Query T0612 YP_001093860.1, Shewanella loihica PV-4, 129 residues Match_columns 129 No_of_seqs 106 out of 143 Neff 6.7 Searched_HMMs 22458 Date Mon Jul 5 08:57:31 2010 Command /home/syshi_2/2008/ferredoxin/manualcheck/update/HHsearch/bin/hhsearch -i /home/syshi_3/CASP9/HHsearch4Targetseq/seq/T0612.hhm -d /home/syshi_2/2008/ferredoxin/manualcheck/update/HHsearch/database/pdb70_15May10_hhmdb -o /home/syshi_3/CASP9/HHsearch4Targetseq/pdb70search/T0612.hhr No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM 1 1p5v_A CAF1M chaperone, chaper 89.9 0.89 4E-05 23.2 9.7 82 41-126 12-102 (235) 2 1s3r_A Intermedilysin; toxin; 81.6 2.4 0.00011 20.7 8.0 63 57-126 420-489 (535) 3 2f2f_C CDT C, cytolethal diste 80.9 0.24 1.1E-05 26.4 0.0 19 1-20 1-19 (186) 4 3hvn_A Hemolysin, suilysin; be 80.4 2.7 0.00012 20.4 7.2 49 73-126 405-460 (508) 5 2co7_B SAFB chaperone, putativ 65.7 6.3 0.00028 18.3 9.6 82 41-126 12-100 (221) 6 1pfo_A Perfringolysin O, PFO; 65.4 6.4 0.00028 18.3 7.3 49 73-126 404-459 (500) 7 3hrz_B Cobra venom factor; ser 59.7 8.1 0.00036 17.6 11.8 66 43-110 84-151 (252) 8 2wnx_A Glycoside hydrolase, fa 52.2 11 0.00048 16.9 4.2 35 52-87 24-61 (170) 9 3isy_A Bsupi, intracellular pr 48.4 13 0.00056 16.6 13.0 74 50-123 13-99 (120) 10 1y0g_A Protein YCEI; lipid bin 43.4 4 0.00018 19.4 0.1 27 1-27 1-28 (191) 11 3cfu_A Uncharacterized lipopro 43.3 15 0.00067 16.1 7.0 70 55-124 47-125 (159) 12 3but_A Uncharacterized protein 42.3 16 0.0007 16.0 7.3 50 56-109 19-71 (136) 13 1fft_B Ubiquinol oxidase; elec 36.2 5.8 0.00026 18.5 0.0 17 3-19 11-27 (315) 14 1nbc_A Cellulosomal scaffoldin 35.8 20 0.00089 15.4 5.6 33 53-86 14-49 (155) 15 1pkq_A (8-18C5) chimeric FAB, 33.8 17 0.00077 15.7 2.1 14 1-14 1-14 (241) 16 1bev_1 Bovine enterovirus coat 33.2 17 0.00075 15.8 2.0 35 93-127 208-242 (281) 17 2a2u_A Protein (alpha-2U-globu 31.5 9.1 0.0004 17.4 0.4 20 1-21 1-20 (181) 18 3fn9_A Putative beta-galactosi 30.9 24 0.0011 14.9 7.6 65 41-108 173-237 (692) 19 1jbj_A CD3 epsilon and gamma e 29.2 18 0.0008 15.7 1.6 48 76-124 135-185 (186) 20 2a3m_A COG3005: nitrate/TMAO r 28.9 9 0.0004 17.4 0.0 18 1-18 1-18 (130) 21 2p3y_A Hypothetical protein VP 25.2 20 0.00088 15.4 1.2 18 1-18 1-19 (491) 22 1e9y_A Urease alpha subunit; h 24.4 32 0.0014 14.2 3.9 73 38-112 106-189 (238) 23 1us5_A Putative GLUR0 ligand b 22.9 14 0.00065 16.2 0.1 23 1-26 1-23 (314) 24 2uxt_A Protein SUFI, SUFI; oxi 21.2 37 0.0016 13.9 3.7 24 95-118 242-265 (451) No 1 >1p5v_A CAF1M chaperone, chaperone protein CAF1M, CAF1M; chaperone-target complex, chaperone-subunit complex, protein fiber; 1.70A {Yersinia pestis} SCOP: b.1.11.1 b.7.2.1 PDB: 1p5u_A 1z9s_A 2os7_A 3dos_A 3dpb_A 3dsn_A Probab=89.88 E-value=0.89 Score=23.19 Aligned_cols=82 Identities=12% Similarity=-0.019 Sum_probs=53.9 Q ss_pred CEEEEEEEEEEECCCEEEEEEEEEECCCCCEEEEEEEEEECCCCCEECCC----CCCCEEEEECCCCEEEEEEECC---- Q ss_conf 50477421022048748999999846687628999999976889683888----8760389977995089998637---- Q T0612 41 SDVDVSAVTTQAEAGFLRARGTIISKSPKDQRLQYKFTWYDINGATVEDE----GVSWKSLKLHGKQQMQVTALSP---- 112 (129) Q Consensus 41 ~~i~v~~~~~~~~~g~~~~~v~l~N~~~~~~~l~Yrf~WyD~~Gl~v~~~----~~~W~~l~l~~~~~~~i~~vap---- 112 (129) .+|.+..-+.....+...++++|.|+.+.|.-+|= |.|+.+-+-... -+| --+.|.++++.+|+-+.. T Consensus 12 ~gv~l~~TRvI~~~~~~~~si~l~N~~~~p~lvQs---wv~d~~~~~~~~~pfivtP-Pl~rl~p~~~q~vRI~~~~~~l 87 (235) T 1p5v_A 12 YGVTIGESRIIYPLDAAGVMVSVKNTQDYPVLIQS---RIYDENKEKESEDPFVVTP-PLFRLDAKQQNSLRIAQAGGVF 87 (235) T ss_dssp EEEEESCSEEEEETTCSCEEEEEEECSSSCEEEEE---EECC---------CEEEES-SEEEECTTCEEEEEEEECSCCC T ss_pred EEEEECCEEEEEECCCCEEEEEEEECCCCCEEEEE---EEECCCCCCCCCCCEEECC-CCEEECCCCCEEEEEEECCCCC T ss_conf 13797870999908995889999959999689999---9865987767779769789-5113289982289998368889 Q ss_pred -CCCEEEEEEEEEEE Q ss_conf -98405899999972 Q T0612 113 -NATAVRCELYVREA 126 (129) Q Consensus 113 -~~~a~~~RlylRe~ 126 (129) .-+-+-|||.++|. T Consensus 88 p~DrEs~f~l~i~eI 102 (235) T 1p5v_A 88 PRDKESLKWLCVKGI 102 (235) T ss_dssp CSSSCEEEEEEEEEE T ss_pred CCCEEEEEEEEEEEC T ss_conf 965279999999843 No 2 >1s3r_A Intermedilysin; toxin; 2.60A {Streptococcus intermedius} Probab=81.58 E-value=2.4 Score=20.66 Aligned_cols=63 Identities=11% Similarity=-0.012 Sum_probs=35.1 Q ss_pred EEEEEEEEECCCCCEEEEEEEEE----ECCCCCEECC---CCCCCEEEEECCCCEEEEEEECCCCCEEEEEEEEEEE Q ss_conf 89999998466876289999999----7688968388---8876038997799508999863798405899999972 Q T0612 57 LRARGTIISKSPKDQRLQYKFTW----YDINGATVED---EGVSWKSLKLHGKQQMQVTALSPNATAVRCELYVREA 126 (129) Q Consensus 57 ~~~~v~l~N~~~~~~~l~Yrf~W----yD~~Gl~v~~---~~~~W~~l~l~~~~~~~i~~vap~~~a~~~RlylRe~ 126 (129) ...-..+.+....- -+|..+| ||++|-|+-. =+..|+.-+.|=.. +|+ --++|++.||++||. T Consensus 420 ~~g~i~ldh~Gayv--a~~~v~wde~syd~~g~e~~~~k~w~~n~~~rta~f~t--~i~---l~~n~rni~i~~~ec 489 (535) T 1s3r_A 420 KDGALTLNHDGAFV--ARFYVYWEELGHDADGYETIRSRSWSGNGYNRGAHYST--TLR---FKGNVRNIRVKVLGA 489 (535) T ss_dssp ECEEEEEEECSSSC--EEEEEEEEEEEECTTSCEEEEEEECTTTTCCBCTTCEE--EEE---ECTTEEEEEEEEEEE T ss_pred ECCCEEEECCCCEE--EEEEEEEEECCCCCCCCEEEEEECCCCCCCCCCCCCEE--EEE---CCCCCCEEEEEEEEC T ss_conf 12535884258367--77899834502078986875310234688545556327--874---488742248998751 No 3 >2f2f_C CDT C, cytolethal distending toxin C; actinobacillus actinomycetemcomitans, oligomerization, stability and toxic activity; 2.40A {Aggregatibacter actinomycetemcomitans} SCOP: b.42.2.1 Probab=80.88 E-value=0.24 Score=26.44 Aligned_cols=19 Identities=32% Similarity=0.256 Sum_probs=16.3 Q ss_pred CHHHHHHHHHHHHHHCCCCC Q ss_conf 92488999998887145788 Q T0612 1 MNKGLVLACLLLGLSACAPH 20 (129) Q Consensus 1 Mkk~l~~~~~~l~L~GCas~ 20 (129) |||.+|++++++.+ ||+++ T Consensus 1 mkK~~i~f~~~l~~-~~~s~ 19 (186) T 2f2f_C 1 MKKYLLSFLLSMIL-TLTSH 19 (186) T ss_dssp -------------------- T ss_pred CCHHHHHHHHHHHH-HCCCC T ss_conf 93237999999997-51245 No 4 >3hvn_A Hemolysin, suilysin; beta-strand rich, elongated ROD like, pore forming, toxin; HET: CFH HTO; 2.85A {Streptococcus suis} Probab=80.39 E-value=2.7 Score=20.41 Aligned_cols=49 Identities=22% Similarity=0.376 Sum_probs=34.6 Q ss_pred EEEEEEE----ECCCCCEECC---CCCCCEEEEECCCCEEEEEEECCCCCEEEEEEEEEEE Q ss_conf 9999999----7688968388---8876038997799508999863798405899999972 Q T0612 73 LQYKFTW----YDINGATVED---EGVSWKSLKLHGKQQMQVTALSPNATAVRCELYVREA 126 (129) Q Consensus 73 l~Yrf~W----yD~~Gl~v~~---~~~~W~~l~l~~~~~~~i~~vap~~~a~~~RlylRe~ 126 (129) -+|..+| ||++|-|+-. =+..|+.-+.|-..++.+ -+.|++.|+++||. T Consensus 405 a~f~i~wde~~yd~~g~e~~~~k~w~~n~~~~ta~f~t~i~~-----~~n~rni~v~~~e~ 460 (508) T 3hvn_A 405 AKYNITWEEVSYNEAGEEVWEPKAWDKNGVNLTSHWSETIQI-----PGNARNLHVNIQEC 460 (508) T ss_dssp EEEEEEEEEEEECGGGCEEEEEEECTTTTCEEEEEEEEEEEE-----CTTEEEEEEEEEEE T ss_pred EEEEEEEEECCCCCCCCEEEEECCCCCCCCCCCCCCEEEEEC-----CCCCEEEEEEEEEC T ss_conf 999998643230788877875033047884454573589745-----89830358999974 No 5 >2co7_B SAFB chaperone, putative fimbriae assembly chaperone; pilus subunit, adhesion, strand complementation, pathogenesis, fibril protein; 1.8A {Salmonella typhimurium} SCOP: b.1.11.1 b.7.2.1 PDB: 2co6_B Probab=65.71 E-value=6.3 Score=18.29 Aligned_cols=82 Identities=13% Similarity=0.074 Sum_probs=51.9 Q ss_pred CEEEEEEEEEEECCCEEEEEEEEEECCCCCEEEEEEEEEECCCCCEEC-CC-CCCCEEEEECCCCEEEEEEEC-----CC Q ss_conf 504774210220487489999998466876289999999768896838-88-876038997799508999863-----79 Q T0612 41 SDVDVSAVTTQAEAGFLRARGTIISKSPKDQRLQYKFTWYDINGATVE-DE-GVSWKSLKLHGKQQMQVTALS-----PN 113 (129) Q Consensus 41 ~~i~v~~~~~~~~~g~~~~~v~l~N~~~~~~~l~Yrf~WyD~~Gl~v~-~~-~~~W~~l~l~~~~~~~i~~va-----p~ 113 (129) ++|.+..-+.....+-.++++++.|+.+.|.-+| -|-|+.+=+.. |. -.| --+.|.++++..|+-+. |. T Consensus 12 a~v~l~~TRvIy~~~~~~~s~~l~N~~~~p~LvQ---swv~~~d~~~~~pFivtP-Plfrl~p~~~q~lRI~~~~~~LP~ 87 (221) T 2co7_B 12 FSVKLGATRVIYHAGTAGATLSVSNPQNYPILVQ---SSVKAADKSSPAPFLVMP-PLFRLEANQQSQLRIVRTGGDMPT 87 (221) T ss_dssp EECEESCSEEEEETTSSCEEEEEECCSSSCEEEE---EEEEETTSSSBCSEEEES-SEEEECTTCEEEEEEEECCCCCCS T ss_pred EEEEECCCEEEECCCCCEEEEEEEECCCCEEEEE---EEEECCCCCCCCCEEECC-CCEEECCCCCEEEEEEECCCCCCC T ss_conf 8899788699990898678999996999839999---998548985448889679-614789999418999944889985 Q ss_pred CCEEEEEEEEEEE Q ss_conf 8405899999972 Q T0612 114 ATAVRCELYVREA 126 (129) Q Consensus 114 ~~a~~~RlylRe~ 126 (129) -+-+=|+|-++|. T Consensus 88 DrESlf~lnv~~I 100 (221) T 2co7_B 88 DRETLQWVCIKAV 100 (221) T ss_dssp SSCEEEEEEEEEE T ss_pred CEEEEEEEEEEEC T ss_conf 3168999999834 No 6 >1pfo_A Perfringolysin O, PFO; toxin, thiol-activated cytolysin, hemolysis, cytolysis; 2.20A {Clostridium perfringens} SCOP: f.9.1.1 PDB: 1m3i_A 1m3j_A 2bk2_A 2bk1_A 3cqf_A Probab=65.41 E-value=6.4 Score=18.25 Aligned_cols=49 Identities=22% Similarity=0.381 Sum_probs=31.6 Q ss_pred EEEEEEE----ECCCCCEECCC---CCCCEEEEECCCCEEEEEEECCCCCEEEEEEEEEEE Q ss_conf 9999999----76889683888---876038997799508999863798405899999972 Q T0612 73 LQYKFTW----YDINGATVEDE---GVSWKSLKLHGKQQMQVTALSPNATAVRCELYVREA 126 (129) Q Consensus 73 l~Yrf~W----yD~~Gl~v~~~---~~~W~~l~l~~~~~~~i~~vap~~~a~~~RlylRe~ 126 (129) -+|..+| ||++|-|+-.. +..|+.-+.|=..+.. --+.|++-|+++||. T Consensus 404 a~f~i~wde~~yd~~g~~~~~~~~w~~n~~~~t~~~~t~i~-----~~~n~~ni~v~~~e~ 459 (500) T 1pfo_A 404 AQFEVAWDEVSYDKEGNEVLTHKTWDGNYQDKTAHYSTVIP-----LEANARNIRIKAREC 459 (500) T ss_dssp EEEEEEEEEEEECTTSCEEEEEEECTTTTCCBCSSEEEEEE-----ECTTEEEEEEEEEEC T ss_pred EEEEEEEEECCCCCCCCEECCCCCCCCCCCCCCCCEEEEEE-----CCCCCEEEEEEEEEC T ss_conf 99999833123278886850113346787545443158864-----388840458999974 No 7 >3hrz_B Cobra venom factor; serine protease, glycosilated, multi-domain, complement system, convertase, complement alternate pathway, complement pathway; HET: NAG P6G; 2.20A {Naja kaouthia} PDB: 3frp_G* 3hs0_B* Probab=59.69 E-value=8.1 Score=17.64 Aligned_cols=66 Identities=6% Similarity=0.007 Sum_probs=46.9 Q ss_pred EEEEEEEEEECCCEEEEEEEEEECCCCCEEEEEEEEEECCCCCEECCCCCC--CEEEEECCCCEEEEEEE Q ss_conf 477421022048748999999846687628999999976889683888876--03899779950899986 Q T0612 43 VDVSAVTTQAEAGFLRARGTIISKSPKDQRLQYKFTWYDINGATVEDEGVS--WKSLKLHGKQQMQVTAL 110 (129) Q Consensus 43 i~v~~~~~~~~~g~~~~~v~l~N~~~~~~~l~Yrf~WyD~~Gl~v~~~~~~--W~~l~l~~~~~~~i~~v 110 (129) +...-|.....++..++.+.+.|....++ .++......+|+........ =+.+.+.+++...+... T Consensus 84 v~~~lP~~v~~GD~~~i~v~v~N~~~~~~--~v~v~l~~~~~~~~~~~~~~~~~~~~~v~~~~~~~v~~~ 151 (252) T 3hrz_B 84 IDLQMPYSVVKNEQVEIRAILHNYVNEDI--YVRVELLYNPAFCSASTKGQRYRQQFPIKALSSRAVPFV 151 (252) T ss_dssp EEECCCSCEETTCCEEEEEEEEECSSSCE--EEEEEECCCTTEEESCCSSCCEEEEEEECTTEEEEEEEE T ss_pred EEECCCCEEECCCEEEEEEEEEECCCCCE--EEEEEEECCCCEEECCCCCCCEEEEEEECCCCCEEEEEE T ss_conf 99358968976989999999996779866--899999647761602367871479998428985278778 No 8 >2wnx_A Glycoside hydrolase, family 9; cellulose degradation; 1.31A {Clostridium thermocellum} PDB: 2wo4_A 2wob_A Probab=52.25 E-value=11 Score=16.91 Aligned_cols=35 Identities=14% Similarity=0.324 Sum_probs=23.8 Q ss_pred ECCCEEEEEEEEEECCCCCEE---EEEEEEEECCCCCEE Q ss_conf 048748999999846687628---999999976889683 Q T0612 52 AEAGFLRARGTIISKSPKDQR---LQYKFTWYDINGATV 87 (129) Q Consensus 52 ~~~g~~~~~v~l~N~~~~~~~---l~Yrf~WyD~~Gl~v 87 (129) ...+.++..+.|.|+...|+. |..| |||+.+|..- T Consensus 24 ~~~n~I~~~~~I~N~g~~pi~Lsdl~iR-Yyft~dg~~~ 61 (170) T 2wnx_A 24 GTKNTIRATINIKNTGTTPVNLSDIKVR-YWFTSDGNEQ 61 (170) T ss_dssp SSCCEEEEEEEEEECSSSCEEGGGEEEE-EEECCTTCSC T ss_pred CCCCEEEEEEEEEECCCCCCCCCCEEEE-EEECCCCCCC T ss_conf 8776681799999898887654645899-9996688752 No 9 >3isy_A Bsupi, intracellular proteinase inhibitor; NP_388994.1, intracellular proteinase inhibitor (bsupi) from bacillus subtilis, structural genomics; HET: PG4; 2.61A {Bacillus subtilis} Probab=48.37 E-value=13 Score=16.55 Aligned_cols=74 Identities=12% Similarity=0.167 Sum_probs=54.2 Q ss_pred EEECCCEEEEEEEEEECCCCCEEEEE------EEEEECCCCCEECCC------CCCCEEEEECCCCEEEEEEECCC-CCE Q ss_conf 22048748999999846687628999------999976889683888------87603899779950899986379-840 Q T0612 50 TQAEAGFLRARGTIISKSPKDQRLQY------KFTWYDINGATVEDE------GVSWKSLKLHGKQQMQVTALSPN-ATA 116 (129) Q Consensus 50 ~~~~~g~~~~~v~l~N~~~~~~~l~Y------rf~WyD~~Gl~v~~~------~~~W~~l~l~~~~~~~i~~vap~-~~a 116 (129) ....++.++....|.|.++.++.|+| -|.=+|++|=+|-.- -.--+...|.++++.+.+..-+. +.. T Consensus 13 ~~~~~e~v~~~ltl~N~~~~~v~l~F~sg~~~d~~v~d~~G~~V~~~S~~k~Ftqa~~~~~l~~gE~~~f~~~~~~~~~p 92 (120) T 3isy_A 13 AIQEPEQIKFNMSLKNQSERAIEFQFSTGQKFELVVYDSEHKERYRYSKEKMFTQAFQNLTLESGETYDFSDVWKEVPEP 92 (120) T ss_dssp EEECSSCEEEEEEEEECSSSCEEEEESSSCCEEEEEECTTCCEEEETTTTCCCCCCCEEEEECTTCEEEEEEEESSCCCS T ss_pred ECCCCCEEEEEEEEEECCCCCEEEEECCCCEEEEEEECCCCCEEEEECCCCHHHHHHHEEEECCCCEEEEEEECCCCCCC T ss_conf 00278529999999918997689897799889999997999899998688423652410870899889998532776889 Q ss_pred EEEEEEE Q ss_conf 5899999 Q T0612 117 VRCELYV 123 (129) Q Consensus 117 ~~~Rlyl 123 (129) -.|.+.. T Consensus 93 G~Ytl~a 99 (120) T 3isy_A 93 GTYEVKV 99 (120) T ss_dssp EEEEEEE T ss_pred CEEEEEE T ss_conf 5089999 No 10 >1y0g_A Protein YCEI; lipid binding protein, lipocalin, cofactor, coenzyme, dehydrogenase, hydrolase, predicted, structural genomics; HET: 8PP; 2.20A {Escherichia coli} SCOP: b.61.6.1 Probab=43.38 E-value=4 Score=19.41 Aligned_cols=27 Identities=15% Similarity=0.086 Sum_probs=16.8 Q ss_pred CHHHHHHHHHHHHHHCCCC-CCCCCCCC Q ss_conf 9248899999888714578-86673026 Q T0612 1 MNKGLVLACLLLGLSACAP-HTGGIMIS 27 (129) Q Consensus 1 Mkk~l~~~~~~l~L~GCas-~~~~~~~~ 27 (129) |||.++.+.++++|.+|++ ....+.++ T Consensus 1 Mkk~~l~l~l~al~~~~~~a~a~~~~id 28 (191) T 1y0g_A 1 MKKSLLGLTFASLMFSAGSAVAADYKID 28 (191) T ss_dssp ----------------------CEEEEC T ss_pred CCHHHHHHHHHHHHHHHHHCCCCCEEEC T ss_conf 9246999999999976324036637975 No 11 >3cfu_A Uncharacterized lipoprotein YJHA; YJHA_bacsu, SR562, NESG, structural genomics, PSI-2, protein structure initiative; 2.40A {Bacillus subtilis} Probab=43.35 E-value=15 Score=16.09 Aligned_cols=70 Identities=14% Similarity=0.069 Sum_probs=50.1 Q ss_pred CEEEEEEEEEECCCCCEEEE-EEEEEECCCCCEECCC------CCCCEEEEECCCCEEEE--EEECCCCCEEEEEEEEE Q ss_conf 74899999984668762899-9999976889683888------87603899779950899--98637984058999999 Q T0612 55 GFLRARGTIISKSPKDQRLQ-YKFTWYDINGATVEDE------GVSWKSLKLHGKQQMQV--TALSPNATAVRCELYVR 124 (129) Q Consensus 55 g~~~~~v~l~N~~~~~~~l~-Yrf~WyD~~Gl~v~~~------~~~W~~l~l~~~~~~~i--~~vap~~~a~~~RlylR 124 (129) -++.+.+++.|+.+.++.+. +.|+.+|.+|-...+. ..--..-.|.|+++++= ....|.-+++.|+|..+ T Consensus 47 ~fviV~vtV~N~g~e~~~~~~~~F~L~d~dg~~y~~~~~~~~~~~~l~~g~L~pG~kvtG~ivFeVPkgd~k~y~l~y~ 125 (159) T 3cfu_A 47 ERLIIEVTMENIGEDSISYNFIGFDLRDKNDQSVRPVFSIEEKGRILMGGTLVSGKKVTGVLSYVIPKGEQKHYTLVYN 125 (159) T ss_dssp EEEEEEEEEEECSSSCEEEEGGGEEEECTTCCBCCCEECSTTTTTBCCEEEECTTCEEEEEEEEEESTTCGGGCEEEEC T ss_pred EEEEEEEEEEECCCCCEEECCCEEEEEECCCCEECCEEEECCCCCEEEEEEECCCCEEEEEEEEEECCCCCCEEEEEEC T ss_conf 9999999999788785670765189990899896221752146760422576799989999999977999720799981 No 12 >3but_A Uncharacterized protein AF_0446; lipid binding protein, beta barrel, protein structure initiative, PSI-2; 1.91A {Archaeoglobus fulgidus dsm 4304} Probab=42.26 E-value=16 Score=15.99 Aligned_cols=50 Identities=12% Similarity=0.119 Sum_probs=37.6 Q ss_pred EEEEEEEEEECCCCCE---EEEEEEEEECCCCCEECCCCCCCEEEEECCCCEEEEEE Q ss_conf 4899999984668762---89999999768896838888760389977995089998 Q T0612 56 FLRARGTIISKSPKDQ---RLQYKFTWYDINGATVEDEGVSWKSLKLHGKQQMQVTA 109 (129) Q Consensus 56 ~~~~~v~l~N~~~~~~---~l~Yrf~WyD~~Gl~v~~~~~~W~~l~l~~~~~~~i~~ 109 (129) -+.+.+.+.|-.+.|+ .+.|.+++ +|.++.....+ +...++++++.++.. T Consensus 19 ~i~~~l~V~NPN~~~l~i~~~~y~l~~---ng~~i~~G~~~-~~~~ip~~~~~~v~v 71 (136) T 3but_A 19 EIVALAKVRNEDVVPIVVSGYHYTIEM---NGVKVADGYEN-SPVTVKPASATTLKF 71 (136) T ss_dssp EEEEEEEEECCSSSCEEEEEEEEEEEE---TTEEEEEEEEC-CCEEECTTCEEEEEE T ss_pred EEEEEEEEECCCCCCEEECCEEEEEEE---CCEEEEEEECC-CCCEECCCCCEEEEE T ss_conf 999999998989867542336999999---99999977507-862788999589999 No 13 >1fft_B Ubiquinol oxidase; electron transport, cytochrome oxidase, membrane protein, oxidoreductase; HET: HEM HEO; 3.50A {Escherichia coli} SCOP: b.6.1.2 f.17.2.1 Probab=36.23 E-value=5.8 Score=18.50 Aligned_cols=17 Identities=29% Similarity=0.200 Sum_probs=12.1 Q ss_pred HHHHHHHHHHHHHCCCC Q ss_conf 48899999888714578 Q T0612 3 KGLVLACLLLGLSACAP 19 (129) Q Consensus 3 k~l~~~~~~l~L~GCas 19 (129) .|+.+++.+++|+||.. T Consensus 11 ~~l~l~~~~~lLsGC~~ 27 (315) T 1fft_B 11 GWLSLFAGTVLLSGCNS 27 (315) T ss_dssp ----------------C T ss_pred HHHHHHHHHHHHCCCCC T ss_conf 99999999999705775 No 14 >1nbc_A Cellulosomal scaffolding protein A; cellulose degradation, cellulose-binding domain, cellulosome, scafoldin; 1.75A {Clostridium thermocellum} SCOP: b.2.2.2 Probab=35.76 E-value=20 Score=15.39 Aligned_cols=33 Identities=9% Similarity=0.287 Sum_probs=21.1 Q ss_pred CCCEEEEEEEEEECCCCCEE---EEEEEEEECCCCCE Q ss_conf 48748999999846687628---99999997688968 Q T0612 53 EAGFLRARGTIISKSPKDQR---LQYKFTWYDINGAT 86 (129) Q Consensus 53 ~~g~~~~~v~l~N~~~~~~~---l~Yrf~WyD~~Gl~ 86 (129) ....++....|.|++..|+. |..| ||||.+|.. T Consensus 14 ~~n~i~~~~~i~N~~~~~i~lsdl~~R-Yyft~d~~~ 49 (155) T 1nbc_A 14 TTNSINPQFKVTNTGSSAIDLSKLTLR-YYYTVDGQK 49 (155) T ss_dssp EESCBCEEEEEEECSSSCEEGGGEEEE-EEECCSSCC T ss_pred CCCEEEEEEEEEECCCCCCCCCEEEEE-EEEECCCCC T ss_conf 787594899999898884002608999-999357873 No 15 >1pkq_A (8-18C5) chimeric FAB, light chain; autoantibody, multiple sclerosis, EAE, immune system; 3.00A {Mus musculus} SCOP: b.1.1.1 b.1.1.2 Probab=33.76 E-value=17 Score=15.75 Aligned_cols=14 Identities=29% Similarity=0.292 Sum_probs=10.1 Q ss_pred CHHHHHHHHHHHHH Q ss_conf 92488999998887 Q T0612 1 MNKGLVLACLLLGL 14 (129) Q Consensus 1 Mkk~l~~~~~~l~L 14 (129) |++++++++++++| T Consensus 1 ~~~~~~~~~~l~ll 14 (241) T 1pkq_A 1 MKQSTIALALLPLL 14 (241) T ss_dssp -------------- T ss_pred CCHHHHHHHHHHHH T ss_conf 95168999999997 No 16 >1bev_1 Bovine enterovirus coat proteins VP1 to VP4; bovine enterovirus VG-5-27, picornavirus, icosahedral virus; HET: MYR; 3.00A {Bovine enterovirus} SCOP: b.121.4.1 Probab=33.24 E-value=17 Score=15.81 Aligned_cols=35 Identities=20% Similarity=0.160 Sum_probs=27.2 Q ss_pred CCEEEEECCCCEEEEEEECCCCCEEEEEEEEEEEC Q ss_conf 60389977995089998637984058999999720 Q T0612 93 SWKSLKLHGKQQMQVTALSPNATAVRCELYVREAI 127 (129) Q Consensus 93 ~W~~l~l~~~~~~~i~~vap~~~a~~~RlylRe~~ 127 (129) .+-...+...++..++.+........+|||+|-++ T Consensus 208 ~YG~~p~N~mGtl~vR~v~~~~~~~~vRVY~kpKh 242 (281) T 1bev_1 208 RYGILPSNFLGFMYFRTLEDAAHQVRFRIYAKIKH 242 (281) T ss_dssp GBTCCGGGCCCEEEEEESSCCSSCCEEEEEEEEEE T ss_pred CCCCCCCCCCEEEEEEEECCCCCCEEEEEEEEECC T ss_conf 47866667863589998628888479999986033 No 17 >2a2u_A Protein (alpha-2U-globulin); lipid binding protein; 2.50A {Rattus norvegicus} SCOP: b.60.1.1 PDB: 2a2g_A Probab=31.48 E-value=9.1 Score=17.36 Aligned_cols=20 Identities=40% Similarity=0.571 Sum_probs=14.9 Q ss_pred CHHHHHHHHHHHHHHCCCCCC Q ss_conf 924889999988871457886 Q T0612 1 MNKGLVLACLLLGLSACAPHT 21 (129) Q Consensus 1 Mkk~l~~~~~~l~L~GCas~~ 21 (129) ||-.++++++.|+|. |+..+ T Consensus 1 ~~~~~~~~~l~l~l~-c~~~~ 20 (181) T 2a2u_A 1 MKLLLLLLCLGLTLV-CGHAE 20 (181) T ss_dssp --------------------C T ss_pred CCCCHHHHHHHHHHH-HCCCC T ss_conf 973124669999867-44887 No 18 >3fn9_A Putative beta-galactosidase; structural genomics, glycosidase, hydrolase, PSI-2; 2.70A {Bacteroides fragilis nctc 9343} Probab=30.86 E-value=24 Score=14.91 Aligned_cols=65 Identities=11% Similarity=0.134 Sum_probs=45.4 Q ss_pred CEEEEEEEEEEECCCEEEEEEEEEECCCCCEEEEEEEEEECCCCCEECCCCCCCEEEEECCCCEEEEE Q ss_conf 50477421022048748999999846687628999999976889683888876038997799508999 Q T0612 41 SDVDVSAVTTQAEAGFLRARGTIISKSPKDQRLQYKFTWYDINGATVEDEGVSWKSLKLHGKQQMQVT 108 (129) Q Consensus 41 ~~i~v~~~~~~~~~g~~~~~v~l~N~~~~~~~l~Yrf~WyD~~Gl~v~~~~~~W~~l~l~~~~~~~i~ 108 (129) .++.+..+......+.+++.+.+.|....+..+..++.=+|.+|-.+.... +.+.+.+.++.++. T Consensus 173 ~gv~i~~~~~~~~~a~v~v~~~v~n~~~~~~~~~l~~~i~~~~g~~v~~~~---~~~~~~~~~~~~~~ 237 (692) T 3fn9_A 173 PGVYITQKDVSKKSADITVKVKLDNAGLQPAAVTLENTIYTQEGQKVGTHS---RSFDLSPQGTQTYL 237 (692) T ss_dssp CSEEEEEESCSSSEEEEEEEEEEEECSSSCEEEEEEEEEECTTSCEEEEEE---EEEEECSSSCEEEE T ss_pred CCEEEEEEECCCCEEEEEEEEEECCCCCCCEEEEEEEEEECCCCCEEEEEE---EEEEECCCCCEEEE T ss_conf 735887763267657999999963688762479999999878898987877---67761578733799 No 19 >1jbj_A CD3 epsilon and gamma ectodomain fragment complex; beta-sheet, C2-SET immunoglobulin superfamily, H-bonded G strand PAIR, single-chain; NMR {Mus musculus} SCOP: b.1.1.4 b.1.1.4 PDB: 1xmw_A Probab=29.24 E-value=18 Score=15.66 Aligned_cols=48 Identities=13% Similarity=0.272 Sum_probs=25.6 Q ss_pred EEEEECCCCCEECCCCCCCEEEEEC---CCCEEEEEEECCCCCEEEEEEEEE Q ss_conf 9999768896838888760389977---995089998637984058999999 Q T0612 76 KFTWYDINGATVEDEGVSWKSLKLH---GKQQMQVTALSPNATAVRCELYVR 124 (129) Q Consensus 76 rf~WyD~~Gl~v~~~~~~W~~l~l~---~~~~~~i~~vap~~~a~~~RlylR 124 (129) .+.||- +|-++.+....=..|.|. ....=...=.|-|...+.+++|+| T Consensus 135 ~i~W~k-~g~~i~~~~~~~~tL~i~~v~~~d~G~Y~C~a~N~~~~~~~v~~~ 185 (186) T 1jbj_A 135 TIKWLK-DGSIISPLNATKNTWNLGNNAKDPRGTYQCQGAKETSNPLQVYYR 185 (186) T ss_dssp CEEEEE-TTEECCCSSCCSSCCEEEETTSCCEEEEEEEESSCEEEEEEEECC T ss_pred EEEEEE-CCEECCCCCCCCCEEEECCCCHHCCEEEEEEEEECCCCCEEEEEE T ss_conf 379988-998965777564799999989113999999989899981999995 No 20 >2a3m_A COG3005: nitrate/TMAO reductases, membrane-bound tetraheme cytochrome C subunit; electron transport; HET: HEM; 1.50A {Desulfovibrio desulfuricans subsp} PDB: 2a3p_A* Probab=28.91 E-value=9 Score=17.38 Aligned_cols=18 Identities=33% Similarity=0.324 Sum_probs=14.2 Q ss_pred CHHHHHHHHHHHHHHCCC Q ss_conf 924889999988871457 Q T0612 1 MNKGLVLACLLLGLSACA 18 (129) Q Consensus 1 Mkk~l~~~~~~l~L~GCa 18 (129) |||.|+++.++.+.++.+ T Consensus 1 m~k~l~~~~vl~~~~~~~ 18 (130) T 2a3m_A 1 MRKSLFAVMVLALVAAFA 18 (130) T ss_dssp ------------------ T ss_pred CCHHHHHHHHHHHHHHHH T ss_conf 906899999999999998 No 21 >2p3y_A Hypothetical protein VPA0735; structural genomics, PSI-2, protein structure initiative; 1.80A {Vibrio parahaemolyticus rimd 2210633} SCOP: e.65.1.1 Probab=25.16 E-value=20 Score=15.42 Aligned_cols=18 Identities=28% Similarity=0.272 Sum_probs=7.7 Q ss_pred CHHHHHHH-HHHHHHHCCC Q ss_conf 92488999-9988871457 Q T0612 1 MNKGLVLA-CLLLGLSACA 18 (129) Q Consensus 1 Mkk~l~~~-~~~l~L~GCa 18 (129) |||-++.+ +++++|++|+ T Consensus 1 mkk~~l~~a~~~~~l~~~~ 19 (491) T 2p3y_A 1 MKKRILAVAVTSMLLSASV 19 (491) T ss_dssp ------------------- T ss_pred CCHHHHHHHHHHHHHHHHH T ss_conf 9178999999999877762 No 22 >1e9y_A Urease alpha subunit; hydrolase, dodecamer, acetohydroxamic acid; HET: KCX; 3.0A {Helicobacter pylori} SCOP: b.85.3.1 d.8.1.1 PDB: 1e9z_A* Probab=24.38 E-value=32 Score=14.23 Aligned_cols=73 Identities=7% Similarity=0.186 Sum_probs=50.0 Q ss_pred CCCCEEEEEEEEEEECCCEEEEEEEEEECCCCCEEEEEEEEEECCC-----------CCEECCCCCCCEEEEECCCCEEE Q ss_conf 2125047742102204874899999984668762899999997688-----------96838888760389977995089 Q T0612 38 SFHSDVDVSAVTTQAEAGFLRARGTIISKSPKDQRLQYKFTWYDIN-----------GATVEDEGVSWKSLKLHGKQQMQ 106 (129) Q Consensus 38 ~l~~~i~v~~~~~~~~~g~~~~~v~l~N~~~~~~~l~Yrf~WyD~~-----------Gl~v~~~~~~W~~l~l~~~~~~~ 106 (129) .+...+...+-.+....|+-...+.+.|+.+.|+++--.|-+|..| |+-.+ ..+. ..+.+-|+++.+ T Consensus 106 ~iPGei~~~~~~I~ln~gr~~~~l~V~N~GDRPIQVGSH~HF~E~N~aL~FDR~~a~G~RLd-IpaG-tavRFEPG~~k~ 183 (238) T 1e9y_A 106 LVPGELFLKNEDITINEGKKAVSVKVKNVGDRPVQIGSHFHFFEVNRCLDFDREKTFGKRLD-IAAG-TAVRFEPGEEKS 183 (238) T ss_dssp CCTTCEECCSCEEETTTTCCCCEEEEEECSSSCEEEETTSCGGGSCTTEESCGGGGTTEEEC-SSTT-CEEEECTTCEEE T ss_pred CCCCCEECCCCCCCCCCCCCEEEEEEECCCCCCEEECCCCCHHHCCCHHHCCHHHHCCCCCC-CCCC-CEEEECCCCEEE T ss_conf 68975545998601379986699999569987505436542453282010458772686436-6787-747668898048 Q ss_pred EEEECC Q ss_conf 998637 Q T0612 107 VTALSP 112 (129) Q Consensus 107 i~~vap 112 (129) +..+.- T Consensus 184 V~LV~~ 189 (238) T 1e9y_A 184 VELIDI 189 (238) T ss_dssp EEEEEC T ss_pred EEEEEC T ss_conf 999970 No 23 >1us5_A Putative GLUR0 ligand binding core; receptor, membrane protein, glutamate receptor, L-glutamate; HET: GLU; 1.5A {Thermus thermophilus} SCOP: c.94.1.1 PDB: 1us4_A* Probab=22.86 E-value=14 Score=16.19 Aligned_cols=23 Identities=26% Similarity=0.208 Sum_probs=14.3 Q ss_pred CHHHHHHHHHHHHHHCCCCCCCCCCC Q ss_conf 92488999998887145788667302 Q T0612 1 MNKGLVLACLLLGLSACAPHTGGIMI 26 (129) Q Consensus 1 Mkk~l~~~~~~l~L~GCas~~~~~~~ 26 (129) |||.++. +|+|+||+.....+.+ T Consensus 1 ~~~~ila---~l~~~g~a~A~~~l~i 23 (314) T 1us5_A 1 MRKPILA---ALTLAGLGLAQEFITI 23 (314) T ss_dssp -------------------CCEEEEE T ss_pred CCHHHHH---HHHHHHHHHHCCEEEE T ss_conf 9279999---9997335634413899 No 24 >2uxt_A Protein SUFI, SUFI; oxidoreductase, periplasmic, cupredoxin-like, FTS mutant suppressor; 1.90A {Escherichia coli} PDB: 2uxv_A Probab=21.22 E-value=37 Score=13.86 Aligned_cols=24 Identities=21% Similarity=0.219 Sum_probs=15.3 Q ss_pred EEEEECCCCEEEEEEECCCCCEEE Q ss_conf 389977995089998637984058 Q T0612 95 KSLKLHGKQQMQVTALSPNATAVR 118 (129) Q Consensus 95 ~~l~l~~~~~~~i~~vap~~~a~~ 118 (129) ..+.|.++|...|--.++.+.... T Consensus 242 ~~l~i~pGqR~dvlv~~~~~~~~~ 265 (451) T 2uxt_A 242 KQLSLAPGERREILVDMSNGDEVS 265 (451) T ss_dssp SSEEECTTCEEEEEEECTTCCCEE T ss_pred EEEEECCCCEEEEEEECCCCCCEE T ss_conf 589966885599999928998479 Done!