Query T0552 BtR376, , 122 residues
Match_columns 122
No_of_seqs 48 out of 50
Neff 2.9
Searched_HMMs 11830
Date Fri May 21 18:06:21 2010
Command /home/syshi_2/2008/ferredoxin/manualcheck/update/HHsearch/bin/hhsearch -i /home/syshi_3/CASP9/HHsearch4Targetseq/pfamAsearch/hhm/T0552.hhm -d /home/syshi_2/2008/ferredoxin/manualcheck/update/HHsearch/database/pfamA_24_hhmdb -o /home/syshi_3/CASP9/HHsearch4Targetseq/pfamAsearch/hhm/T0552.hhr
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF04465 DUF499: Protein of un 47.8 8.1 0.00068 17.3 3.7 73 12-89 824-902 (1035)
2 PF07686 V-set: Immunoglobulin 42.1 9.9 0.00084 16.8 6.8 46 15-63 4-49 (114)
3 PF07705 CARDB: CARDB; InterP 33.8 13 0.0011 16.0 9.9 82 12-100 3-84 (101)
4 PF08770 SoxZ: Sulphur oxidati 33.5 14 0.0012 15.9 7.8 83 20-112 5-99 (100)
5 PF08980 DUF1883: Domain of un 30.5 9 0.00076 17.1 1.6 16 21-36 8-23 (94)
6 PF08022 FAD_binding_8: FAD-bi 30.2 15 0.0012 15.8 2.7 16 90-105 88-103 (105)
7 PF00609 DAGK_acc: Diacylglyce 29.1 14 0.0012 15.9 2.4 26 21-57 135-160 (161)
8 PF07472 PA-IIL: Fucose-bindin 26.2 14 0.0011 16.0 1.9 25 79-103 7-31 (107)
9 PF11512 Atu4866: Agrobacteriu 24.5 10 0.00086 16.7 1.0 24 29-52 14-43 (78)
10 PF00116 COX2: Cytochrome C ox 19.9 11 0.0009 16.6 0.4 46 69-115 44-94 (120)
No 1
>PF04465 DUF499: Protein of unknown function (DUF499); InterPro: IPR007555 This is a family of uncharacterised hypothetical prokaryotic proteins.
Probab=47.80 E-value=8.1 Score=17.33 Aligned_cols=73 Identities=18% Similarity=0.240 Sum_probs=49.7
Q ss_pred CCEEEEEECCHHCCCCCEEEEEEEEEECCCCCCCEEEEEEEEECCCEEEEECCCCE-----ECC-CCCCCCCCCEEEEEE
Q ss_conf 85368732331204897379998871078604756899888668967988589846-----625-556517887189998
Q T0552 12 PFSIETMPVPKKLKVGETAEIRCQLHRDGRFEETKYFIRYFQPDGAGTLKMSDGTV-----LLP-NDLYPLPGETFRLYY 85 (122)
Q Consensus 12 pF~v~tmPv~k~I~~GetvEIRc~L~reG~y~~t~Y~IRYFQ~dG~G~L~~~dg~~-----l~p-nD~ypL~~e~FrLYY 85 (122)
.|.+++-|--=+..+|+.+|+|..+++-|||..+.+--. + -|.|.-+.|.+ ..- +=.-|-.++.++++-
T Consensus 824 ~~~l~v~p~~v~~~p~e~~~~~v~~~~~~~~~~~v~l~~----~-~g~l~~~~~~~~~~~~~~~w~~~~~~~~~~~~i~~ 898 (1035)
T PF04465_consen 824 GFELEVEPSEVEGKPGEKIEVEVKIKPIGDYRFKVKLSV----N-YGELDSDEGILEGESFKVTWRITIPRERRIAKIRA 898 (1035)
T ss_pred CCEEEECHHHCCCCCCCEEEEEEEEEECCCCCEEEEEEE----C-CCEEEEEEEEECCCCCEEEEEEECCCCCCEEEEEE
T ss_conf 735996424403799963899999877477735899973----1-55333101466167634799973255564279985
Q ss_pred CCCC
Q ss_conf 0368
Q T0552 86 TSAS 89 (122)
Q Consensus 86 tS~s 89 (122)
.|-+
T Consensus 899 ~~~~ 902 (1035)
T PF04465_consen 899 KSDD 902 (1035)
T ss_pred ECCC
T ss_conf 2266
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=42.14 E-value=9.9 Score=16.79 Aligned_cols=46 Identities=20% Similarity=0.450 Sum_probs=33.4
Q ss_pred EEEEECCHHCCCCCEEEEEEEEEECCCCCCCEEEEEEEEECCCEEEEEC
Q ss_conf 6873233120489737999887107860475689988866896798858
Q T0552 15 IETMPVPKKLKVGETAEIRCQLHRDGRFEETKYFIRYFQPDGAGTLKMS 63 (122)
Q Consensus 15 v~tmPv~k~I~~GetvEIRc~L~reG~y~~t~Y~IRYFQ~dG~G~L~~~ 63 (122)
|..-|-+.....|++|+|.|... . -.......-|++..|.+...+-
T Consensus 4 v~~~~~~v~~~~G~~v~L~C~~~-~--~~~~~~v~W~~~~~~~~~~~i~ 49 (114)
T PF07686_consen 4 VTQPPTPVTVKEGDSVTLPCSYS-S--PDKNQSVYWYKQSPGSGPQQII 49 (114)
T ss_dssp EEEEESEEEEETTSEEEEEEEEE-S--SGGGSEEEEEEEETTSEEEEEE
T ss_pred EEEECCCEEEECCCCEEEEEEEC-C--CCCCEEEEEEEECCCCCCEEEE
T ss_conf 79909838997199799999987-8--8875089999937999836766
No 3
>PF07705 CARDB: CARDB; InterPro: IPR011635 The APHP (acidic peptide-dependent hydrolases/peptidase) domain is found in a variety of different proteins.
Probab=33.82 E-value=13 Score=15.98 Aligned_cols=82 Identities=18% Similarity=0.311 Sum_probs=54.7
Q ss_pred CCEEEEEECCHHCCCCCEEEEEEEEEECCCCCCCEEEEEEEEECCCEEEEECCCCEECCCCCCCCCCCEEEEEECCCCCC
Q ss_conf 85368732331204897379998871078604756899888668967988589846625556517887189998036887
Q T0552 12 PFSIETMPVPKKLKVGETAEIRCQLHRDGRFEETKYFIRYFQPDGAGTLKMSDGTVLLPNDLYPLPGETFRLYYTSASTD 91 (122)
Q Consensus 12 pF~v~tmPv~k~I~~GetvEIRc~L~reG~y~~t~Y~IRYFQ~dG~G~L~~~dg~~l~pnD~ypL~~e~FrLYYtS~s~~ 91 (122)
++.|..-..|.....|+.+.|.++++-.|...-.-..+++. .+|... +...+ ..+-|=+.....+..+.....
T Consensus 3 DL~I~~~~~~~~~~~g~~~~i~~~V~N~G~~~a~~~~v~~~-~~~~~~-----~~~~i-~~L~~g~~~~v~~~~~~~~~G 75 (101)
T PF07705_consen 3 DLTISISVSPSSPTPGESVTITVTVKNQGTADAENVTVSFY-LDGDLV-----STVTI-PSLAPGESATVTFTWTPPTSG 75 (101)
T ss_pred CEEEEEECCCCCCCCCCEEEEEEEEEECCCCCCCCEEEEEE-ECCCCC-----CCEEE-CCCCCCCEEEEEEEEEECCCC
T ss_conf 78999601788556898899999999778776665899999-899820-----67794-448899689999998717898
Q ss_pred CCEEEEEEE
Q ss_conf 742799998
Q T0552 92 QQTVDVYFQ 100 (122)
Q Consensus 92 ~q~idv~ve 100 (122)
..++.+.+.
T Consensus 76 ~~~l~~~iD 84 (101)
T PF07705_consen 76 NYTLTAVID 84 (101)
T ss_pred EEEEEEEEE
T ss_conf 199999995
No 4
>PF08770 SoxZ: Sulphur oxidation protein SoxZ; InterPro: IPR014880 SoxZ forms an anti parallel beta structure and forms a complex with SoxY. Sulphur oxidation occurs at the thiol of a conserved cysteine residue of the SoxY subunit . ; PDB: 2ox5_Z 2oxh_E 2oxg_E 1v8h_A.
Probab=33.52 E-value=14 Score=15.95 Aligned_cols=83 Identities=17% Similarity=0.322 Sum_probs=55.8
Q ss_pred CCHHCCCCCEEEEEEEEEE----------CCCCCCCEEEEEEEEE--CCCEEEEECCCCEECCCCCCCCCCCEEEEEECC
Q ss_conf 3312048973799988710----------7860475689988866--896798858984662555651788718999803
Q T0552 20 VPKKLKVGETAEIRCQLHR----------DGRFEETKYFIRYFQP--DGAGTLKMSDGTVLLPNDLYPLPGETFRLYYTS 87 (122)
Q Consensus 20 v~k~I~~GetvEIRc~L~r----------eG~y~~t~Y~IRYFQ~--dG~G~L~~~dg~~l~pnD~ypL~~e~FrLYYtS 87 (122)
+|+.-..|+.+|+|+-+.- .|.+-.+ .+|..++. +|+-.+.++-|...-. +-.|+.++..
T Consensus 5 ~p~~~~~g~v~~v~~li~HPMetGlrkd~tg~~iPa-~~I~~~~~~~ng~~v~~~~~~~svS~-------NP~~~F~~~~ 76 (100)
T PF08770_consen 5 MPRAAKKGDVVEVRLLISHPMETGLRKDQTGKLIPA-HYIEEVEVTYNGKPVFSADWGPSVSE-------NPYLRFKFKG 76 (100)
T ss_dssp -SSCEE---EEEEEEEE----B---BB-----BB---B-EEEEEEEE---EEEEEEE-TTB-S-------S-EEEEEEE-
T ss_pred CCCHHCCCCCEEEEEEEECCCCCCCCCCCCCCCCCH-HHEEEEEEEECCEEEEEEEECCCCCC-------CCCEEEEEEC
T ss_conf 552004899599999998988643411778889775-85589999999999999884885237-------9808999704
Q ss_pred CCCCCCEEEEEEEECCCCEEEEEEE
Q ss_conf 6887742799998288865899985
Q T0552 88 ASTDQQTVDVYFQDSFGQLQQLTFS 112 (122)
Q Consensus 88 ~s~~~q~idv~veDnfgq~~ql~f~ 112 (122)
.... ++.+...||-|+..+-+..
T Consensus 77 ~~~g--~l~v~~~Dn~G~~~~~~~~ 99 (100)
T PF08770_consen 77 KKAG--TLTVTWTDNKGNSFEAEVK 99 (100)
T ss_dssp S------EEEEEEE----EEEEEE-
T ss_pred CCCC--EEEEEEEECCCCEEEEEEE
T ss_conf 8897--6999999799999888885
No 5
>PF08980 DUF1883: Domain of unknown function (DUF1883); InterPro: IPR015073 This protein is found in a set of hypothetical bacterial proteins.
Probab=30.47 E-value=9 Score=17.05 Aligned_cols=16 Identities=6% Similarity=0.113 Sum_probs=13.2
Q ss_pred CHHCCCCCEEEEEEEE
Q ss_conf 3120489737999887
Q T0552 21 PKKLKVGETAEIRCQL 36 (122)
Q Consensus 21 ~k~I~~GetvEIRc~L 36 (122)
-+....|++|||+|.-
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 6
>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=30.21 E-value=15 Score=15.78 Aligned_cols=16 Identities=19% Similarity=0.625 Sum_probs=7.9
Q ss_pred CCCCEEEEEEEECCCC
Q ss_conf 8774279999828886
Q T0552 90 TDQQTVDVYFQDSFGQ 105 (122)
Q Consensus 90 ~~~q~idv~veDnfgq 105 (122)
.....+.++|+--+|.
T Consensus 88 ~~~~~~~v~ieGPYG~ 103 (105)
T PF08022_consen 88 SQSVRIRVYIEGPYGS 103 (105)
T ss_pred CCCCCEEEEEECCCCC
T ss_conf 6888579999988999
No 7
>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=29.12 E-value=14 Score=15.92 Aligned_cols=26 Identities=35% Similarity=0.437 Sum_probs=16.9
Q ss_pred CHHCCCCCEEEEEEEEEECCCCCCCEEEEEEEEECCC
Q ss_conf 3120489737999887107860475689988866896
Q T0552 21 PKKLKVGETAEIRCQLHRDGRFEETKYFIRYFQPDGA 57 (122)
Q Consensus 21 ~k~I~~GetvEIRc~L~reG~y~~t~Y~IRYFQ~dG~ 57 (122)
+++|++ ..+||++++.+ -=|||.||+
T Consensus 135 ~~rl~Q--~~~i~i~~~~~---------~~~~QvDGE 160 (161)
T PF00609_consen 135 PIRLAQ--GRPIRITTKKD---------KIPFQVDGE 160 (161)
T ss_pred CEEEEC--CCEEEEEECCC---------CEEEEECCC
T ss_conf 648740--77699998667---------510783899
No 8
>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=26.23 E-value=14 Score=15.96 Aligned_cols=25 Identities=32% Similarity=0.387 Sum_probs=14.3
Q ss_pred CEEEEEECCCCCCCCEEEEEEEECC
Q ss_conf 7189998036887742799998288
Q T0552 79 ETFRLYYTSASTDQQTVDVYFQDSF 103 (122)
Q Consensus 79 e~FrLYYtS~s~~~q~idv~veDnf 103 (122)
-.|.+---.-|+.+|+|+|||-|.-
T Consensus 7 i~Fgvta~~Nsa~~Qti~v~iDd~~ 31 (107)
T PF07472_consen 7 IRFGVTAYANSAHQQTIKVYIDDDP 31 (107)
T ss_dssp -EEEEEEEEECSS-EEEEEEETTEE
T ss_pred CEEEEEEEECCCCCEEEEEEECCCH
T ss_conf 1684999961687327999978820
No 9
>PF11512 Atu4866: Agrobacterium tumefaciens protein Atu4866
Probab=24.45 E-value=10 Score=16.72 Aligned_cols=24 Identities=38% Similarity=0.677 Sum_probs=18.1
Q ss_pred EEEEEEEEEECCCCCCCE------EEEEEE
Q ss_conf 379998871078604756------899888
Q T0552 29 TAEIRCQLHRDGRFEETK------YFIRYF 52 (122)
Q Consensus 29 tvEIRc~L~reG~y~~t~------Y~IRYF 52 (122)
.-.||-+|...|+|.+|+ |+=||-
T Consensus 14 DG~Ir~ELlp~GRYdEaRg~r~sAyqGrY~ 43 (78)
T PF11512_consen 14 DGRIRHELLPNGRYDEARGNRESAYQGRYE 43 (78)
T ss_pred CCCEEEEECCCCCCHHHCCCCCCCCEEEEE
T ss_conf 972431205798513321786331102789
No 10
>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=19.93 E-value=11 Score=16.60 Aligned_cols=46 Identities=26% Similarity=0.331 Sum_probs=23.3
Q ss_pred CCCCCCCCCCCEEEEEECCCCCCCCEEEEE-----EEECCCCEEEEEEEECC
Q ss_conf 255565178871899980368877427999-----98288865899985348
Q T0552 69 LPNDLYPLPGETFRLYYTSASTDQQTVDVY-----FQDSFGQLQQLTFSFNN 115 (122)
Q Consensus 69 ~pnD~ypL~~e~FrLYYtS~s~~~q~idv~-----veDnfgq~~ql~f~Fnn 115 (122)
.||.+..-..+.-+|--|| ++.-++|-|- +.-.=|+...+.|.++.
T Consensus 44 ~~~~l~lp~g~~v~~~ltS-~DViHsF~ip~l~ik~d~~PG~~~~~~~~~~~ 94 (120)
T PF00116_consen 44 TPNELVLPVGEPVRFLLTS-SDVIHSFWIPELGIKMDAIPGRVNSVTFTPDK 94 (120)
T ss_dssp BSSSEEEETTSEEEEEEEE-SSS-EEEEETTGTEEEEE-TT-EEEEEEE-S-
T ss_pred CCEEEEEECCCCCEEEEEC-CCEECCCCCCCCCCCCCCCCCCCCEEEEECCC
T ss_conf 1136774136642467705-75164403776572213243243202234167
Done!