Query T0577 BvR155, , 116 residues
Match_columns 116
No_of_seqs 42 out of 44
Neff 2.9
Searched_HMMs 11830
Date Fri Jun 4 14:27:07 2010
Command /home/syshi_2/2008/ferredoxin/manualcheck/update/HHsearch/bin/hhsearch -i /home/syshi_3/CASP9/HHsearch4Targetseq/seq/T0577.hhm -d /home/syshi_2/2008/ferredoxin/manualcheck/update/HHsearch/database/pfamA_24_hhmdb -o /home/syshi_3/CASP9/HHsearch4Targetseq/pfamAsearch/T0577.hhr
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF04465 DUF499: Protein of un 50.9 6.8 0.00057 17.7 3.7 74 10-88 823-902 (1035)
2 PF07686 V-set: Immunoglobulin 39.3 11 0.00092 16.5 6.6 85 14-101 4-100 (114)
3 PF08980 DUF1883: Domain of un 33.3 7.6 0.00064 17.4 1.6 16 20-35 8-23 (94)
4 PF08022 FAD_binding_8: FAD-bi 29.8 14 0.0012 15.7 2.6 13 93-105 91-103 (105)
5 PF11512 Atu4866: Agrobacteriu 28.7 7.7 0.00065 17.4 1.0 25 27-51 13-43 (78)
6 PF00609 DAGK_acc: Diacylglyce 28.2 14 0.0012 15.7 2.4 26 20-56 135-160 (161)
7 PF07472 PA-IIL: Fucose-bindin 22.8 21 0.0017 14.7 2.3 25 77-103 6-31 (107)
8 PF07809 RTP801_C: RTP801 C-te 21.8 6.2 0.00052 18.0 -0.5 46 64-109 12-58 (116)
9 PF00116 COX2: Cytochrome C ox 21.8 9.9 0.00083 16.7 0.5 42 68-114 44-93 (120)
10 PF07610 DUF1573: Protein of u 20.6 20 0.0017 14.8 1.9 21 13-34 24-44 (45)
No 1
>PF04465 DUF499: Protein of unknown function (DUF499); InterPro: IPR007555 This is a family of uncharacterised hypothetical prokaryotic proteins.
Probab=50.92 E-value=6.8 Score=17.72 Aligned_cols=74 Identities=20% Similarity=0.219 Sum_probs=48.9
Q ss_pred CCCEEEEEECCHHCCCCCEEEEEEEEEECCCCCCCEEEEEEEEECCCEEEEECCCCE-----ECC-CCCCCCCCCEEEEE
Q ss_conf 686367722221204897389998870088604756899888658967988589836-----725-45663787539999
Q T0577 10 YPFTVESMPVADEIAGDETVEIRLEIKPSGNFIGTVYTLRYFQPDGKGSLKMEDGTV-----LKP-NDRYLLNEWKFRLY 83 (116)
Q Consensus 10 YpF~v~tmpv~k~I~~geTvEIRc~L~reG~y~~t~Y~IrYfQ~dG~G~L~~~dg~~-----l~p-nD~ypL~~~~FrLY 83 (116)
-.|.+++-|--=+..+||.+|+|..+++-|||..+.+-- -+ -|.|.-+.|.+ ..- +=.-|-.++.++++
T Consensus 823 ~~~~l~v~p~~v~~~p~e~~~~~v~~~~~~~~~~~v~l~----~~-~g~l~~~~~~~~~~~~~~~w~~~~~~~~~~~~i~ 897 (1035)
T PF04465_consen 823 GGFELEVEPSEVEGKPGEKIEVEVKIKPIGDYRFKVKLS----VN-YGELDSDEGILEGESFKVTWRITIPRERRIAKIR 897 (1035)
T ss_pred CCCEEEECHHHCCCCCCCEEEEEEEEEECCCCCEEEEEE----EC-CCEEEEEEEEECCCCCEEEEEEECCCCCCEEEEE
T ss_conf 573599642440379996389999987747773589997----31-5533310146616763479997325556427998
Q ss_pred EECCC
Q ss_conf 81368
Q T0577 84 YTSQS 88 (116)
Q Consensus 84 YtS~S 88 (116)
-.|-+
T Consensus 898 ~~~~~ 902 (1035)
T PF04465_consen 898 AKSDD 902 (1035)
T ss_pred EECCC
T ss_conf 52266
No 2
>PF07686 V-set: Immunoglobulin V-set domain; InterPro: IPR013106 The basic structure of immunoglobulin (Ig) molecules is a tetramer of two light chains and two heavy chains linked by disulphide bonds. There are two types of light chains: kappa and lambda, each composed of a constant domain (CL) and a variable domain (VL). There are five types of heavy chains: alpha, delta, epsilon, gamma and mu, all consisting of a variable domain (VH) and three (in alpha, delta and gamma) or four (in epsilon and mu) constant domains (CH1 to CH4). Ig molecules are highly modular proteins, in which the variable and constant domains have clear, conserved sequence patterns. The domains in Ig and Ig-like molecules are grouped into four types: V-set (variable; IPR013106 from INTERPRO), C1-set (constant-1; IPR003597 from INTERPRO), C2-set (constant-2; IPR008424 from INTERPRO) and I-set (intermediate; IPR013098 from INTERPRO) . Structural studies have shown that these domains share a common core Greek-key beta-sandwich structure, with the types differing in the number of strands in the beta-sheets as well as in their sequence patterns , . Immunoglobulin-like domains that are related in both sequence and structure can be found in several diverse protein families. Ig-like domains are involved in a variety of functions, including cell-cell recognition, cell-surface receptors, muscle structure and the immune system . This entry represents the V-set domains, which are Ig-like domains resembling the antibody variable domain. V-set domains are found in diverse protein families, including immunoglobulin light and heavy chains; in several T-cell receptors such as CD2 (Cluster of Differentiation 2), CD4, CD80, and CD86; in myelin membrane adhesion molecules; in junction adhesion molecules (JAM); in tyrosine-protein kinase receptors; and in the programmed cell death protein 1 (PD1).; PDB: 2dru_A 2ptv_A 2ptt_A 2edo_A 2if7_B 1xed_C 1u9k_A 1q8m_C 1smo_A 1hkf_A ....
Probab=39.33 E-value=11 Score=16.46 Aligned_cols=85 Identities=14% Similarity=0.120 Sum_probs=48.6
Q ss_pred EEEEECCHHCCCCCEEEEEEEEEECCCCCCCEEEEEEEEECCCEEEEEC----CCCEECCCCCCC--------CCCCEEE
Q ss_conf 6772222120489738999887008860475689988865896798858----983672545663--------7875399
Q T0577 14 VESMPVADEIAGDETVEIRLEIKPSGNFIGTVYTLRYFQPDGKGSLKME----DGTVLKPNDRYL--------LNEWKFR 81 (116)
Q Consensus 14 v~tmpv~k~I~~geTvEIRc~L~reG~y~~t~Y~IrYfQ~dG~G~L~~~----dg~~l~pnD~yp--------L~~~~Fr 81 (116)
|..=|-+.....|++|+|.|... . -.......-|++..|.+...+- ......+...|. .....|.
T Consensus 4 v~~~~~~v~~~~G~~v~L~C~~~-~--~~~~~~v~W~~~~~~~~~~~i~~~~~~~~~~~~~~~~~~r~~~~~~~~~~~~~ 80 (114)
T PF07686_consen 4 VTQPPTPVTVKEGDSVTLPCSYS-S--PDKNQSVYWYKQSPGSGPQQIIYYSSSSGRPIVSPQYKGRVSLSGNGSNGNFS 80 (114)
T ss_dssp EEEEESEEEEETTSEEEEEEEEE-S--SGGGSEEEEEEEETTSEEEEEEEETTTEEEEEESTTEETTEEEEEETTTTEEE
T ss_pred EEEECCCEEEECCCCEEEEEEEC-C--CCCCEEEEEEEECCCCCCEEEEEEECCCCCEECCCCCCEEEEEEEECCCCEEE
T ss_conf 79909838997199799999987-8--88750899999379998367667743655300177640269997606798999
Q ss_pred EEEECCCCCCCCEEEEEEEE
Q ss_conf 99813688756327999982
Q T0577 82 LYYTSQSDKEAQTIDLYFED 101 (116)
Q Consensus 82 LYYtS~S~~~~qtidv~v~D 101 (116)
|--.+....|+-....-+..
T Consensus 81 L~I~~~~~~D~G~Y~C~v~~ 100 (114)
T PF07686_consen 81 LTISNLTPSDSGTYTCQVSS 100 (114)
T ss_dssp EEESSETGGGEEEEEEEEEE
T ss_pred EEECCCCHHHCEEEEEEEEE
T ss_conf 99889983679999999988
No 3
>PF08980 DUF1883: Domain of unknown function (DUF1883); InterPro: IPR015073 This protein is found in a set of hypothetical bacterial proteins.
Probab=33.29 E-value=7.6 Score=17.41 Aligned_cols=16 Identities=13% Similarity=0.131 Sum_probs=13.2
Q ss_pred CHHCCCCCEEEEEEEE
Q ss_conf 2120489738999887
Q T0577 20 ADEIAGDETVEIRLEI 35 (116)
Q Consensus 20 ~k~I~~geTvEIRc~L 35 (116)
-+..+.|++|||+|.-
T Consensus 8 ~~~~~~Gd~V~V~ls~ 23 (94)
T PF08980_consen 8 LGHQRAGDIVVVTLSQ 23 (94)
T ss_pred HHHHCCCCEEEEEECC
T ss_conf 5400489889999568
No 4
>PF08022 FAD_binding_8: FAD-binding domain; InterPro: IPR013112 This FAD binding domain is associated with ferric reductase NAD binding proteins and the heavy chain of Cytochrome b-245.
Probab=29.85 E-value=14 Score=15.69 Aligned_cols=13 Identities=31% Similarity=0.692 Sum_probs=6.2
Q ss_pred CEEEEEEEECCCC
Q ss_conf 3279999828996
Q T0577 93 QTIDLYFEDNWGN 105 (116)
Q Consensus 93 qtidv~v~Dnfgq 105 (116)
..+.++|+--+|.
T Consensus 91 ~~~~v~ieGPYG~ 103 (105)
T PF08022_consen 91 VRIRVYIEGPYGS 103 (105)
T ss_pred CCEEEEEECCCCC
T ss_conf 8579999988999
No 5
>PF11512 Atu4866: Agrobacterium tumefaciens protein Atu4866
Probab=28.69 E-value=7.7 Score=17.37 Aligned_cols=25 Identities=32% Similarity=0.464 Sum_probs=18.6
Q ss_pred CEEEEEEEEEECCCCCCCE------EEEEEE
Q ss_conf 7389998870088604756------899888
Q T0577 27 ETVEIRLEIKPSGNFIGTV------YTLRYF 51 (116)
Q Consensus 27 eTvEIRc~L~reG~y~~t~------Y~IrYf 51 (116)
..-.||-+|-..|+|.+|| |+=||-
T Consensus 13 ~DG~Ir~ELlp~GRYdEaRg~r~sAyqGrY~ 43 (78)
T PF11512_consen 13 ADGRIRHELLPNGRYDEARGNRESAYQGRYE 43 (78)
T ss_pred CCCCEEEEECCCCCCHHHCCCCCCCCEEEEE
T ss_conf 7972431205798513321786331102789
No 6
>PF00609 DAGK_acc: Diacylglycerol kinase accessory domain; InterPro: IPR000756 Protein kinases are a group of enzymes that possess a catalytic subunit which transfers the gamma phosphate from nucleotide triphosphates (often ATP) to one or more amino acid residues in a protein substrate side chain, resulting in a conformational change affecting protein function. The enzymes fall into two broad classes, characterised with respect to substrate specificity: serine/threonine specific and tyrosine specific . Protein kinase function has been evolutionarily conserved from Escherichia coli to Homo sapiens. Protein kinases play a role in a mulititude of cellular processes, including division, proliferation, apoptosis, and differentiation . Phosphorylation usually results in a functional change of the target protein by changing enzyme activity, cellular location, or association with other proteins. The catalytic subunits of protein kinases are highly conserved, and several structures have been solved , leading to large screens to develop kinase-specific inhibitors for the treatments of a number of diseases . Diacylglycerol (DAG) is a second messenger that acts as a protein kinase C activator. The DAG kinase domain is assumed to be an accessory domain. Upon cell stimulation, DAG kinase converts DAG into phosphatidate, initiating the resynthesis of phosphatidylinositols and attenuating protein kinase C activity. It catalyzes the reaction: ATP + 1,2-diacylglycerol = ADP + 1,2-diacylglycerol 3-phosphate. The enzyme is stimulated by calcium and phosphatidylserine and phosphorylated by protein kinase C. This domain is always associated with IPR001206 from INTERPRO.; GO: 0004143 diacylglycerol kinase activity, 0007205 protein kinase C activation
Probab=28.22 E-value=14 Score=15.69 Aligned_cols=26 Identities=31% Similarity=0.346 Sum_probs=16.4
Q ss_pred CHHCCCCCEEEEEEEEEECCCCCCCEEEEEEEEECCC
Q ss_conf 2120489738999887008860475689988865896
Q T0577 20 ADEIAGDETVEIRLEIKPSGNFIGTVYTLRYFQPDGK 56 (116)
Q Consensus 20 ~k~I~~geTvEIRc~L~reG~y~~t~Y~IrYfQ~dG~ 56 (116)
+++|+ |..+||++++.+ -=|||.||+
T Consensus 135 ~~rl~--Q~~~i~i~~~~~---------~~~~QvDGE 160 (161)
T PF00609_consen 135 PIRLA--QGRPIRITTKKD---------KIPFQVDGE 160 (161)
T ss_pred CEEEE--CCCEEEEEECCC---------CEEEEECCC
T ss_conf 64874--077699998667---------510783899
No 7
>PF07472 PA-IIL: Fucose-binding lectin II (PA-IIL); InterPro: IPR010907 This entry represents calcium-mediated lectins. Structures have been determined for both fucose-binding lectin II (PA-IIL) and mannose-specific lectin II (RS-IIL) . These proteins have homologous structures, their monomers consisting of a 9-stranded beta sandwich with Greek-key topology. Each monomer contains two calcium ions that mediate an exceptionally high binding affinity to the monosaccharide ligand in a recognition mode unique among carbohydrate-protein interactions. In Pseudomonas aeruginosa, PA-IIL contributes to the pathogenic virulence of the bacterium, functioning as a tetramer when binding fucose . In the plant pathogen Ralstonia solanacearum (Pseudomonas solanacearum), RS-IIL recognises fucose, but displays much higher affinity to mannose and fructose, which is opposite to the preference of PA-IIL. ; PDB: 2vnv_E 2boi_B 2bv4_B 2chh_A 1uqx_A 1w8h_A 2boj_C 1our_A 1ous_D 1oux_B ....
Probab=22.75 E-value=21 Score=14.74 Aligned_cols=25 Identities=28% Similarity=0.575 Sum_probs=14.7
Q ss_pred CCEEEE-EEECCCCCCCCEEEEEEEECC
Q ss_conf 753999-981368875632799998289
Q T0577 77 EWKFRL-YYTSQSDKEAQTIDLYFEDNW 103 (116)
Q Consensus 77 ~~~FrL-YYtS~S~~~~qtidv~v~Dnf 103 (116)
...|.+ .|.+.+ .+|+|+|||-|.-
T Consensus 6 ni~Fgvta~~Nsa--~~Qti~v~iDd~~ 31 (107)
T PF07472_consen 6 NIRFGVTAYANSA--HQQTIKVYIDDDP 31 (107)
T ss_dssp T-EEEEEEEEECS--S-EEEEEEETTEE
T ss_pred CCEEEEEEEECCC--CCEEEEEEECCCH
T ss_conf 5168499996168--7327999978820
No 8
>PF07809 RTP801_C: RTP801 C-terminal region; InterPro: IPR012918 The members of this family are sequences similar to the C-terminal region of RTP801, the protein product of a hypoxia-inducible factor 1 (HIF-1)- responsive gene . Two members of this family expressed by Drosophila melanogaster, Scylla (Q9NHN4 from SWISSPROT) and Charybde (Q9NHN5 from SWISSPROT), are designated as Hox targets . RTP801 is thought to be involved in various cellular processes . Over expression of the gene caused the apoptosis-resistant phenotype in cycling cells, and apoptosis sensitivity in growth arrested cells . Moreover, the protein product of the mouse homolog of RTP801 (dig2 (Q9D3F7 from SWISSPROT)) is thought to be induced by diverse apoptotic signals, and also by dexamethasone treatment . ; GO: 0009968 negative regulation of signal transduction, 0005737 cytoplasm
Probab=21.80 E-value=6.2 Score=17.97 Aligned_cols=46 Identities=26% Similarity=0.258 Sum_probs=32.5
Q ss_pred CCEECCCCCCC-CCCCEEEEEEECCCCCCCCEEEEEEEECCCCEEEE
Q ss_conf 83672545663-78753999981368875632799998289965999
Q T0577 64 GTVLKPNDRYL-LNEWKFRLYYTSQSDKEAQTIDLYFEDNWGNLQQL 109 (116)
Q Consensus 64 g~~l~pnD~yp-L~~~~FrLYYtS~S~~~~qtidv~v~Dnfgq~~ql 109 (116)
.-+++|+|+-+ ...+++||=+.--|+-..-+|++.+||.-++.+++
T Consensus 12 t~vllP~~L~~~Ia~evlrlS~~EPCGlRGc~i~i~~E~e~~~~~~i 58 (116)
T PF07809_consen 12 TEVLLPEDLTPRIAQEVLRLSESEPCGLRGCTIYIEFEDEPKNCRRI 58 (116)
T ss_pred EEEECCHHHHHHHHHHHHHHHCCCCCCCCEEEEEEEECCCCCCEEEE
T ss_conf 36766188889999999986037987631028999974587501352
No 9
>PF00116 COX2: Cytochrome C oxidase subunit II, periplasmic domain This family corresponds to chains b and o.; InterPro: IPR002429 Cytochrome c oxidase (1.9.3.1 from EC) , is an oligomeric enzymatic complex which is a component of the respiratory chain and is involved in the transfer of electrons from cytochrome c to oxygen. In eukaryotes this enzyme complex is located in the mitochondrial inner membrane; in aerobic prokaryotes it is found in the plasma membrane. The number of polypeptides in the complex ranges from 3-4 (prokaryotes), up to 13(mammals). Subunit 2 (CO II) transfers the electrons from cytochrome c to the catalytic subunit 1. It contains two adjacent transmembrane regions in its N-terminus and the major part of the protein is exposed to the periplasmic or to the mitochondrial intermembrane space, respectively. CO II provides the substrate-binding site and contains a copper centre called Cu(A), probably the primary acceptor in cytochrome c oxidase. An exception is the corresponding subunit of the cbb3-type oxidase which lacks the copper A redox-centre. Several bacterial CO II have a C-terminal extension that contains a covalently bound heme c.; GO: 0004129 cytochrome-c oxidase activity, 0005507 copper ion binding, 0006118 electron transport, 0016020 membrane; PDB: 2iwk_A 2iwf_A 1fwx_B 1qni_D 2zxw_B 1ocz_O 1v55_O 2ein_B 1ocr_B 2eil_O ....
Probab=21.77 E-value=9.9 Score=16.71 Aligned_cols=42 Identities=21% Similarity=0.278 Sum_probs=19.2
Q ss_pred CCCCCCCCCCCEEEEEEECCCCCCCCEEEEEEEECC--------CCEEEEEEEEC
Q ss_conf 254566378753999981368875632799998289--------96599998635
Q T0577 68 KPNDRYLLNEWKFRLYYTSQSDKEAQTIDLYFEDNW--------GNLQQLTYDFN 114 (116)
Q Consensus 68 ~pnD~ypL~~~~FrLYYtS~S~~~~qtidv~v~Dnf--------gq~~ql~f~Fn 114 (116)
.||.+..-..+.-+|--||. + .-.++- | .++ |+...+.|.++
T Consensus 44 ~~~~l~lp~g~~v~~~ltS~-D-ViHsF~--i-p~l~ik~d~~PG~~~~~~~~~~ 93 (120)
T PF00116_consen 44 TPNELVLPVGEPVRFLLTSS-D-VIHSFW--I-PELGIKMDAIPGRVNSVTFTPD 93 (120)
T ss_dssp BSSSEEEETTSEEEEEEEES-S-S-EEEE--E-TTGTEEEEE-TT-EEEEEEE-S
T ss_pred CCEEEEEECCCCCEEEEECC-C-EECCCC--C-CCCCCCCCCCCCCCCEEEEECC
T ss_conf 11367741366424677057-5-164403--7-7657221324324320223416
No 10
>PF07610 DUF1573: Protein of unknown function (DUF1573); InterPro: IPR011467 These hypothetical proteins from bacteria, such as Rhodopirellula baltica, Bacteroides thetaiotaomicron and Porphyromonas gingivalis, share a region of conserved sequence towards their N termini.
Probab=20.59 E-value=20 Score=14.81 Aligned_cols=21 Identities=29% Similarity=0.317 Sum_probs=14.3
Q ss_pred EEEEEECCHHCCCCCEEEEEEE
Q ss_conf 3677222212048973899988
Q T0577 13 TVESMPVADEIAGDETVEIRLE 34 (116)
Q Consensus 13 ~v~tmpv~k~I~~geTvEIRc~ 34 (116)
+...++- +.|++||+.+|+.+
T Consensus 24 t~~~~~k-~~i~PGes~~i~v~ 44 (45)
T PF07610_consen 24 TTAEYSK-KPIAPGESGEIKVT 44 (45)
T ss_pred EEECCCC-CEECCCCEEEEEEE
T ss_conf 8605776-40889998899998
Done!