Query T0579 SR518, , 124 residues Match_columns 124 No_of_seqs 37 out of 39 Neff 2.5 Searched_HMMs 22458 Date Sun Jun 13 15:16:16 2010 Command /home/syshi_2/2008/ferredoxin/manualcheck/update/HHsearch/bin/hhsearch -i /home/syshi_3/CASP9/HHsearch4Targetseq/seq/T0579.hhm -d /home/syshi_2/2008/ferredoxin/manualcheck/update/HHsearch/database/pdb70_15May10_hhmdb -o /home/syshi_3/CASP9/HHsearch4Targetseq/pdb70search/T0579.hhr No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM 1 2qqr_A JMJC domain-containing 70.6 5.4 0.00024 19.3 7.1 95 1-110 6-103 (118) 2 2akk_A RP4479, PHNA-like prote 37.3 19 0.00083 16.3 2.8 35 55-91 3-37 (74) 3 2akl_A PHNA-like protein PA012 30.1 22 0.00098 15.9 2.1 42 47-90 50-100 (138) 4 3a0j_A Cold shock protein; OB- 28.1 30 0.0013 15.1 4.4 43 41-87 21-63 (73) 5 2nqc_A Filamin-C; immunoglobul 23.2 38 0.0017 14.6 3.0 35 80-116 84-118 (138) 6 1k0h_A Gpfii; twisted beta-san 21.5 41 0.0018 14.4 4.3 78 4-109 24-101 (117) 7 1fm0_D Molybdopterin convertin 19.1 46 0.0021 14.1 2.4 24 49-73 51-74 (81) 8 2ki8_A Tungsten formylmethanof 18.8 32 0.0014 15.0 1.2 46 52-99 54-99 (146) 9 2jk1_A HUPR, hydrogenase trans 17.4 41 0.0018 14.4 1.5 16 6-21 46-61 (139) 10 1s8n_A Putative antiterminator 15.8 41 0.0018 14.4 1.2 16 6-21 60-75 (205) No 1 >2qqr_A JMJC domain-containing histone demethylation protein 3A; histone lysine demethylase, tandem hybrid tudor domains, metal binding protein; 1.80A {Homo sapiens} SCOP: b.34.9.1 b.34.9.1 PDB: 2qqs_A* 2gfa_A* 2gf7_A* Probab=70.62 E-value=5.4 Score=19.25 Aligned_cols=95 Identities=19% Similarity=0.291 Sum_probs=62.0 Q ss_pred CCCCCEEEEEECCCCCCCCCCEEEEEECCCEEEEEEEECCCCCCCCCCCEEEEEECCCCC---CCCCCCCCCEEEEECCC Q ss_conf 987875799606756536872268741020688887321788962345401333002687---75547898779997011 Q T0579 1 MKVGSQVIINTSHMKGMKGAEATVTGAYDTTAYVVSYTPTNGGQRVDHHKWVIQEEIKDA---GDKTLQPGDQVILEASH 77 (124) Q Consensus 1 y~vGs~v~l~adHM~GM~GA~atIvgAydTt~Y~VsYtPt~Gg~~V~nHKWVv~EEl~~a---g~~~~~~G~eV~l~AdH 77 (124) +.+|+.|. |-+-.| +=-.|+|+.......|.|.|.--+-...+. .+.|... ...+++.|+.|...-. T Consensus 6 l~vG~~V~--ak~~~g-~~y~g~I~~v~~~~~y~V~fdDg~~~~~~~------~~~i~~~~~~~~~~~~vG~~V~a~~~- 75 (118) T 2qqr_A 6 ITAGQKVI--SKHKNG-RFYQCEVVRLTTETFYEVNFDDGSFSDNLY------PEDIVSQDCLQFGPPAEGEVVQVRWT- 75 (118) T ss_dssp CCTTCEEE--EECTTS-SEEEEEEEEEEEEEEEEEEETTSCEEEEEC------GGGBCSSCHHHHCCCCTTCEEEEECT- T ss_pred CCCCCEEE--EEECCC-CEEEEEEEEECCCCEEEEEECCCCCEECCC------HHHEEECCCCCCCCCCCCCEEEEECC- T ss_conf 67899999--993899-898999999924888999987999211368------67568724334688788989999948- Q ss_pred CCCCCCCCEEEEECCCCEEEEEEEEECCCCCEE Q ss_conf 455478706886036860688864326999465 Q T0579 78 MKGMKGATAEIDSAEKTTVYMVDYTSTTSGEKV 110 (124) Q Consensus 78 M~GMkgA~a~Id~~~~tTVYmVDy~~t~~g~~v 110 (124) .| +-..|+|........|.|.|. +|.+. T Consensus 76 -~~-~~y~g~v~~~~~~~~Y~V~fd---DG~~~ 103 (118) T 2qqr_A 76 -DG-QVYGAKFVASHPIQMYQVEFE---DGSQL 103 (118) T ss_dssp -TS-CEEEEEEEEEEEEEEEEEEET---TSCEE T ss_pred -CC-EEEEEEEEEEECCCEEEEEEC---CCCEE T ss_conf -98-498899999955988999997---89989 No 2 >2akk_A RP4479, PHNA-like protein; beta-strand protein, structural genomics, PSI, protein structure initiative; NMR {Rhodopseudomonas palustris CGA009} SCOP: b.34.11.2 Probab=37.31 E-value=19 Score=16.29 Aligned_cols=35 Identities=26% Similarity=0.414 Sum_probs=27.7 Q ss_pred ECCCCCCCCCCCCCCEEEEECCCCCCCCCCCEEEEEC Q ss_conf 0026877554789877999701145547870688603 Q T0579 55 EEIKDAGDKTLQPGDQVILEASHMKGMKGATAEIDSA 91 (124) Q Consensus 55 EEl~~ag~~~~~~G~eV~l~AdHM~GMkgA~a~Id~~ 91 (124) -|++|+.-..|++||.|+|--|- --||+..+|-.- T Consensus 3 ~~vkD~nGn~L~dGDsV~liKDL--kVKGss~~lK~G 37 (74) T 2akk_A 3 IEVRDCNGALLADGDNVSLIKDL--KLKGSSTVLKRG 37 (74) T ss_dssp CCCBCSSCCBCCTTEEEEESSCE--EETTTTEEECTT T ss_pred EEEEECCCCCCCCCCEEEEEEEE--EECCCCCCCCCC T ss_conf 38993889893379989999622--744666212275 No 3 >2akl_A PHNA-like protein PA0128; two domains, Zn binding protein, beta-strand protein, structural genomics, PSI; NMR {Pseudomonas aeruginosa PAO1} SCOP: b.34.11.2 g.41.3.5 Probab=30.08 E-value=22 Score=15.91 Aligned_cols=42 Identities=29% Similarity=0.448 Sum_probs=30.4 Q ss_pred CCCEEEEEE---------CCCCCCCCCCCCCCEEEEECCCCCCCCCCCEEEEE Q ss_conf 454013330---------02687755478987799970114554787068860 Q T0579 47 DHHKWVIQE---------EIKDAGDKTLQPGDQVILEASHMKGMKGATAEIDS 90 (124) Q Consensus 47 ~nHKWVv~E---------El~~ag~~~~~~G~eV~l~AdHM~GMkgA~a~Id~ 90 (124) --|-|--.+ .++|+.-..|++||.|+|--|- -.||+..+|-. T Consensus 50 C~hEW~~~~~~~~~~~~~vvkDaNGn~L~dGDsVtvIKDL--kVKGss~~iK~ 100 (138) T 2akl_A 50 CAHEWSPNEAATASDDGKVIKDSVGNVLQDGDTITVIKDL--KVKGSSLVVKV 100 (138) T ss_dssp TTEEECTTTTTCCCCSCCSCBCTTSCBCCTTCEEECCSCE--ECSSSSCEECT T ss_pred CCCCCCCCCCCCCCCCCCEEECCCCCCCCCCCEEEEEECC--EECCCCCCEEC T ss_conf 6374785535555667746882899994579979998301--22576631337 No 4 >3a0j_A Cold shock protein; OB-fold, cytoplasm, transcription, structural genomics, NPPSFA; 1.65A {Thermus thermophilus} Probab=28.09 E-value=30 Score=15.15 Aligned_cols=43 Identities=30% Similarity=0.405 Sum_probs=31.9 Q ss_pred CCCCCCCCCEEEEEECCCCCCCCCCCCCCEEEEECCCCCCCCCCCEE Q ss_conf 88962345401333002687755478987799970114554787068 Q T0579 41 NGGQRVDHHKWVIQEEIKDAGDKTLQPGDQVILEASHMKGMKGATAE 87 (124) Q Consensus 41 ~Gg~~V~nHKWVv~EEl~~ag~~~~~~G~eV~l~AdHM~GMkgA~a~ 87 (124) +||+.| +|-+-.|+..+-..|.+|+.|..+...-+.-+|..|. T Consensus 21 d~g~Dv----FvH~s~i~~~g~~~l~~G~~V~f~~~~~~~~kg~~A~ 63 (73) T 3a0j_A 21 EGDTDV----FVHYTAINAKGFRTLNEGDIVTFDVEPGRNGKGPQAV 63 (73) T ss_dssp TTSCCE----EEEGGGBCSSSCSSCCTTCEEEEEEECCSCCSSSEEE T ss_pred CCCCEE----EEEEHHHCCCCCCCCCCCCEEEEEEEECCCCCCCEEE T ss_conf 899709----9983671513798689999999999989999887788 No 5 >2nqc_A Filamin-C; immunoglobulin, metal binding, immune system; 2.05A {Homo sapiens} SCOP: b.1.18.10 PDB: 2d7q_A 2k3t_A Probab=23.20 E-value=38 Score=14.63 Aligned_cols=35 Identities=17% Similarity=0.232 Sum_probs=23.4 Q ss_pred CCCCCCEEEEECCCCEEEEEEEEECCCCCEEEEEECE Q ss_conf 5478706886036860688864326999465300011 Q T0579 80 GMKGATAEIDSAEKTTVYMVDYTSTTSGEKVKNHKWV 116 (124) Q Consensus 80 GMkgA~a~Id~~~~tTVYmVDy~~t~~g~~v~NHKWV 116 (124) |=.+....+...... |-|.|+|+.-|.-.-+=+|- T Consensus 84 gp~~~~v~v~~~~dg--y~V~YtP~~~G~y~I~V~~~ 118 (138) T 2nqc_A 84 GPSKVQLDCRECPEG--HVVTYTPMAPGNYLIAIKYG 118 (138) T ss_dssp SSSCCEEEEEEETTE--EEEEEECCSCEEEEEEEEES T ss_pred CCCCCCEEEEECCCC--CEEEEECCCCEEEEEEEEEC T ss_conf 888751278863896--38999728988799999999 No 6 >1k0h_A Gpfii; twisted beta-sandwich, viral protein; NMR {Enterobacteria phage lambda} SCOP: b.106.1.2 Probab=21.55 E-value=41 Score=14.44 Aligned_cols=78 Identities=18% Similarity=0.344 Sum_probs=49.6 Q ss_pred CCEEEEEECCCCCCCCCCEEEEEECCCEEEEEEEECCCCCCCCCCCEEEEEECCCCCCCCCCCCCCEEEEECCCCCCCCC Q ss_conf 87579960675653687226874102068888732178896234540133300268775547898779997011455478 Q T0579 4 GSQVIINTSHMKGMKGAEATVTGAYDTTAYVVSYTPTNGGQRVDHHKWVIQEEIKDAGDKTLQPGDQVILEASHMKGMKG 83 (124) Q Consensus 4 Gs~v~l~adHM~GM~GA~atIvgAydTt~Y~VsYtPt~Gg~~V~nHKWVv~EEl~~ag~~~~~~G~eV~l~AdHM~GMkg 83 (124) |..++++-. .|...+|.|-||.- |+.+..+ ||-++....=+.+--..|.. .++.||.|++. T Consensus 24 G~~a~~tp~-----~g~~~~I~gIFd~p-~~~~~~~--Gg~~v~~~~P~l~vr~sDv~--~~~~gD~v~I~--------- 84 (117) T 1k0h_A 24 GTSATITSG-----EQSGAVIRGVFDDP-ENISYAG--QGVRVEGSSPSLFVRTDEVR--QLRRGDTLTIG--------- 84 (117) T ss_dssp CCEEEEECT-----TTCCEEEEEEEECS-SCCCSSS--CSCCSSCSSCEEEESSSSTT--TCCSSCEEEET--------- T ss_pred CCCEEEECC-----CCCCEEEEEEECCC-CCCCCCC--CCEEEEEECCEEEEECHHCC--CCCCCCEEEEC--------- T ss_conf 883599828-----99837999997880-0045578--84577635859998900166--87889989999--------- Q ss_pred CCEEEEECCCCEEEEEEEEECCCCCE Q ss_conf 70688603686068886432699946 Q T0579 84 ATAEIDSAEKTTVYMVDYTSTTSGEK 109 (124) Q Consensus 84 A~a~Id~~~~tTVYmVDy~~t~~g~~ 109 (124) ..+-..++.+|...|++ T Consensus 85 ---------g~~Y~V~~v~PDg~G~t 101 (117) T 1k0h_A 85 ---------EENFWVDRVSPDDGGSC 101 (117) T ss_dssp ---------TTCEEBCCCCSSSCCCT T ss_pred ---------CEEEEEEEECCCCCCEE T ss_conf ---------98999976635999769 No 7 >1fm0_D Molybdopterin convertin factor, subunit 1; molybdenum cofactor biosynthesis, transferase; 1.45A {Escherichia coli} SCOP: d.15.3.1 PDB: 1fma_D 1jw9_D 1jwa_D* 1jwb_D* 3bii_D 1nvi_D Probab=19.07 E-value=46 Score=14.13 Aligned_cols=24 Identities=21% Similarity=0.328 Sum_probs=18.4 Q ss_pred CEEEEEECCCCCCCCCCCCCCEEEE Q ss_conf 4013330026877554789877999 Q T0579 49 HKWVIQEEIKDAGDKTLQPGDQVIL 73 (124) Q Consensus 49 HKWVv~EEl~~ag~~~~~~G~eV~l 73 (124) -++.++.++.+. +.++++||||.+ T Consensus 51 ~~vavn~~~~~~-~~~l~dgDeVA~ 74 (81) T 1fm0_D 51 LLAAVNQTLVSF-DHPLTDGDEVAF 74 (81) T ss_dssp CEEEETTEECCT-TCBCCTTCEEEE T ss_pred EEEECCCEECCC-CCCCCCCCEEEE T ss_conf 899728459799-978599999999 No 8 >2ki8_A Tungsten formylmethanofuran dehydrogenase, subunit D (FWDD-2); beta-barrel, structural genomics, PSI-2, protein structure initiative; NMR {Archaeoglobus fulgidus} Probab=18.79 E-value=32 Score=15.03 Aligned_cols=46 Identities=20% Similarity=0.206 Sum_probs=31.8 Q ss_pred EEEECCCCCCCCCCCCCCEEEEECCCCCCCCCCCEEEEECCCCEEEEE Q ss_conf 333002687755478987799970114554787068860368606888 Q T0579 52 VIQEEIKDAGDKTLQPGDQVILEASHMKGMKGATAEIDSAEKTTVYMV 99 (124) Q Consensus 52 Vv~EEl~~ag~~~~~~G~eV~l~AdHM~GMkgA~a~Id~~~~tTVYmV 99 (124) +|.=--+||.+-.+++||.|.+.... |---+.|.+....+.+|+|- T Consensus 54 ~ieinP~DA~~lGi~~Gd~V~V~s~~--G~v~~~a~~~di~~G~vf~P 99 (146) T 2ki8_A 54 YAEINEEDWNALGLQEGDRVKVKTEF--GEVVVFAKKGDVPKGMIFIP 99 (146) T ss_dssp EEEECHHHHHHHTCCTTCEEEEECSS--CEEEEEEEECSCCTTEEEEE T ss_pred EEEECHHHHHHCCCCCCCEEEEECCC--EEEEEEEEECCCCCCEEEEE T ss_conf 99999999988599999999998799--68999999912578859973 No 9 >2jk1_A HUPR, hydrogenase transcriptional regulatory protein HUPR1; nucleotide-binding, transcription regulation; 2.10A {Rhodobacter capsulatus} PDB: 2vui_B 2vuh_B Probab=17.37 E-value=41 Score=14.44 Aligned_cols=16 Identities=44% Similarity=0.650 Sum_probs=10.0 Q ss_pred EEEEEECCCCCCCCCC Q ss_conf 5799606756536872 Q T0579 6 QVIINTSHMKGMKGAE 21 (124) Q Consensus 6 ~v~l~adHM~GM~GA~ 21 (124) .++|.+=+||||+|-+ T Consensus 46 dlil~D~~mP~~~G~~ 61 (139) T 2jk1_A 46 QVIICDQRMPGRTGVD 61 (139) T ss_dssp EEEEEESCCSSSCHHH T ss_pred CEEEEECCCCCCCHHH T ss_conf 8899634454243899 No 10 >1s8n_A Putative antiterminator; structural genomics, transcriptional antiterminator, two component system, PSI; 1.48A {Mycobacterium tuberculosis H37RV} SCOP: c.23.1.1 PDB: 1sd5_A Probab=15.80 E-value=41 Score=14.42 Aligned_cols=16 Identities=19% Similarity=0.360 Sum_probs=8.8 Q ss_pred EEEEEECCCCCCCCCC Q ss_conf 5799606756536872 Q T0579 6 QVIINTSHMKGMKGAE 21 (124) Q Consensus 6 ~v~l~adHM~GM~GA~ 21 (124) .++|.+=+||||+|-+ T Consensus 60 DlillDi~MP~mdGle 75 (205) T 1s8n_A 60 DLVIMDVKMPRRDGID 75 (205) T ss_dssp SEEEEESSCSSSCHHH T ss_pred CEEEEECCCCCCCHHH T ss_conf 9999964045860799 Done!