEFERIGERISPVMIAHGSYADDRIMK   81 (120)
Q Consensus         6 ~~i~e~~p~gi~~--~~~g--~i~~~N~~~~~~~G~~~~el~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~   81 (120)
                      ..|-...|...++  .+++  ++..+-...++++|+   ++.|+.+.+++.+.. .....+.+........+........
T Consensus        31 ~~i~~lLp~i~ile~~~~~~~r~RLaGt~i~~~~G~---d~tG~~~~~l~~~~~-~~~~~~~~~~v~~~~~p~~~~~~~~  106 (137)
T PF07310_consen   31 AEIPRLLPHIFILEVEDPGRFRYRLAGTRIVELFGR---DLTGRRLDELFAPED-RERVFRALRAVVDEPCPVRARGRAR  106 (137)
T ss_pred             HHHHHHHCCEEEEEEECCCCEEEEEECHHHHHHHCC---CCCCCCHHHHCCHHH-HHHHHHHHHHHHCCCCEEEEEEEEE
T ss_conf             899987196299998289957999966899998199---888989778418166-9999999999981895299997872


Q ss_pred             CCCCCEEEEEEEEEEE-CCCCCEEEEEEEE
Q ss_conf             2211013433245676-3799888999988
Q T0523            82 RAGGELFWCHVTGRAL-DRTAPLAAGVWTF  110 (120)
Q Consensus        82 ~~dG~~~~v~~~~~~i-~~~~~~~~~v~~~  110 (120)
                      ..+|.....+...-|+ +++|.+..+++.+
T Consensus       107 ~~~~~~~~~e~l~LPL~~~~g~v~~ilG~l  136 (137)
T PF07310_consen  107 TEDGRYLRFERLLLPLRDDDGEVDRILGAL  136 (137)
T ss_pred             CCCCCEEEEEEEECCCCCCCCCCCEEEEEC
T ss_conf             489983355689723588999806797723


No 7  
>PF06785 UPF0242:  Uncharacterised protein family (UPF0242);  InterPro: IPR009623   This is a group of proteins of unknown function.
Probab=84.15  E-value=0.031  Score=29.34  Aligned_cols=95  Identities=8%  Similarity=0.112  Sum_probs=61.0

Q ss_pred             CHHHHHHHHHC---CCCE-EE-EC-CCEEEEECHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
Q ss_conf             42688998718---9748-99-65-9868760368886420133311100122344333322222222222222222222
Q T0523             2 AIDYKTAFHLA---PIGL-VL-SR-DRVIEDCNDELAAIFRCARADLIGRSFEVLYPSSDEFERIGERISPVMIAHGSYA   75 (120)
Q Consensus         2 ~~~~~~i~e~~---p~gi-~~-~~-~g~i~~~N~~~~~~~G~~~~el~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   75 (120)
                      +++-|.+|++.   ..|| ++ .. +.+.+++|.-|-..+||..++++...-....-.-..   ..+.+...  .....+
T Consensus       282 slecRqLFDnLreEnlGmlfVya~qsQr~vFAN~lfKtwtGy~~edfl~~~~diV~sGl~q---W~~dL~~~--~r~E~s  356 (401)
T PF06785_consen  282 SLECRQLFDNLREENLGMLFVYAPQSQRAVFANSLFKTWTGYGAEDFLSDFSDIVISGLNQ---WERDLRLL--DRAERS  356 (401)
T ss_pred             HHHHHHHHHHHHHHCCCEEEEECCHHHHHHHHHHHHHHHHCCCHHHHHHHCHHHHHHHHHH---HHHHHHHH--HHHHHC
T ss_conf             3899999755545128669997510378998788888875246999873122889851889---98888875--468654


Q ss_pred             CCCCCCCCCCCEEEEEEEEEEECCCCC
Q ss_conf             222222221101343324567637998
Q T0523            76 DDRIMKRAGGELFWCHVTGRALDRTAP  102 (120)
Q Consensus        76 ~e~~~~~~dG~~~~v~~~~~~i~~~~~  102 (120)
                      +-+...+|+|..++.......+ +.|.
T Consensus       357 gkiiiKtKn~g~ipf~ycL~il-~kGp  382 (401)
T PF06785_consen  357 GKIIIKTKNHGQIPFYYCLTIL-NKGP  382 (401)
T ss_pred             CEEEEECCCCCCCEEEEEEEEE-CCCC
T ss_conf             7278871678842058889850-6752


No 8  
>PF08348 PAS_6:  YheO-like PAS domain;  InterPro: IPR013559   This domain is found in various hypothetical bacterial proteins that are similar to the Escherichia coli protein YheO (P64624 from SWISSPROT). Their function is unknown, but a few members are annotated as being HTH-containing proteins and putative DNA-binding proteins. 
Probab=39.35  E-value=9.9  Score=16.05  Aligned_cols=45  Identities=11%  Similarity=0.070  Sum_probs=32.8

Q ss_pred             CCCCCCCCCCCCCCEEEEEEEEEEE-CCCCCEEEEEEEEEEHHHHHHC
Q ss_conf             2222222222211013433245676-3799888999988840147331
Q T0523            73 SYADDRIMKRAGGELFWCHVTGRAL-DRTAPLAAGVWTFEDLSATRRV  119 (120)
Q Consensus        73 ~~~~e~~~~~~dG~~~~v~~~~~~i-~~~~~~~~~v~~~~DITerkra  119 (120)
                      .+...+.-+.+||+..  +.+..++ +.+|.+.|++.+=.|+|.-.++
T Consensus        67 ~~~~~Y~~~~~dGr~l--kSsT~~ird~~g~~iG~LCIN~D~s~~~~~  112 (118)
T PF08348_consen   67 DDIVNYKTRTKDGRTL--KSSTIFIRDENGKPIGALCINFDISALEQA  112 (118)
T ss_pred             CCCCCEEEECCCCCEE--EEEEEEEECCCCCEEEEEEEEECCHHHHHH
T ss_conf             6144605678999898--999999999999999999997576789999


No 9  
>PF09547 Spore_IV_A:  Stage IV sporulation protein A (spore_IV_A)
Probab=11.23  E-value=34  Score=13.21  Aligned_cols=46  Identities=26%  Similarity=0.339  Sum_probs=25.3

Q ss_pred             HHHHHCCCCEEEECCCEEEEECHHHHH-HHHCCCCCC--CCCCCCCCCC
Q ss_conf             998718974899659868760368886-420133311--1001223443
Q T0523             7 TAFHLAPIGLVLSRDRVIEDCNDELAA-IFRCARADL--IGRSFEVLYP   52 (120)
Q Consensus         7 ~i~e~~p~gi~~~~~g~i~~~N~~~~~-~~G~~~~el--~g~~~~~~~~   52 (120)
                      .|-+|+.+|++++.||.|..+.+.-.. .-..--+||  +|++|-.++.
T Consensus       140 VI~dHSTIGiVVTTDGSitdIpRe~Y~eAEervI~ELk~igKPFvillN  188 (492)
T PF09547_consen  140 VIQDHSTIGIVVTTDGSITDIPRENYVEAEERVIEELKEIGKPFVILLN  188 (492)
T ss_pred             EECCCCCEEEEEECCCCCCCCCHHHHHHHHHHHHHHHHHCCCCEEEEEE
T ss_conf             3205770449995688745666566667899999999862999899982


No 10 
>PF01731 Arylesterase:  Arylesterase;  InterPro: IPR002640    The serum paraoxonases/arylesterases are enzymes that catalyse the hydrolysis of the toxic metabolites of a variety of organophosphorus insecticides. The enzymes hydrolyse a broad spectrum of organophosphate substrates, including paraoxon and a number of aromatic carboxylic acid esters (e.g., phenyl acetate), and hence confer resistance to organophosphate toxicity .     Mammals have 3 distinct paraoxonase types, termed PON1-3 , . In mice and humans, the PON genes are found on the same chromosome in close proximity. PON activity has been found in variety of tissues, with highest levels in liver and serum - the source of serum PON is thought to be the liver. Unlike mammals, fish and avian species lack paraoxonase activity.     Human and rabbit PONs appear to have two distinct Ca2+ binding sites, one required for stability and one required for catalytic activity. The Ca2+ dependency of PONs suggests a mechanism of hydrolysis where Ca2+ acts as the electrophilic catalyst, like that proposed for phospholipase A2. The paraoxonase enzymes, PON1 and PON3, are high density lipoprotein (HDL)- associated proteins capable of preventing oxidative modification of low density lipoproteins (LPL) . Although PON2 has oxidative properties, the enzyme does not associate with HDL.     Within a given species, PON1, PON2 and PON3 share ~60% amino acid sequence identity, whereas between mammalian species particular PONs (1,2 or 3) share 79-90% identity at the amino acid level. Human PON1 and PON3 share numerous conserved phosphorylation and N-glycosylation sites; however, it is not known whether the PON proteins are modified at these sites, or whether modification at these sites is required for activity in vivo .  This family consists of arylesterases (Also known as serum paraoxonase) 3.1.1.2 from EC. These enzymes hydrolyse organophosphorus esters such as paraoxon and are found in the liver and blood. They confer resistance to organophosphate toxicity . Human arylesterase (PON1) P27169 from SWISSPROT is associated with HDL and may protect against LDL oxidation .; GO: 0004064 arylesterase activity; PDB: 1v04_A.
Probab=8.45  E-value=38  Score=12.94  Aligned_cols=14  Identities=14%  Similarity=0.242  Sum_probs=7.4

Q ss_pred             CCCCCCCCEEEEEE
Q ss_conf             22222110134332
Q T0523            79 IMKRAGGELFWCHV   92 (120)
Q Consensus        79 ~~~~~dG~~~~v~~   92 (120)
                      ....+||+.+++.-
T Consensus        59 I~~s~d~k~vyVa~   72 (86)
T PF01731_consen   59 INISPDGKYVYVAS   72 (86)
T ss_dssp             -EE-----EEEEEE
T ss_pred             EEECCCCCEEEEEC
T ss_conf             58889988999941


Done!