Query 002653
Match_columns 896
No_of_seqs 123 out of 236
Neff 2.7
Searched_HMMs 29240
Date Tue Mar 26 16:26:50 2013
Command hhsearch -i /local_scratch/syshi/lefta3m/002653.a3m -d /local_scratch/syshi/pdb70.hhm -v 0 -o /local_scratch/syshi/H1_1370-1374//hhsearch_pdb/002653hhsearch_pdb
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 1v54_D Cytochrome C oxidase su 1.0 1 1 20.9 3.5 37 844-882 94-131 (147)
2 2y69_D Cytochrome C oxidase su 1.0 1 1 20.5 3.5 37 844-882 116-153 (169)
3 2wj8_A Nucleoprotein; RNA bind 1.0 1 1 18.8 -2.0 106 229-337 197-302 (391)
4 1deq_A Fibrinogen (alpha chain 1.0 1 1 16.8 4.2 31 849-879 210-243 (390)
5 1s9u_A Putative component of a 1.0 1 1 15.9 1.7 97 288-413 80-191 (207)
6 1n1c_A TORA specific chaperone 1.0 1 1 15.6 2.2 108 288-413 83-196 (217)
7 3u8p_A Cytochrome B562 integra 1.0 1 1 14.9 -2.7 15 451-466 155-169 (347)
8 3iqt_A Signal transduction his 1.0 1 1 14.7 3.6 48 561-608 40-92 (123)
9 2kk1_A Tyrosine-protein kinase 1.0 1 1 14.6 2.8 38 572-612 91-128 (135)
10 1zzp_A P150, C-ABL, proto-onco 1.0 1 1 14.4 1.3 39 572-612 83-121 (130)
No 1
>1v54_D Cytochrome C oxidase subunit IV isoform 1; oxidoreductase; HET: FME TPO HEA TGL PGV CHD CDL PEK PSC DMU; 1.80A {Bos taurus} SCOP: f.23.1.1 PDB: 1oco_D* 1occ_D* 1ocz_D* 1ocr_D* 1v55_D* 2dyr_D* 2dys_D* 2eij_D* 2eik_D* 2eil_D* 2eim_D* 2ein_D* 2occ_D* 2ybb_O* 2zxw_D* 3abk_D* 3abl_D* 3abm_D* 3ag1_D* 3ag2_D* ...
Probab=1.00 E-value=1 Score=20.92 Aligned_cols=37 Identities=22% Similarity=0.398 Sum_probs=25.4
Q ss_pred HHHHHHHHC-CCCCCCCCCHHHHHHHHHHHHHHHHHHCCC
Q ss_conf 999999981-998899885028999999999985320268
Q 002653 844 MLAAIQRYV-PGLIPSTYGPERLDLLRQLEKVKEMESSEV 882 (896)
Q Consensus 844 LLPvilKlF-PnMLPSTFeseR~e~lrkL~kvKkme~~e~ 882 (896)
++-+++|.| -.-+|-||+.+.+ .+++++++.|.++-.
T Consensus 94 ~~f~~~r~~v~~p~P~T~~~Ewq--eaq~erm~~~~~nPi 131 (147)
T 1v54_D 94 LLLIWEKHYVYGPIPHTFEEEWV--AKQTKRMLDMKVAPI 131 (147)
T ss_dssp HHHHHHHHHTCCCCCGGGSHHHH--HHHHHHHHHTTSSTT
T ss_pred HHHHHHHHHCCCCCCCCCCHHHH--HHHHHHHHHCCCCCC
T ss_conf 99999999706999998999999--999999998068998
No 2
>2y69_D Cytochrome C oxidase subunit 4 isoform 1; electron transport, complex IV, proton pumps, membrane prote; HET: TPO HEA CHD PEK PGV DMU; 1.95A {Bos taurus}
Probab=1.00 E-value=1 Score=20.48 Aligned_cols=37 Identities=22% Similarity=0.398 Sum_probs=25.4
Q ss_pred HHHHHHHHC-CCCCCCCCCHHHHHHHHHHHHHHHHHHCCC
Q ss_conf 999999981-998899885028999999999985320268
Q 002653 844 MLAAIQRYV-PGLIPSTYGPERLDLLRQLEKVKEMESSEV 882 (896)
Q Consensus 844 LLPvilKlF-PnMLPSTFeseR~e~lrkL~kvKkme~~e~ 882 (896)
++-+++|.| -.-+|-||+.+.+ .+++++++.|.++-.
T Consensus 116 ~~f~~~r~~v~~p~P~T~~~Ewq--eaq~erml~~~~NPi 153 (169)
T 2y69_D 116 LLLIWEKHYVYGPIPHTFEEEWV--AKQTKRMLDMKVAPI 153 (169)
T ss_dssp HHHHHHHHHTCCCCCGGGSHHHH--HHHHHHHHHTTSSTT
T ss_pred HHHHHHHHHCCCCCCCCCCHHHH--HHHHHHHHHCCCCCC
T ss_conf 99999999706999998999999--999999998278998
No 3
>2wj8_A Nucleoprotein; RNA binding protein RNA complex, nucleocapsid (N), ribonucleoprotein, respiratory syncytial virus (RSV); 3.29A {Human respiratory syncytial virus astrain long} PDB: 2yhm_A 2yhp_A 2yhq_A
Probab=1.00 E-value=1 Score=18.78 Aligned_cols=106 Identities=14% Similarity=0.144 Sum_probs=64.5
Q ss_pred HHCCCCHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHCCCCCCCCCCCHHHHHHHHHH
Q ss_conf 43025402566734100126333200001357865689998852689999999999852188621244310235678997
Q 002653 229 FWSEQVPAVVTSFINYFERDQRFTAATAVSGKGMSLGSGSSSDTSLLMLALTCIAAITKLGPAKVSCSQFSSMISDITGR 308 (896)
Q Consensus 229 fws~Q~P~vv~sFvn~le~d~rf~~at~~~~~~~~~~~~~~SdvslL~Lalsc~aAi~kLGsa~vSCp~F~S~i~d~~gr 308 (896)
|--...|.++.||-..||+.+.|-..---|++..... +.||-+..|.+.|++.|-- -|.+-.-|-..--..-.|.--
T Consensus 197 yp~~~~~~ia~sfyelfe~k~yy~~~fi~~g~a~~s~-~~gsk~e~lf~~ifm~ayg--agq~mlrwgviars~~nimlg 273 (391)
T 2wj8_A 197 YKGLLPKDIANSFYEVFEKHPHFIDVFVHFGIAQSST-RGGSRVEGIFAGLFMNAYG--AGQVMLRWGVLAKSVKNIMLG 273 (391)
T ss_dssp CTTCCHHHHHHHHHHHHHHCHHHHHHHHHHHHHHTTS-SCCCHHHHHHHHHHHTTTT--TTCHHHHHHHHHHHTTCGGGG
T ss_pred CCCCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHHCCC-CCCCHHHHHHHHHHHHHHC--CCCCEEEEHHHHHCCCCEEEE
T ss_conf 7788879999999999851606778898860553478-7772178899999998615--640102002311104555530
Q ss_pred HHHHHCCCEEHHHHHHHHHHHHHHHHHHH
Q ss_conf 89640024011358888864223477775
Q 002653 309 LMDTLVDLVPISQAYYSIKDIGLHREFLA 337 (896)
Q Consensus 309 LMdml~~fvpv~q~Y~~~k~iGl~rEFL~ 337 (896)
-.-..-|+--|.++|.+....|=+--||-
T Consensus 274 h~svqae~~qv~evy~~~~k~G~EsG~~H 302 (391)
T 2wj8_A 274 HASVQAEMEQVVEVYEYAQKLGGEAGFYH 302 (391)
T ss_dssp SHHHHHHHHHHHHHHHHHHHHGGGGGGTT
T ss_pred HHHHHHHHHHHHHHHHHHHHHCCCCHHHH
T ss_conf 11889999999999999998686410035
No 4
>1deq_A Fibrinogen (alpha chain); coiled-coil, blood clotting; 3.50A {Bos taurus} SCOP: i.9.1.1
Probab=1.00 E-value=1 Score=16.84 Aligned_cols=31 Identities=10% Similarity=0.210 Sum_probs=22.5
Q ss_pred HHHCCCCCCCCCCHH---HHHHHHHHHHHHHHHH
Q ss_conf 998199889988502---8999999999985320
Q 002653 849 QRYVPGLIPSTYGPE---RLDLLRQLEKVKEMES 879 (896)
Q Consensus 849 lKlFPnMLPSTFese---R~e~lrkL~kvKkme~ 879 (896)
.+-||.++|+-|.++ ..-.++++..+++|..
T Consensus 210 ~~p~kd~vP~~fKsq~q~a~~Ew~al~~~~Qm~~ 243 (390)
T 1deq_A 210 MSTITGPVPREFKSQLQEAPLEWKALLEMQQTKM 243 (390)
T ss_pred CCCCCCCCCHHHCCCCCCCCHHHHHHHHHHHHEE
T ss_conf 4556555874431444113667899986664500
No 5
>1s9u_A Putative component of anaerobic dehydrogenases; structural genomics, anaerobic dehydrogenases component, PSI structure initiative; 1.38A {Salmonella typhimurium} SCOP: a.184.1.1 PDB: 3efp_A 3cw0_A
Probab=1.00 E-value=1 Score=15.88 Aligned_cols=97 Identities=18% Similarity=0.192 Sum_probs=51.3
Q ss_pred CCCCCCCCCCCHHHHHHHHHHHHHHH----------CCCEEHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCE
Q ss_conf 18862124431023567899789640----------02401135888886422347777520987545566687786321
Q 002653 288 LGPAKVSCSQFSSMISDITGRLMDTL----------VDLVPISQAYYSIKDIGLHREFLAHFGPRASACRVKNDRDSEEV 357 (896)
Q Consensus 288 LGsa~vSCp~F~S~i~d~~grLMdml----------~~fvpv~q~Y~~~k~iGl~rEFL~hFGpraa~~~~~~d~~~eEv 357 (896)
+|+.+.++|++-|.-.+.-|++|... .++.+-.......-+||+..||+.+.
T Consensus 80 ~g~~~~~~~py~S~yl~~e~~l~g~~~~~l~~~y~~~Gl~~~~~~~ep~Dhi~~~Lef~a~L------------------ 141 (207)
T 1s9u_A 80 IGPYALPSPPWGSVWLDRESVLFGDSTLALRQWMRENGIQFEMQQNEPEDHFGSLLLLAAWL------------------ 141 (207)
T ss_dssp TCSSCCSSCCBHHHHHSTTCCSSCHHHHHHHHHHHHTTCC------CCTTBHHHHHHHHHHH------------------
T ss_pred CCCCCCCCCCCEEEECCCCCCCCCHHHHHHHHHHHHCCCCCCCCCCCCCCHHHHHHHHHHHH------------------
T ss_conf 89998807980103328877656789999999999869988889999977999999999999------------------
Q ss_pred EHHHHHHHH---HHHHHHHHHHH--HHCCCCCHHHHHHHHHHHHHHHHHHHCCCHHHHHHC
Q ss_conf 044999999---99999968644--302555224899864345788998731101342201
Q 002653 358 IFWVDLVQK---QLQRAIDREKI--WSRLTTSESIEVLERDLAIFGFFIALGRSTQSFLSR 413 (896)
Q Consensus 358 ~FWV~L~qk---qL~~AidRE~I--wsrL~tsesiEvlE~dLAifGfFiaLGRsTr~fLs~ 413 (896)
+.+ ..++.+-.+-+ |.. .=.+.++. -+..+|+.++++=++.||..
T Consensus 142 ------~~~~~~~~~~~fl~~hL~~W~~----~f~~~~~~-~~~~~fY~~la~l~~~fl~~ 191 (207)
T 1s9u_A 142 ------AENDRHHECEQLLAWHLFPWSS----RFLDVFID-HAGHPFYQALGQLARLTLAQ 191 (207)
T ss_dssp ------HHTTCHHHHHHHHHHHTHHHHH----HHHHHHHH-HCCSHHHHHHHHHHHHHHHH
T ss_pred ------HCCCCHHHHHHHHHHHHHHHHH----HHHHHHHH-CCCCCHHHHHHHHHHHHHHH
T ss_conf ------8189899999999999999999----99999986-55983999999999999999
No 6
>1n1c_A TORA specific chaperone; TORD, 3D-domain swapping; 2.40A {Shewanella massilia} SCOP: a.184.1.1
Probab=1.00 E-value=1 Score=15.60 Aligned_cols=108 Identities=19% Similarity=0.163 Sum_probs=59.4
Q ss_pred CCCCCCCCCCCHHHHHHHH--HHHHHHHCCCEEHHHHHHHHHHHHHHHHHHHHCCCCCC-CCCCCCCCCCCCEEHHHHHH
Q ss_conf 1886212443102356789--97896400240113588888642234777752098754-55666877863210449999
Q 002653 288 LGPAKVSCSQFSSMISDIT--GRLMDTLVDLVPISQAYYSIKDIGLHREFLAHFGPRAS-ACRVKNDRDSEEVIFWVDLV 364 (896)
Q Consensus 288 LGsa~vSCp~F~S~i~d~~--grLMdml~~fvpv~q~Y~~~k~iGl~rEFL~hFGpraa-~~~~~~d~~~eEv~FWV~L~ 364 (896)
+|+.+.++|++-|.-.+.- +++|.... +.+ |+|+..+|=... .++.-.|+=.-+.+|--.|+
T Consensus 83 ~g~~~~~~~pyeS~yl~~~~e~~l~g~~~--~~l-------------~~~y~~~Gl~~~~~~~Ep~DHi~~~Lefma~L~ 147 (217)
T 1n1c_A 83 LVGTKHSASPYASLYLSGEDEPLLFGEQH--QQM-------------SEFLHQSKLQVQSHFPEPADHLAVMLAYMAHLC 147 (217)
T ss_dssp TSCC--CCCCBGGGGC------CCSGGGH--HHH-------------HHHHHHHCCCCCCSSCCGGGBHHHHHHHHHHHH
T ss_pred CCCCCCCCCCEEEEEECCCCCCCCCCHHH--HHH-------------HHHHHHCCCEECCCCCCCCCHHHHHHHHHHHHH
T ss_conf 89999855984324647875566673899--999-------------999999689008899999538999999999999
Q ss_pred HHH---HHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHCCCHHHHHHC
Q ss_conf 999---9999968644302555224899864345788998731101342201
Q 002653 365 QKQ---LQRAIDREKIWSRLTTSESIEVLERDLAIFGFFIALGRSTQSFLSR 413 (896)
Q Consensus 365 qkq---L~~AidRE~IwsrL~tsesiEvlE~dLAifGfFiaLGRsTr~fLs~ 413 (896)
.+. .++.+-.+-+-.=.. .=.+.++. -+..+|+.++++=|+.|+..
T Consensus 148 ~~~~~~~q~~Fl~~HL~~W~~--~f~~~l~~-~~~~~FY~~la~l~~~fl~~ 196 (217)
T 1n1c_A 148 CHSENSVQLSFLQTCVNSWLA--KFINHLTQ-CNKNGFYSAVATLTLAWVKQ 196 (217)
T ss_dssp HHSCHHHHHHHHHHHTTTTHH--HHHHHHHH-HCSSCHHHHHHHHHHHHHHH
T ss_pred HCCCHHHHHHHHHHHHHHHHH--HHHHHHHH-CCCCCHHHHHHHHHHHHHHH
T ss_conf 767699999999999999999--99999981-65672999999999999999
No 7
>3u8p_A Cytochrome B562 integral fusion with enhanced GRE fluorescent protein; directed evolution, domain insertion, energy transfer, fluor quenching; HET: CRO HEM; 2.75A {Aequorea victoria}
Probab=1.00 E-value=1 Score=14.87 Aligned_cols=15 Identities=13% Similarity=0.140 Sum_probs=6.6
Q ss_pred EEEEECCCCCCCCCCC
Q ss_conf 2132122454335789
Q 002653 451 VEVVCEELDWLLFYPG 466 (896)
Q Consensus 451 vEVVcEEl~WLpFYp~ 466 (896)
+-.||+. +=|||-..
T Consensus 155 ~K~v~t~-GPLPFs~d 169 (347)
T 3u8p_A 155 LKFICTT-GKLPVPWP 169 (347)
T ss_dssp EEEEETT-SSCSSCGG
T ss_pred EEEEECC-CCCCCCHH
T ss_conf 9999817-88787488
No 8
>3iqt_A Signal transduction histidine-protein kinase BARA; histidine phosphotransfer domain, HTP, structural genomics, protein structure initiative; HET: MSE BTB; 1.40A {Escherichia coli}
Probab=1.00 E-value=1 Score=14.71 Aligned_cols=48 Identities=31% Similarity=0.451 Sum_probs=35.2
Q ss_pred HHHHHHHHHHHHHHH-----HHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHH
Q ss_conf 169997788999999-----999998776224685327899986413999998
Q 002653 561 DSFDKALESVEEALI-----RLEKLLQALHVSSSNSGKEQLKAACSDLEKIRK 608 (896)
Q Consensus 561 ~s~dkalesv~~Al~-----rlE~Llqel~~sss~sgke~l~aacsDLekIr~ 608 (896)
.+..+.++.++.|+- .+..+.-.+|-++++.|...|+++|..||..-|
T Consensus 40 ~~~~~~~~~l~~a~~~~d~~~l~~~aHkLkGaa~~~Ga~~L~~~c~~LE~~~r 92 (123)
T 3iqt_A 40 DFLPEVRNKVEEQLVGENPEGLVDLIHKLHGSCGYSGVPRMKNLCQLIEQQLR 92 (123)
T ss_dssp HHHHHHHHHHHHHHTTCCCTTHHHHHHHHHHHHTTSCCHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHH
T ss_conf 87799999999998867899999999999899998389999999999999987
No 9
>2kk1_A Tyrosine-protein kinase ABL2; methods development, tyrosin protein kinase ABL2, F-actin binding domain, NESG, alternative splicing, ATP-binding; NMR {Homo sapiens}
Probab=1.00 E-value=1 Score=14.62 Aligned_cols=38 Identities=34% Similarity=0.410 Sum_probs=0.0
Q ss_pred HHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHHHH
Q ss_conf 99999999987762246853278999864139999987888
Q 002653 572 EALIRLEKLLQALHVSSSNSGKEQLKAACSDLEKIRKLKKE 612 (896)
Q Consensus 572 ~Al~rlE~Llqel~~sss~sgke~l~aacsDLekIr~Lkke 612 (896)
||+-|||..+|||-++|...| -.++-+|+.+.-.--||
T Consensus 91 EavsrLe~slqeL~~~sa~ag---~p~~~~~~n~LLssVKE 128 (135)
T 2kk1_A 91 EAVSKLELSLQELQVSSAAAG---VPGTNPVLNNLLSCVQE 128 (135)
T ss_dssp HHHHHHHHHHHHHHHSCSSSS---CTTCCTHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHCCCCCCCC---CCCCCHHHHHHHHHHHH
T ss_conf 999998889999646887779---99888889999999999
No 10
>1zzp_A P150, C-ABL, proto-oncogene tyrosine-protein kinase ABL1; four helix bundle, nuclear export signal, transferase; NMR {Homo sapiens}
Probab=1.00 E-value=1 Score=14.45 Aligned_cols=39 Identities=33% Similarity=0.438 Sum_probs=0.0
Q ss_pred HHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHHHH
Q ss_conf 99999999987762246853278999864139999987888
Q 002653 572 EALIRLEKLLQALHVSSSNSGKEQLKAACSDLEKIRKLKKE 612 (896)
Q Consensus 572 ~Al~rlE~Llqel~~sss~sgke~l~aacsDLekIr~Lkke 612 (896)
||.-|||+-+|||-+++++.|- --++-.||.|+-.--||
T Consensus 83 eAv~klE~sl~elq~~~a~~gg--~p~a~~~~s~LlssVkE 121 (130)
T 1zzp_A 83 EAINKLENNLRELQICPATAGS--GPAATQDFSKLLSSVKE 121 (130)
T ss_dssp HHHHHHHHHHHHHSCCSSSSCS--SSCCCCCCHHHHHHHHH
T ss_pred HHHHHHHCCHHHHHCCCCCCCC--CCCCCHHHHHHHHHHHH
T ss_conf 9998740498998617545689--99875789999999999
Done!