Query         T0557 NeR70A, , 145 residues
Match_columns 145
No_of_seqs    116 out of 927
Neff          8.2 
Searched_HMMs 22458
Date          Tue May 25 15:40:25 2010
Command       /home/syshi_2/2008/ferredoxin/manualcheck/update/HHsearch/bin/hhsearch -i /home/syshi_3/CASP9/HHsearch4Targetseq/seq/T0557.hhm -d /home/syshi_2/2008/ferredoxin/manualcheck/update/HHsearch/database/pdb70_15May10_hhmdb -o /home/syshi_3/CASP9/HHsearch4Targetseq/pdb70search/T0557.hhr 

 No Hit                             Prob E-value P-value  Score    SS Cols Query HMM  Template HMM
  1 3lmm_A Uncharacterized protein  99.9 7.5E-23 3.3E-27  136.6   9.4  108   15-144    35-159 (583)
  2 2q22_A Uncharacterized protein  66.5     3.7 0.00016   19.3   3.1   78   29-144    36-113 (139)
  3 1gh9_A 8.3 kDa protein (gene M  19.4      36  0.0016   14.2   1.5   14  132-145    12-25  (71)
  4 1q02_A Sequestosome 1; helical   8.4      92  0.0041   12.1   1.0   21   30-50      8-29  (52)
  5 1af7_A Chemotaxis receptor met   7.6   1E+02  0.0046   11.8   1.1   13   47-59    136-148 (274)
  6 3daw_B Twinfilin-1, protein A6   6.1 1.2E+02  0.0055   11.4   6.5   33   28-63     24-56  (164)
  7 1wcu_A CBM29_1, non-catalytic    5.8 1.3E+02  0.0058   11.3   1.3   73   45-125    59-132 (153)
  8 2apo_A Probable tRNA pseudouri   4.7 1.5E+02  0.0069   10.9   1.7   13   48-60    107-119 (357)
  9 1yud_A Hypothetical protein SO   3.6 1.9E+02  0.0084   10.5   1.4   25    1-27     11-37  (170)
 10 1pav_A Hypothetical protein TA   3.0 2.2E+02  0.0099   10.1   2.9   43    9-58     25-67  (78)

No 1  
>3lmm_A Uncharacterized protein; multi-domained alpha-beta protein, structural genomics, PSI- 2, protein structure initiative; 3.00A {Corynebacterium diphtheriae}
Probab=99.88  E-value=7.5e-23  Score=136.58  Aligned_cols=108  Identities=25%  Similarity=0.370  Sum_probs=77.8

Q ss_pred             CCCCEEEEEECCC-------------C---HHHHHHHHHHHHCCCCCCCCEEEEEEECCCCCCCCCCCCEEECC-CHHHH
Q ss_conf             8996577741578-------------8---47999999997088778970799986327763366532202202-03578
Q T0557            15 DESARIEAKRASD-------------M---GKSVMETVIAFANEPGLDGGYLLLGVDWAINDKGDTVYRPVGLP-DPDKV   77 (145)
Q Consensus        15 ~E~~~lEfK~~~~-------------~---~~~l~k~i~AFAN~~~~~GG~liiGV~d~~~~~~~~~~~~~~~~-~~~~~   77 (145)
                      .|++++|||+.+.             .   .++|+++||||||+  .+||+|+|||+|++..+.       |++ +.+  
T Consensus        35 ~E~~~~efK~~~~~~~~~~~~~~~~~~~~~~~~l~~~v~afAN~--~~GG~Ii~GV~D~~g~iv-------Gv~~d~~--  103 (583)
T 3lmm_A           35 KETQSVDFKEEAGRRNGPQIEPGKPENPEAADKLADEVACMANT--PGGGALIVGIEDKTGRII-------GTELDID--  103 (583)
T ss_dssp             GGGTTCEEECCSSCBCSSSBCCCCSCCHHHHHHHHHHHHHHHHS--TTCEEEEETBCTTTCBBC-------CCCCCHH--
T ss_pred             CCCCEEEEEECCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHCCC--CCCCEEEEEEECCCCCEE-------CCCCCHH--
T ss_conf             66650686552455665444666656871298999999884379--999889999988998371-------6368999--


Q ss_pred             HHHHHHHHHCCCCCCCEEEEEEEEECCCEEEEEEEECCCCCCCCEEECCCCCCCCEEEEECCCCCEE
Q ss_conf             9999998760388530245889984697899998335999888588758799861689826875211
Q T0557            78 QRDLASQCASMLNVALRPEMQLEQVGGKTLLVVYVPEADVTHKPIYKKATGLPGGAYRRIGSSDQRC  144 (145)
Q Consensus        78 ~~~l~~~~~~~~~p~~~~~i~~~~~~g~~i~vi~Ip~s~~~~~P~~~~~~~~~~~~Y~R~g~~~~~~  144 (145)
                        .+.+.+.+.+.|.  ++++.+.++|+.|++|+||+++  . |+|.    ..+++|+|+|+++++|
T Consensus       104 --~l~~~i~~~~~~~--p~i~~~~i~gk~vlvi~Vp~~~--~-~py~----~~g~~yiRvG~~~~~~  159 (583)
T 3lmm_A          104 --WLRQGIFTRIDVA--PDVVAKRVLGQRVLAIYVAAAA--E-PIED----TSDRLRWRVGDSCRPV  159 (583)
T ss_dssp             --HHHHHHHHHHSCC--CEEEEEESSSCEEEEEEECCCS--S-CCCC----TTSCCEEECSSSEEEC
T ss_pred             --HHHHHHHHCCCCC--CCEEEEEECCCEEEEEEECCCC--C-CCEE----CCCEEEEECCCCCCCC
T ss_conf             --9999876247998--7439999899789999986898--7-8877----6886799848877579


No 2  
>2q22_A Uncharacterized protein; YP_323524.1, structural genomics, joint center for structural genomics, JCSG; HET: PG4; 2.11A {Anabaena variabilis atcc 29413} SCOP: d.365.1.1
Probab=66.51  E-value=3.7  Score=19.33  Aligned_cols=78  Identities=21%  Similarity=0.269  Sum_probs=48.6

Q ss_pred             HHHHHHHHHHHHCCCCCCCCEEEEEEECCCCCCCCCCCCEEECCCHHHHHHHHHHHHHCCCCCCCEEEEEEEEECCCEEE
Q ss_conf             47999999997088778970799986327763366532202202035789999998760388530245889984697899
Q T0557            29 GKSVMETVIAFANEPGLDGGYLLLGVDWAINDKGDTVYRPVGLPDPDKVQRDLASQCASMLNVALRPEMQLEQVGGKTLL  108 (145)
Q Consensus        29 ~~~l~k~i~AFAN~~~~~GG~liiGV~d~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~p~~~~~i~~~~~~g~~i~  108 (145)
                      .+.|.+.+.+.+..    --|+-|||=-.               ..+.....|++.....-.+..               
T Consensus        36 ~~~Lr~eL~~~~~~----sdw~tiGImA~---------------s~~~Ai~ALrs~~~~~~~~~~---------------   81 (139)
T 2q22_A           36 KESVRRALILITKL----SDYQILGICAD---------------TADEGLLAMKTYSHALGYEVP---------------   81 (139)
T ss_dssp             HHHHHHHHHHHHHT----SSEEEEEEEES---------------SHHHHHHHHHHHHHHTTCCCC---------------
T ss_pred             HHHHHHHHHHHHHH----CCCEEEEEECC---------------CHHHHHHHHHHHHHHCCCCCC---------------
T ss_conf             99999999999862----78079986558---------------889999999999998099756---------------


Q ss_pred             EEEEECCCCCCCCEEECCCCCCCCEEEEECCCCCEE
Q ss_conf             998335999888588758799861689826875211
Q T0557           109 VVYVPEADVTHKPIYKKATGLPGGAYRRIGSSDQRC  144 (145)
Q Consensus       109 vi~Ip~s~~~~~P~~~~~~~~~~~~Y~R~g~~~~~~  144 (145)
                       +..|   ..+-|+|+|.|...+.+|+|.-.|..+=
T Consensus        82 -~d~~---~~~GpVfLK~NqktG~~~ir~e~Glg~G  113 (139)
T 2q22_A           82 -IDLP---VVEGPVYIKLNGKNGLCYLDSYAGHHRG  113 (139)
T ss_dssp             --CCC---CCSSSEEEEEETTTCCEEEEECCSCCBE
T ss_pred             -CCCC---CCCCCEEEEECCCCCCEEEEECCCCCCE
T ss_conf             -7677---8888779984588886899723786416


No 3  
>1gh9_A 8.3 kDa protein (gene MTH1184); beta+alpha complex structure, structural genomics, PSI, protein structure initiative; NMR {Methanothermobacterthermautotrophicus} SCOP: g.41.6.1
Probab=19.41  E-value=36  Score=14.22  Aligned_cols=14  Identities=36%  Similarity=0.852  Sum_probs=8.0

Q ss_pred             CEEEEECCCCCEEC
Q ss_conf             16898268752119
Q T0557           132 GAYRRIGSSDQRCV  145 (145)
Q Consensus       132 ~~Y~R~g~~~~~~~  145 (145)
                      ..|-|.|..+|+||
T Consensus        12 alysregaktrkcv   25 (71)
T 1gh9_A           12 ALYSREGAKTRKCV   25 (71)
T ss_dssp             CEEEETTCSEEEET
T ss_pred             HHHHCCCCCEEEEE
T ss_conf             76611464300134


No 4  
>1q02_A Sequestosome 1; helical bundle, protein binding; NMR {Homo sapiens} SCOP: a.5.2.1 PDB: 2jy7_A 2jy8_A 2k0b_X 2knv_A
Probab=8.38  E-value=92  Score=12.10  Aligned_cols=21  Identities=19%  Similarity=0.422  Sum_probs=14.6

Q ss_pred             HHHHHHHHHHHCCC-CCCCCEE
Q ss_conf             79999999970887-7897079
Q T0557            30 KSVMETVIAFANEP-GLDGGYL   50 (145)
Q Consensus        30 ~~l~k~i~AFAN~~-~~~GG~l   50 (145)
                      ..+.+++.+|.+.. .++||||
T Consensus         8 p~l~~al~qM~aMGFsneGGWL   29 (52)
T 1q02_A            8 PRLIESLSQMLSMGFSDEGGWL   29 (52)
T ss_dssp             HHHHHHHHHHHTTTCCCTTSHH
T ss_pred             HHHHHHHHHHHHCCCCCCCHHH
T ss_conf             6899999999982878765299


No 5  
>1af7_A Chemotaxis receptor methyltransferase CHER; chemotaxis receptor methylation; HET: SAH; 2.00A {Salmonella typhimurium} SCOP: a.58.1.1 c.66.1.8 PDB: 1bc5_A*
Probab=7.57  E-value=1e+02  Score=11.85  Aligned_cols=13  Identities=15%  Similarity=0.355  Sum_probs=7.4

Q ss_pred             CCEEEEEEECCCC
Q ss_conf             7079998632776
Q T0557            47 GGYLLLGVDWAIN   59 (145)
Q Consensus        47 GG~liiGV~d~~~   59 (145)
                      ..+-|+|.+=+..
T Consensus       136 ~~~~I~aTDIs~~  148 (274)
T 1af7_A          136 GRWKVFASDIDTE  148 (274)
T ss_dssp             TSEEEEEEESCHH
T ss_pred             CCEEEEEECCCHH
T ss_conf             9648999819999


No 6  
>3daw_B Twinfilin-1, protein A6; actin depolymerisation, actin binding proteins, cytoskeleton, structural protein/contractIle protein complex; HET: ATP; 2.55A {Mus musculus} PDB: 2hd7_A
Probab=6.14  E-value=1.2e+02  Score=11.44  Aligned_cols=33  Identities=9%  Similarity=0.155  Sum_probs=25.0

Q ss_pred             CHHHHHHHHHHHHCCCCCCCCEEEEEEECCCCCCCC
Q ss_conf             847999999997088778970799986327763366
Q T0557            28 MGKSVMETVIAFANEPGLDGGYLLLGVDWAINDKGD   63 (145)
Q Consensus        28 ~~~~l~k~i~AFAN~~~~~GG~liiGV~d~~~~~~~   63 (145)
                      ..+++.+.+-.|.+.   ..-||+|+|++++..+..
T Consensus        24 v~~e~~~a~~~lk~~---~~~~iif~Id~~~e~Iv~   56 (164)
T 3daw_B           24 ISRDAFQALEKLSKK---QLNYVQLEIDIKNETIIL   56 (164)
T ss_dssp             BCHHHHHHHHHHHTT---SCSEEEEEEETTTTEEEE
T ss_pred             CCHHHHHHHHHHHCC---CCCEEEEEECCCCEEEEE
T ss_conf             699999999999749---977899998689629999


No 7  
>1wcu_A CBM29_1, non-catalytic protein 1; carbohydrate binding, carbohydrate binding module; 1.5A {Piromyces equi}
Probab=5.75  E-value=1.3e+02  Score=11.32  Aligned_cols=73  Identities=15%  Similarity=0.146  Sum_probs=38.1

Q ss_pred             CCCCEEEEEEECCCCCCCCCCCCEEECCCHHHHHHHHHHHHHCCCCCCCEEEEEEEEEC-CCEEEEEEEECCCCCCCCEE
Q ss_conf             89707999863277633665322022020357899999987603885302458899846-97899998335999888588
Q T0557            45 LDGGYLLLGVDWAINDKGDTVYRPVGLPDPDKVQRDLASQCASMLNVALRPEMQLEQVG-GKTLLVVYVPEADVTHKPIY  123 (145)
Q Consensus        45 ~~GG~liiGV~d~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~p~~~~~i~~~~~~-g~~i~vi~Ip~s~~~~~P~~  123 (145)
                      +.||-|.|-++-..+-.    .++.++...+..+.. .   ...+.|.-...-+..+++ .-.+..|.+..+|...-|++
T Consensus        59 gkGG~i~~~~Kte~EG~----VKv~gV~~~~~~E~F-~---V~s~~~S~~~~~Y~~~VD~~~~FDRI~~QD~P~~~~~I~  130 (153)
T 1wcu_A           59 GKGGCIYLQVKTETEGL----VKVQGVRGYDETEAF-N---VGSFRSSSDFTEYKFEVDDEYQFDRIIVQDGPASNIPIY  130 (153)
T ss_dssp             EEEEEEEEEEEESSCEE----EEEESCTTSCTTCCE-E---EEEECCEEEEEEEEEEEEEEEEESEEEEEETTCCCCCEE
T ss_pred             CCCCEEEEEEECCCCCE----EEEEEECCCCCCCCE-E---EEEECCCCCCEEEEEECCCCCCCCEEEEECCCCCCCEEE
T ss_conf             46866999876266745----899975277743114-4---310036542079999615766523788713898898588


Q ss_pred             EC
Q ss_conf             75
Q T0557           124 KK  125 (145)
Q Consensus       124 ~~  125 (145)
                      ++
T Consensus       131 ~r  132 (153)
T 1wcu_A          131 MR  132 (153)
T ss_dssp             EE
T ss_pred             EE
T ss_conf             88


No 8  
>2apo_A Probable tRNA pseudouridine synthase B; protein-protein complex, box H/ACA, snoRNP, pseudouridine synthase, RNA modification; 1.95A {Methanocaldococcus jannaschii} SCOP: b.122.1.1 d.265.1.2
Probab=4.67  E-value=1.5e+02  Score=10.93  Aligned_cols=13  Identities=23%  Similarity=0.386  Sum_probs=6.4

Q ss_pred             CEEEEEEECCCCC
Q ss_conf             0799986327763
Q T0557            48 GYLLLGVDWAIND   60 (145)
Q Consensus        48 G~liiGV~d~~~~   60 (145)
                      |.|++++...+..
T Consensus       107 GvL~i~ig~aTKl  119 (357)
T 2apo_A          107 GVLPVALERATKT  119 (357)
T ss_dssp             EEEEEEEGGGGGG
T ss_pred             CCHHHEECHHHHH
T ss_conf             6553211865322


No 9  
>1yud_A Hypothetical protein SO0799; SOR12, Q8E1N8, PSI, protein structure initiative, northeast structural genomics consortium, NESG; 2.70A {Shewanella oneidensis mr-1} SCOP: b.82.1.16
Probab=3.63  E-value=1.9e+02  Score=10.46  Aligned_cols=25  Identities=20%  Similarity=0.267  Sum_probs=16.9

Q ss_pred             CCCHHHHHHHHHHCC--CCCEEEEEECCC
Q ss_conf             973799999997178--996577741578
Q T0557             1 MRSATDLLDELNAVD--ESARIEAKRASD   27 (145)
Q Consensus         1 m~~~~e~l~~L~~~~--E~~~lEfK~~~~   27 (145)
                      |.+++++|+.|...+  |+-++  ++.+.
T Consensus        11 m~~a~~lI~~L~L~pHPEGG~f--~et~r   37 (170)
T 1yud_A           11 MQNADDFIKFLELEQHVEGGFY--RSSYR   37 (170)
T ss_dssp             CCCHHHHHHHTTCEECTTSSEE--EEEEE
T ss_pred             CCCHHHHHHHCCCCCCCCCCEE--EEEEE
T ss_conf             8999999998099768998669--98885


No 10 
>1pav_A Hypothetical protein TA1170/TA1414; structural genomics, structure, fast NMR, semiautomated analysis; NMR {Thermoplasma acidophilum} SCOP: d.68.3.3
Probab=2.99  E-value=2.2e+02  Score=10.11  Aligned_cols=43  Identities=14%  Similarity=0.057  Sum_probs=22.1

Q ss_pred             HHHHHCCCCCEEEEEECCCCHHHHHHHHHHHHCCCCCCCCEEEEEEECCC
Q ss_conf             99971789965777415788479999999970887789707999863277
Q T0557             9 DELNAVDESARIEAKRASDMGKSVMETVIAFANEPGLDGGYLLLGVDWAI   58 (145)
Q Consensus         9 ~~L~~~~E~~~lEfK~~~~~~~~l~k~i~AFAN~~~~~GG~liiGV~d~~   58 (145)
                      ..|.++..++.+++......   ..++|-+||..    -|+-++.+.+.+
T Consensus        25 kal~~l~~G~~l~v~~dd~~---~~~di~~~~~~----~g~~~~~~~~~~   67 (78)
T 1pav_A           25 KAYKQAKVGEVISVYSTDAG---TKKDAPAWIQK----SGQELVGVFDRN   67 (78)
T ss_dssp             HHHTTSCTTCCEECCBSSSC---HHHHHHHHHHH----HTEEECCCCCCS
T ss_pred             HHHHHCCCCCEEEEEECCCC---HHHHHHHHHHH----CCCEEEEEEEEC
T ss_conf             99984799979999908964---59999999998----699999999719


Done!