Query T0549 CvR118A, , 84 residues
Match_columns 84
No_of_seqs 101 out of 205
Neff 5.7
Searched_HMMs 11830
Date Fri May 21 18:05:38 2010
Command /home/syshi_2/2008/ferredoxin/manualcheck/update/HHsearch/bin/hhsearch -i /home/syshi_3/CASP9/HHsearch4Targetseq/pfamAsearch/hhm/T0549.hhm -d /home/syshi_2/2008/ferredoxin/manualcheck/update/HHsearch/database/pfamA_24_hhmdb -o /home/syshi_3/CASP9/HHsearch4Targetseq/pfamAsearch/hhm/T0549.hhr
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF04384 DUF528: Protein of un 84.2 0.14 1.2E-05 27.8 1.2 44 26-69 3-46 (64)
2 PF00538 Linker_histone: linke 63.6 3 0.00026 20.1 3.6 37 8-45 4-41 (77)
3 PF06479 Ribonuc_2-5A: Ribonuc 53.9 2.8 0.00023 20.4 2.1 54 2-60 17-70 (129)
4 PF01885 PTS_2-RNA: RNA 2'-pho 38.9 4.1 0.00035 19.4 1.0 55 8-67 11-70 (185)
5 PF10264 Stork_head: Winged he 36.3 13 0.0011 16.5 4.9 64 2-65 5-70 (80)
6 PF05480 Staph_haemo: Staphylo 32.1 7.9 0.00066 17.8 1.6 27 7-34 2-28 (43)
7 PF09421 FRQ: Frequency clock 21.3 7.7 0.00065 17.8 -0.1 40 18-66 470-514 (989)
8 PF09079 Cdc6_C: CDC6, C termi 17.1 31 0.0026 14.4 5.2 57 23-81 12-75 (85)
9 PF02387 IncFII_repA: IncFII R 16.3 15 0.0013 16.2 0.5 61 12-81 93-156 (281)
10 PF02504 FA_synthesis: Fatty a 16.2 32 0.0027 14.3 2.1 41 7-49 242-282 (323)
No 1
>PF04384 DUF528: Protein of unknown function (DUF528); InterPro: IPR007479 Iron-sulphur (FeS) clusters are important cofactors for numerous proteins involved in electron transfer, in redox and non-redox catalysis, in gene regulation, and as sensors of oxygen and iron. These functions depend on the various FeS cluster prosthetic groups, the most common being [2Fe-2S] and [4Fe-4S] . FeS cluster assembly is a complex process involving the mobilisation of Fe and S atoms from storage sources, their assembly into [Fe-S] form, their transport to specific cellular locations, and their transfer to recipient apoproteins. So far, three FeS assembly machineries have been identified, which are capable of synthesising all types of [Fe-S] clusters: ISC (iron-sulphur cluster), SUF (sulphur assimilation), and NIF (nitrogen fixation) systems. The ISC system is conserved in eubacteria and eukaryotes (mitochondria), and has broad specificity, targeting general FeS proteins , . It is encoded by the isc operon (iscRSUA-hscBA-fdx-iscX). IscS is a cysteine desulphurase, which obtains S from cysteine (converting it to alanine) and serves as a S donor for FeS cluster assembly. IscU and IscA act as scaffolds to accept S and Fe atoms, assembling clusters and transfering them to recipient apoproteins. HscA is a molecular chaperone and HscB is a co-chaperone. Fdx is a [2Fe-2S]-type ferredoxin. IscR is a transcription factor that regulates expression of the isc operon. IscX (also known as YfhJ) appears to interact with IscS and may function as an Fe donor during cluster assembly . The SUF system is an alternative pathway to the ISC system that operates under iron starvation and oxidative stress. It is found in eubacteria, archaea and eukaryotes (plastids). The SUF system is encoded by the suf operon (sufABCDSE), and the six encoded proteins are arranged into two complexes (SufSE and SufBCD) and one protein (SufA). SufS is a pyridoxal-phosphate (PLP) protein displaying cysteine desulphurase activity. SufE acts as a scaffold protein that accepts S from SufS and donates it to SufA . SufC is an ATPase with an unorthodox ATP-binding cassette (ABC)-like component. No specific functions have been assigned to SufB and SufD. SufA is homologous to IscA , acting as a scaffold protein in which Fe and S atoms are assembled into [FeS] cluster forms, which can then easily be transferred to apoproteins targets. In the NIF system, NifS and NifU are required for the formation of metalloclusters of nitrogenase in Azotobacter vinelandii, and other organisms, as well as in the maturation of other FeS proteins. Nitrogenase catalyses the fixation of nitrogen. It contains a complex cluster, the FeMo cofactor, which contains molybdenum, Fe and S. NifS is a cysteine desulphurase. NifU binds one Fe atom at its N-terminal, assembling an FeS cluster that is transferred to nitrogenase apoproteins . Nif proteins involved in the formation of FeS clusters can also be found in organisms that do not fix nitrogen . This entry represents IscX proteins (also known as hypothetical protein YfhJ) that are part of the ISC system. IscX is active as a monomer. The structure of YfhJ is an orthogonal alpha-bundle . YfhJ is a small acidic protein that binds IscS, and contains a modified winged helix motif that is usually found in DNA-binding proteins . YfhJ/IscX can bind Fe, and may function as an Fe donor in the assembly of FeS clusters ; GO: 0016226 iron-sulfur cluster assembly; PDB: 1uj8_A 2bzt_A.
Probab=84.15 E-value=0.14 Score=27.75 Aligned_cols=44 Identities=23% Similarity=0.312 Sum_probs=38.1
Q ss_pred EEEHHHHHHHHHHCCCCCCCCCCCCHHHHHHHHHCCCEEEEEEC
Q ss_conf 06388899898741799983305722388999865861366402
Q T0549 26 WAELSAVGSYLAKNDPSFDPRNWGHGRLSQMVKKLDFLTVQESR 69 (84)
Q Consensus 26 W~~l~~vG~~l~k~~PdFdpR~YG~~kls~li~a~~~fei~~~~ 69 (84)
|...-.++-.|...+|+.||++--|-.|.++|-+++-|+=+-..
T Consensus 3 W~D~~~IA~~L~e~~pd~DP~~vrFtdL~~wv~~L~~FdDdp~~ 46 (64)
T PF04384_consen 3 WTDSEDIAIELYEKYPDVDPLTVRFTDLHQWVLELPDFDDDPNR 46 (64)
T ss_dssp TT-TTT---HHHHHSTTS-CCC--HHHHHHHHHCSTT--S-CCG
T ss_pred CCCHHHHHHHHHHHCCCCCCCEECHHHHHHHHHHCCCCCCCCCC
T ss_conf 64699999999988889894722099999999848676888563
No 2
>PF00538 Linker_histone: linker histone H1 and H5 family; InterPro: IPR005818 Linker histone H1 is an essential component of chromatin structure. H1 links nucleosomes into higher order structures. Histone H5 performs the same function as histone H1, and replaces H1 in certain cells. The structure of GH5, the globular domain of the linker histone H5 is known , . The fold is similar to the DNA-binding domain of the catabolite gene activator protein, CAP, thus providing a possible model for the binding of GH5 to DNA.; GO: 0003677 DNA binding, 0006334 nucleosome assembly, 0000786 nucleosome, 0005634 nucleus; PDB: 1ust_A 1uhm_A 1uss_A 1yqa_A 1ghc_A 1hst_A.
Probab=63.60 E-value=3 Score=20.12 Aligned_cols=37 Identities=30% Similarity=0.578 Sum_probs=31.1
Q ss_pred HHHHHHHHHHHHHCCCCCEEEHHHHHHHHHHCCC-CCCC
Q ss_conf 7899999999873057880638889989874179-9983
Q T0549 8 PLQDMFTSAIEAVARDSGWAELSAVGSYLAKNDP-SFDP 45 (84)
Q Consensus 8 ~l~~ll~~Ai~~~~dedGW~~l~~vG~~l~k~~P-dFdp 45 (84)
+...+|.+||.++.+..| +++.++-.||..++| +.++
T Consensus 4 ~y~~MI~eAI~~l~er~G-sS~~aI~kyI~~~y~~~~~~ 41 (77)
T PF00538_consen 4 PYSEMILEAITALKERKG-SSRQAIKKYIESNYPVDLPP 41 (77)
T ss_dssp -HHHHHHHHHHTTTTT----THHHHHHHHHHHSTTSSSH
T ss_pred CHHHHHHHHHHHCCCCCC-CCHHHHHHHHHHHCCCCCCH
T ss_conf 889999999997588799-79999999999865778876
No 3
>PF06479 Ribonuc_2-5A: Ribonuclease 2-5A; InterPro: IPR010513 This domain is found in a group of endoribonucleases . Specifically, these enzymes cleave an intron from Hac1 mRNA in humans, which cause it to be much more efficiently translated.; GO: 0016891 endoribonuclease activity, producing 5'-phosphomonoesters, 0006397 mRNA processing; PDB: 2rio_B 3fbv_D.
Probab=53.89 E-value=2.8 Score=20.36 Aligned_cols=54 Identities=17% Similarity=0.396 Sum_probs=33.4
Q ss_pred CCCCCHHHHHHHHHHHHHHCCCCCEEEHHHHHHHHHHCCCCCCCCCCCCHHHHHHHHHC
Q ss_conf 88531578999999998730578806388899898741799983305722388999865
Q T0549 2 PHKEKHPLQDMFTSAIEAVARDSGWAELSAVGSYLAKNDPSFDPRNWGHGRLSQMVKKL 60 (84)
Q Consensus 2 p~~~~~~l~~ll~~Ai~~~~dedGW~~l~~vG~~l~k~~PdFdpR~YG~~kls~li~a~ 60 (84)
|+...++++..|......+-. ..|..- +...+...--.| |.|-+.++.||++++
T Consensus 17 ~r~~~s~~L~~Le~~~~~v~~-~~W~~k--ld~~l~~~l~k~--RkY~~~sv~DLLR~I 70 (129)
T PF06479_consen 17 PRDPPSPLLQALESNAPDVVG-GDWTKK--LDPELMDNLGKY--RKYDGDSVRDLLRAI 70 (129)
T ss_dssp -TTTT-HHHHHHH---TTTS----GGGG--SBHHHHHTTTTT--S---TT-HHHHHHHH
T ss_pred CCCCCHHHHHHHHHCCCCCCC-CCHHHH--CCHHHHHHHHHC--CCCCCCCHHHHHHHH
T ss_conf 678973999998804767668-528888--279999999841--787846599999999
No 4
>PF01885 PTS_2-RNA: RNA 2'-phosphotransferase, Tpt1 / KptA family; InterPro: IPR002745 The final step of tRNA splicing in Saccharomyces cerevisiae requires 2'-phosphotransferase (Tpt1) to transfer the 2'-phosphate from ligated tRNA to NAD, producing mature tRNA and ADP ribose-1' '-2' '-cyclic phosphate. Yeast and mouse Tpt1 protein and bacterial KptA protein can catalyze the conversion of the generated intermediate to both product and the original substrate, these enzymes likely use the same reaction mechanism. Step 1 of this reaction is strikingly similar to the ADP-ribosylation of proteins catalyzed by a number of bacterial toxins. KptA, a functional Tpt1 protein homologue from Escherichia coli is strikingly similar to yeast Tpt1 in its kinetic parameters, although Escherichia coli is not known to have a 2'-phosphorylated RNA substrate ,.; GO: 0016772 transferase activity, transferring phosphorus-containing groups, 0006388 tRNA splicing; PDB: 1wfx_A.
Probab=38.90 E-value=4.1 Score=19.39 Aligned_cols=55 Identities=11% Similarity=0.099 Sum_probs=35.7
Q ss_pred HHHHHHHHHH---HHHCCCCCEEEHHHHHHHHHHCCCCCCCCCCCCHHHHHHHHHC--CCEEEEE
Q ss_conf 7899999999---8730578806388899898741799983305722388999865--8613664
Q T0549 8 PLQDMFTSAI---EAVARDSGWAELSAVGSYLAKNDPSFDPRNWGHGRLSQMVKKL--DFLTVQE 67 (84)
Q Consensus 8 ~l~~ll~~Ai---~~~~dedGW~~l~~vG~~l~k~~PdFdpR~YG~~kls~li~a~--~~fei~~ 67 (84)
.|--+||.+- .-..|++||+.+..+=..+... .+..-...+..+|++. ..||+..
T Consensus 11 ~LS~lLRH~p~~~gL~~d~~G~v~v~~ll~~~~~~-----~~~~t~~~i~~vV~~~~K~Rfel~~ 70 (185)
T PF01885_consen 11 FLSYLLRHGPEKEGLPMDPDGWVSVDDLLKHLRIK-----GRWVTREDIREVVATDDKQRFELRY 70 (185)
T ss_dssp HH----SS--------------B-HHHHH------------TT--HHHH---TTT-----EEE--
T ss_pred HHHHHHCCCHHHCCCCCCCCCCEEHHHHHHHHHHC-----CCCCCHHHHHHHHHHCCCCCEEEEE
T ss_conf 99999677986779956899779899999768871-----8999999999999729998879882
No 5
>PF10264 Stork_head: Winged helix Storkhead-box1 domain
Probab=36.31 E-value=13 Score=16.52 Aligned_cols=64 Identities=17% Similarity=0.185 Sum_probs=51.8
Q ss_pred CCCCCHHHHHHHHHHHHHHCCCCCEEEHHHHHHHHHHCCCCCCCCCC--CCHHHHHHHHHCCCEEE
Q ss_conf 88531578999999998730578806388899898741799983305--72238899986586136
Q T0549 2 PHKEKHPLQDMFTSAIEAVARDSGWAELSAVGSYLAKNDPSFDPRNW--GHGRLSQMVKKLDFLTV 65 (84)
Q Consensus 2 p~~~~~~l~~ll~~Ai~~~~dedGW~~l~~vG~~l~k~~PdFdpR~Y--G~~kls~li~a~~~fei 65 (84)
++.+=-+|-++|..||-++.....=|+...+-++|.+.+|..-+=+- =|..|..|+++-.++-.
T Consensus 5 ~Q~qfiPL~EvlC~aI~dln~~~~~at~e~l~~~L~~~~p~i~~Ps~e~~~~tL~~L~~e~kIY~t 70 (80)
T PF10264_consen 5 SQSQFIPLGEVLCDAIADLNSQGQPATQEALRQHLTKHFPGIQIPSTEVLYNTLGTLIKERKIYHT 70 (80)
T ss_pred CCCCEEEHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHCCCEEEC
T ss_conf 302410489999999999862798504999999999869899998689999999999971632547
No 6
>PF05480 Staph_haemo: Staphylococcus haemolytic protein; InterPro: IPR008846 This family consists of several different short Staphylococcal proteins, it contains SLUSH A, B and C proteins as well as haemolysin and gonococcal growth inhibitor. Some strains of the coagulase-negative Staphylococcus lugdunensis produce a synergistic hemolytic activity (SLUSH), phenotypically similar to the delta-hemolysin of S. aureus . Gonococcal growth inhibitor from Staphylococcus acts on the cytoplasmic membrane of the gonococcal cell causing cytoplasmic leakage and, eventually, death .; GO: 0009405 pathogenesis
Probab=32.08 E-value=7.9 Score=17.78 Aligned_cols=27 Identities=19% Similarity=0.320 Sum_probs=19.9
Q ss_pred HHHHHHHHHHHHHHCCCCCEEEHHHHHH
Q ss_conf 5789999999987305788063888998
Q T0549 7 HPLQDMFTSAIEAVARDSGWAELSAVGS 34 (84)
Q Consensus 7 ~~l~~ll~~Ai~~~~dedGW~~l~~vG~ 34 (84)
++|.+.|++++++..+ ..|+.||.=--
T Consensus 2 ~~l~eAI~~tV~Ag~~-~Dwa~lgtsIv 28 (43)
T PF05480_consen 2 SKLFEAIKNTVQAGQN-QDWAKLGTSIV 28 (43)
T ss_pred CHHHHHHHHHHHHHHH-CCHHHHHHHHH
T ss_conf 1799999999999983-64999978999
No 7
>PF09421 FRQ: Frequency clock protein
Probab=21.32 E-value=7.7 Score=17.82 Aligned_cols=40 Identities=15% Similarity=0.361 Sum_probs=25.0
Q ss_pred HHHCCCCCEEEHHHHHHHHH----HCCCCCCCCCCCCHHHHHHHHH-CCCEEEE
Q ss_conf 87305788063888998987----4179998330572238899986-5861366
Q T0549 18 EAVARDSGWAELSAVGSYLA----KNDPSFDPRNWGHGRLSQMVKK-LDFLTVQ 66 (84)
Q Consensus 18 ~~~~dedGW~~l~~vG~~l~----k~~PdFdpR~YG~~kls~li~a-~~~fei~ 66 (84)
+..-|.+||+.|..++|..+ ..-|+| .++-|.+ ...|++-
T Consensus 470 D~apdadGWVYLNLL~NmAQLHiiNVTP~F---------IR~AV~E~StkfQLS 514 (989)
T PF09421_consen 470 DVAPDADGWVYLNLLCNMAQLHIINVTPDF---------IRSAVSEKSTKFQLS 514 (989)
T ss_pred CCCCCCCCEEEHHHHHHHHHHHEECCCHHH---------HHHHHHHCCCCEEEC
T ss_conf 567676643334767767777400378899---------999987426643567
No 8
>PF09079 Cdc6_C: CDC6, C terminal ; InterPro: IPR015163 The C terminal domain of CDC6 assumes a winged helix fold, with a five alpha-helical bundle (alpha15-alpha19) structure, backed on one side by three beta strands (beta6-beta8). It has been shown that this domain acts as a DNA-localisation factor, however its exact function is, as yet, unknown. Putative functions include: (1) mediation of protein-protein interactions and (2) regulation of nucleotide binding and hydrolysis. Mutagenesis studies have shown that this domain is essential for appropriate Cdc6 activity . ; PDB: 2qby_B 2v1u_A 1w5t_C 1w5s_A 1fnn_A.
Probab=17.12 E-value=31 Score=14.41 Aligned_cols=57 Identities=18% Similarity=0.200 Sum_probs=35.6
Q ss_pred CCCEEEHHHHHHHHHHCCC--CCCCCCCCCHHHHHHHHHC---CCEEEEEECCC--CCCEEEEEEE
Q ss_conf 7880638889989874179--9983305722388999865---86136640289--9724788752
Q T0549 23 DSGWAELSAVGSYLAKNDP--SFDPRNWGHGRLSQMVKKL---DFLTVQESRNG--SKLHSEIRLR 81 (84)
Q Consensus 23 edGW~~l~~vG~~l~k~~P--dFdpR~YG~~kls~li~a~---~~fei~~~~~~--~~~~~~ir~r 81 (84)
...|+..+.|=..-...-- +.||.++ ..+++++..+ ++.++++...| .+....+.+.
T Consensus 12 ~~~~~~~~~vy~~Y~~lc~~~~~~pls~--~r~~~~l~~L~~~gli~~~~~~~G~~~G~~~~~~L~ 75 (85)
T PF09079_consen 12 GREEVTTGEVYEQYEELCEKIGVDPLSQ--RRFSDILSELEMLGLIESERKSRGRGRGRTREISLN 75 (85)
T ss_dssp -SSSEE-HHHHHHHHHHHHHCTS----H--HHHHHHHHHHHH---EEEEEE--------EEEEEEE
T ss_pred CCCCCCHHHHHHHHHHHHHHHCCCCCCH--HHHHHHHHHHHHCCCEEEEECCCCCCCCEEEEEEEC
T ss_conf 9986308999999999999848999989--999999999985787034332688888815899856
No 9
>PF02387 IncFII_repA: IncFII RepA protein family; InterPro: IPR003446 These proteins are plasmid encoded and essential for plasmid replication, they are also involved in copy control functions .; GO: 0006276 plasmid maintenance
Probab=16.32 E-value=15 Score=16.17 Aligned_cols=61 Identities=18% Similarity=0.352 Sum_probs=38.4
Q ss_pred HHHHHHHHHCCCCCEEEHHHHHHHHHHCCCCCCCCCCCCHHHHHHHHHCCCEEEEEE---CCCCCCEEEEEEE
Q ss_conf 999999873057880638889989874179998330572238899986586136640---2899724788752
Q T0549 12 MFTSAIEAVARDSGWAELSAVGSYLAKNDPSFDPRNWGHGRLSQMVKKLDFLTVQES---RNGSKLHSEIRLR 81 (84)
Q Consensus 12 ll~~Ai~~~~dedGW~~l~~vG~~l~k~~PdFdpR~YG~~kls~li~a~~~fei~~~---~~~~~~~~~ir~r 81 (84)
.+...|+..++|=|++..+.-|+- .-+....-+++|++.+++...++. .++.-.+.+|.+.
T Consensus 93 ~V~~sie~LA~ecGLst~s~~Gn~---------sItRasR~i~e~le~~Gli~~~~~~D~~~~~~~Pk~I~lT 156 (281)
T PF02387_consen 93 IVQASIEQLADECGLSTKSKAGNK---------SITRASRLITEFLEPMGLITCEKEWDPYNGNYIPKHIWLT 156 (281)
T ss_pred CHHCCHHHHHHHHCCCCCCCCCCE---------EHHHHHHHHHHHHHHCCCEEEEEEECHHHCCCCCEEEEEC
T ss_conf 112049999998098752889996---------0789999999999864784433235332236368079987
No 10
>PF02504 FA_synthesis: Fatty acid synthesis protein; InterPro: IPR003664 The plsX gene is part of the bacterial fab gene cluster which encodes several key fatty acid biosynthetic enzymes . The plsX gene encodes a poorly understood enzyme of phospholipid metabolism .; GO: 0003824 catalytic activity, 0006633 fatty acid biosynthetic process; PDB: 1u7n_A 1vi1_B.
Probab=16.19 E-value=32 Score=14.29 Aligned_cols=41 Identities=12% Similarity=0.135 Sum_probs=0.0
Q ss_pred HHHHHHHHHHHHHHCCCCCEEEHHHHHHHHHHCCCCCCCCCCC
Q ss_conf 5789999999987305788063888998987417999833057
Q T0549 7 HPLQDMFTSAIEAVARDSGWAELSAVGSYLAKNDPSFDPRNWG 49 (84)
Q Consensus 7 ~~l~~ll~~Ai~~~~dedGW~~l~~vG~~l~k~~PdFdpR~YG 49 (84)
..+..+|++++...--. +...--+..-+++....|||++||
T Consensus 242 ~~~~~~lk~~~~~~~~~--kl~~ll~~~~l~~~~~~~d~~~~g 282 (323)
T PF02504_consen 242 KFILKLLKEELKKSLLS--KLGALLLKPALKKLKKRFDYEEYG 282 (323)
T ss_dssp HHHHHHHHHHCTTT---------HHHHHCHHHHCCCC-GGG--
T ss_pred HHHHHHHHHHHHHHHHH--HHHHHHHCHHHHHHHHHCCCCCCC
T ss_conf 99999999999874999--999987452368999855766789
Done!