Query 024686
Match_columns 264
No_of_seqs 94 out of 96
Neff 3.7
Searched_HMMs 46136
Date Fri Mar 29 06:35:53 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/024686.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/024686hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF13225 DUF4033: Domain of un 100.0 2.8E-55 6E-60 343.4 6.2 84 154-237 1-86 (86)
2 KOG3196 NADH:ubiquinone oxidor 72.9 1.3 2.9E-05 40.8 0.4 71 120-195 75-167 (233)
3 PF11342 DUF3144: Protein of u 31.1 61 0.0013 25.5 3.2 40 91-152 6-45 (78)
4 PRK15031 5-carboxymethyl-2-hyd 30.9 8.2 0.00018 32.5 -1.8 30 92-121 59-88 (126)
5 PF14196 ATC_hydrolase: L-2-am 30.2 1.1E+02 0.0024 24.5 4.7 55 171-227 88-149 (149)
6 PHA02611 51 baseplate hub asse 29.6 57 0.0012 30.9 3.3 34 90-124 23-56 (249)
7 PF14922 FWWh: Protein of unkn 24.8 88 0.0019 27.3 3.4 50 108-157 98-149 (161)
8 TIGR00273 iron-sulfur cluster- 23.4 40 0.00087 33.6 1.2 48 149-198 251-307 (432)
9 PF02671 PAH: Paired amphipath 22.9 1.6E+02 0.0035 19.9 3.8 44 90-135 3-47 (47)
10 PF04675 DNA_ligase_A_N: DNA l 18.9 1.8E+02 0.0038 24.3 4.0 47 91-137 3-53 (177)
No 1
>PF13225 DUF4033: Domain of unknown function (DUF4033)
Probab=100.00 E-value=2.8e-55 Score=343.38 Aligned_cols=84 Identities=74% Similarity=1.380 Sum_probs=82.8
Q ss_pred ccccceeeEEEe--ecCeeeeccEEEceeceeecccccccccccccCcccchhhhccCCceeeccCCccceeeEeeCCCC
Q 024686 154 WLVGPSEVVEVE--INGEKQRSGVHIKKCRYLENSGCVGMCVNMCKFPTQDFFTREFGLPLTMIPNFEDMSCEMVYGQVP 231 (264)
Q Consensus 154 WLvGP~ev~~ve--v~G~~~~sgV~IeKCRyLEeSgC~GmCvN~CKiPTQ~FF~d~~GlpLtM~PNFeD~SCqm~FG~~P 231 (264)
||||||+|+++| .+|.+++|||+||||||||||||+|||+|+||+|||+||+|+|||||||+||||||||||+||++|
T Consensus 1 WLvGp~~v~~~e~~~~~~~~~sgV~i~kCRyLEes~C~g~C~N~CK~PtQ~Ff~~~~Glpl~M~PNfed~SC~~~FG~~P 80 (86)
T PF13225_consen 1 WLVGPCEVNEVEENGNGRGQKSGVHIEKCRYLEESGCAGMCVNMCKIPTQTFFKEEFGLPLTMEPNFEDFSCQMIFGQTP 80 (86)
T ss_pred CcccccEeeEeeccCCCccccceEEEEEeEEeecCCceeeeehhcccchHHHHHhccCCceEecCCCcCcEEEEEcCCCC
Confidence 999999999999 788999999999999999999999999999999999999999999999999999999999999999
Q ss_pred CCCCCC
Q 024686 232 PSFEDD 237 (264)
Q Consensus 232 Pp~eeD 237 (264)
||+|||
T Consensus 81 pp~eeD 86 (86)
T PF13225_consen 81 PPIEED 86 (86)
T ss_pred CCCCCC
Confidence 999998
No 2
>KOG3196 consensus NADH:ubiquinone oxidoreductase, NDUFV2/24 kD subunit [Energy production and conversion]
Probab=72.92 E-value=1.3 Score=40.78 Aligned_cols=71 Identities=27% Similarity=0.404 Sum_probs=38.4
Q ss_pred hcCCCChHHHHHhhcCCchhHHHHHhhhhhhhhcccccceeeEEEe-----ecC-----------------eeeeccEEE
Q 024686 120 SMLPPGAPAQFRKLFPPTKWAAEFNAALTVPFFHWLVGPSEVVEVE-----ING-----------------EKQRSGVHI 177 (264)
Q Consensus 120 sl~Pp~~~~~fr~lfpp~~~~~e~nA~~T~~~f~WLvGP~ev~~ve-----v~G-----------------~~~~sgV~I 177 (264)
.++|..+..-+.+++--..--.--.|.+-+.||.|=+|---|.--. +-| +..+.+.+
T Consensus 75 GWlpiSAM~~VA~~~~v~~mrvyevatfYtmf~r~p~gKy~v~VC~ttpC~lrg~d~i~ea~~k~lgi~~Gett~d~~F- 153 (233)
T KOG3196|consen 75 GWLPISAMNEVAEVLEVPPMRVYEVATFYTMFFRKPVGKYHVQVCTTTPCMLRGSDDILEACKKQLGIKVGETTKDGLF- 153 (233)
T ss_pred CCcCHHHHHHHHHHHcCChHHHHHHHHHHHHhhccCCCCceEEEecCcHHhhhccHHHHHHHHHHhCccccccccccce-
Confidence 3555554444444432111112224777789999999965443210 001 11122222
Q ss_pred ceeceeeccccccccccc
Q 024686 178 KKCRYLENSGCVGMCVNM 195 (264)
Q Consensus 178 eKCRyLEeSgC~GmCvN~ 195 (264)
-|+|.+|.|-|+|-
T Consensus 154 ----tl~e~eClGaCvna 167 (233)
T KOG3196|consen 154 ----TLEEVECLGACVNA 167 (233)
T ss_pred ----eeecchhhhhhccC
Confidence 48999999999995
No 3
>PF11342 DUF3144: Protein of unknown function (DUF3144); InterPro: IPR021490 This family of proteins with unknown function appears to be restricted to Proteobacteria.
Probab=31.10 E-value=61 Score=25.50 Aligned_cols=40 Identities=23% Similarity=0.356 Sum_probs=26.0
Q ss_pred hhHHHHHHHHHhcCCCHHHHHHHHHHHHHhcCCCChHHHHHhhcCCchhHHHHHhhhhhhhh
Q 024686 91 YESFVDVSKRVMEGRSRQQQQEVVREVLLSMLPPGAPAQFRKLFPPTKWAAEFNAALTVPFF 152 (264)
Q Consensus 91 YdglVe~a~~lm~grs~~~q~~~v~~vL~sl~Pp~~~~~fr~lfpp~~~~~e~nA~~T~~~f 152 (264)
-|.||++||+....-.+-+-..+. |+ =++++||++....|
T Consensus 6 aD~fI~lAN~~~~~~~~g~Vsaal------------------ly----AaARfnAf~~a~~~ 45 (78)
T PF11342_consen 6 ADEFIALANEQNKEEDAGQVSAAL------------------LY----AAARFNAFVAASSF 45 (78)
T ss_pred HHHHHHHHHHhhccCCcchHHHHH------------------HH----HHHHHHHHHHHHcc
Confidence 378999999998765443333332 11 26788888877654
No 4
>PRK15031 5-carboxymethyl-2-hydroxymuconate delta-isomerase; Provisional
Probab=30.88 E-value=8.2 Score=32.54 Aligned_cols=30 Identities=27% Similarity=0.390 Sum_probs=25.5
Q ss_pred hHHHHHHHHHhcCCCHHHHHHHHHHHHHhc
Q 024686 92 ESFVDVSKRVMEGRSRQQQQEVVREVLLSM 121 (264)
Q Consensus 92 dglVe~a~~lm~grs~~~q~~~v~~vL~sl 121 (264)
++||.+.-+||.|||.++.+++...+|..|
T Consensus 59 ~~Fihv~l~i~~GRs~e~k~~l~~~l~~~l 88 (126)
T PRK15031 59 YAFVHMTLKIGAGRSLESRQEVGEMLFALI 88 (126)
T ss_pred CcEEEEEeeecCCCCHHHHHHHHHHHHHHH
Confidence 489999999999999999998887766554
No 5
>PF14196 ATC_hydrolase: L-2-amino-thiazoline-4-carboxylic acid hydrolase
Probab=30.21 E-value=1.1e+02 Score=24.47 Aligned_cols=55 Identities=16% Similarity=0.414 Sum_probs=36.9
Q ss_pred eeccEEEceecee---ecccccccccccccCcccchhhhcc--CCceeeccCCc--cceeeEee
Q 024686 171 QRSGVHIKKCRYL---ENSGCVGMCVNMCKFPTQDFFTREF--GLPLTMIPNFE--DMSCEMVY 227 (264)
Q Consensus 171 ~~sgV~IeKCRyL---EeSgC~GmCvN~CKiPTQ~FF~d~~--GlpLtM~PNFe--D~SCqm~F 227 (264)
..-.+.|.+|-|. .+=||...|.-.|.+ ..-+-+.| |+.|+.+=.-- |--|+|.|
T Consensus 88 ~~~~~~~~~Cp~~~~~k~~G~~e~~~~~C~~--D~~~~~~~~~~~~l~r~~tla~G~~~Cdf~f 149 (149)
T PF14196_consen 88 DEFEFDFTRCPYAEFWKEYGLPELGPIYCDI--DYAMAEGFNPGIRLERTKTLADGDDCCDFRF 149 (149)
T ss_pred CeEEEEEEeChHHHHHHHcCCchHHhHhhhh--hHHHHHhCCCCcEEEEeeEEeCCCCcCccCC
Confidence 3568899999865 567888889999999 44466667 88776543221 33455544
No 6
>PHA02611 51 baseplate hub assembly protein; Provisional
Probab=29.64 E-value=57 Score=30.87 Aligned_cols=34 Identities=41% Similarity=0.736 Sum_probs=28.6
Q ss_pred ChhHHHHHHHHHhcCCCHHHHHHHHHHHHHhcCCC
Q 024686 90 DYESFVDVSKRVMEGRSRQQQQEVVREVLLSMLPP 124 (264)
Q Consensus 90 gYdglVe~a~~lm~grs~~~q~~~v~~vL~sl~Pp 124 (264)
+|-+|+ +|+.-|.|+++.+|++++-.++..++|-
T Consensus 23 Ey~~Ll-lar~~me~~~~~Eq~eii~eli~~~~~e 56 (249)
T PHA02611 23 DYRDFL-LVRNDMEGRSPEEQQEILDELLDEYFPE 56 (249)
T ss_pred HHHHHH-hhhhhhcCCChhhHHHHHHHHHHHHhcc
Confidence 577776 4566799999999999999999998755
No 7
>PF14922 FWWh: Protein of unknown function
Probab=24.81 E-value=88 Score=27.29 Aligned_cols=50 Identities=20% Similarity=0.363 Sum_probs=43.0
Q ss_pred HHHHHHHHHHHHhcCCCChHHHHHhhcCCch--hHHHHHhhhhhhhhccccc
Q 024686 108 QQQQEVVREVLLSMLPPGAPAQFRKLFPPTK--WAAEFNAALTVPFFHWLVG 157 (264)
Q Consensus 108 ~~q~~~v~~vL~sl~Pp~~~~~fr~lfpp~~--~~~e~nA~~T~~~f~WLvG 157 (264)
.+-++.+.+++-.++.-.+-..|-..||.++ |..++-..+.-.++.|+.|
T Consensus 98 ~~~kD~~~~~yp~~laqavy~~f~~~FP~s~~~F~~~FK~~l~~~~~~w~sG 149 (161)
T PF14922_consen 98 SHYKDAFFKVYPDCLAQAVYYSFCECFPQSWHLFNEEFKSNLYNTCSEWISG 149 (161)
T ss_pred chhHHHHHHHHHHHHHHHHHHHHHHHCchHHHHHhHHHHHHHHHHHHHHHcC
Confidence 3446678888888888888889999999976 8888999999999999998
No 8
>TIGR00273 iron-sulfur cluster-binding protein. Members of this family have a perfect 4Fe-4S binding motif C-x(2)-C-x(2)-C-x(3)-CP followed by either a perfect or imperfect (the first Cys replaced by Ser) second copy. Members probably bind two 4fe-4S iron-sulfur clusters.
Probab=23.42 E-value=40 Score=33.59 Aligned_cols=48 Identities=21% Similarity=0.545 Sum_probs=30.6
Q ss_pred hhhhcccccceeeEEEeecCeeeeccEEEcee-------ceeeccccc--ccccccccC
Q 024686 149 VPFFHWLVGPSEVVEVEINGEKQRSGVHIKKC-------RYLENSGCV--GMCVNMCKF 198 (264)
Q Consensus 149 ~~~f~WLvGP~ev~~vev~G~~~~sgV~IeKC-------RyLEeSgC~--GmCvN~CKi 198 (264)
+....|.-||+.-.+ ++|.++...|.|+.= +|-|...|. |.|+|.|++
T Consensus 251 ~~y~~~IsGps~t~D--~~GP~e~hvilldngr~~~~~~~~~e~~~CIrCG~C~~~CPv 307 (432)
T TIGR00273 251 TAYINVLTGPRQEGD--VDGPEEFHLILLDNGRSNILATEFREVLACIRCGACQNECPV 307 (432)
T ss_pred CcceEEeeCCCCCCC--CCCCcEEEEEEeCCCcchhhhhhhhhHhhCCCCCCccccCcc
Confidence 345678889998655 346555444444421 145666665 899999986
No 9
>PF02671 PAH: Paired amphipathic helix repeat; InterPro: IPR003822 This family contains the paired amphipathic helix (PAH) repeat. The family contains the eukaryotic Sin3 proteins, which have at least three PAH domains (PAH1, PAH2, and PAH3). Sin3 proteins are components of a co-repressor complex that silences transcription, playing important roles in the transition between proliferation and differentiation. Sin3 proteins are recruited to the DNA by various DNA-binding transcription factors such as the Mad family of repressors, Mnt/Rox, PLZF, MeCP2, p53, REST/NRSF, MNFbeta, Sp1, TGIF and Ume6 []. Sin3 acts as a scaffold protein that in turn recruits histone-binding proteins RbAp46/RbAp48 and histone deacetylases HDAC1/HDAC2, which deacetylate the core histones resulting in a repressed state of the chromatin []. The PAH domains are protein-protein interaction domains through which Sin3 fulfils its role as a scaffold. The PAH2 domain of Sin3 can interact with a wide range of unrelated and structurally diverse transcription factors that bind using different interaction motifs. For example, the Sin3 PAH2 domain can interact with the unrelated Mad and HBP1 factors using alternative interaction motifs that involve binding in opposite helical orientations [].; GO: 0006355 regulation of transcription, DNA-dependent, 0005634 nucleus; PDB: 1S5Q_B 2L9S_B 1G1E_B 1S5R_B 2CR7_A 2CZY_A 2LD7_B 2RMR_A 2RMS_A 1PD7_A ....
Probab=22.88 E-value=1.6e+02 Score=19.86 Aligned_cols=44 Identities=27% Similarity=0.484 Sum_probs=25.8
Q ss_pred ChhHHHHHHHHHhcC-CCHHHHHHHHHHHHHhcCCCChHHHHHhhcC
Q 024686 90 DYESFVDVSKRVMEG-RSRQQQQEVVREVLLSMLPPGAPAQFRKLFP 135 (264)
Q Consensus 90 gYdglVe~a~~lm~g-rs~~~q~~~v~~vL~sl~Pp~~~~~fr~lfp 135 (264)
-|+.|+++-+...++ .+..+-.+.|...|..- |-+...|+.++|
T Consensus 3 ~Y~~FL~il~~y~~~~~~~~~v~~~v~~Ll~~h--pdLl~~F~~FlP 47 (47)
T PF02671_consen 3 VYNEFLKILNDYKKGRISRSEVIEEVSELLRGH--PDLLEEFNRFLP 47 (47)
T ss_dssp HHHHHHHHHHHHHCTCSCHHHHHHHHHHHTTT---HHHHHHHHHHSS
T ss_pred HHHHHHHHHHHHHhcCCCHHHHHHHHHHHHccC--HHHHHHHHhhCc
Confidence 589999999888875 46666555553333221 124444555544
No 10
>PF04675 DNA_ligase_A_N: DNA ligase N terminus; InterPro: IPR012308 DNA ligase (polydeoxyribonucleotide synthase) is the enzyme that joins two DNA fragments by catalysing the formation of an internucleotide ester bond between phosphate and deoxyribose. It is active during DNA replication, DNA repair and DNA recombination. There are two forms of DNA ligase, one requires ATP (6.5.1.1 from EC), the other NAD (6.5.1.2 from EC), the latter being restricted to eubacteria. Eukaryotic, archaebacterial, viral and some eubacterial DNA ligases are ATP-dependent. The first step in the ligation reaction is the formation of a covalent enzyme-AMP complex. The co-factor ATP is cleaved to pyrophosphate and AMP, with the AMP being covalently joined to a highly conserved lysine residue in the active site of the ligase. The activated AMP residue is then transferred to the 5'phosphate of the nick, before the nick is sealed by phosphodiester-bond formation and AMP elimination [,]. Vertebrate cells encode three well-characterised DNA ligases (DNA ligases I, III and IV), all of which are related in structure and sequence. With the exception of the atypically small PBCV-1 viral enzyme, two regions of primary sequence are common to all members of the family. The catalytic region comprises six conserved sequence motifs (I, III, IIIa, IV, V-VI), motif I includes the lysine residue that is adenylated in the first step of the ligation reaction. The function of the second, less well-conserved region is unknown. When folded, each protein comprises of two distinct sub-domains: a large amino-terminal sub-domain ('domain 1') and a smaller carboxy-terminal sub-domain ('domain 2'). The ATP-binding site of the enzyme lies in the cleft between the two sub-domains. Domain 1 consists of two antiparallel beta sheets flanked by alpha helices, whereas domain 2 consists of a five-stranded beta barrel and a single alpha helix, which form the oligonucleotide-binding fold [, ]. This region is found in many but not all ATP-dependent DNA ligase enzymes (6.5.1.1 from EC). It is thought to be involved in DNA binding and in catalysis. In human DNA ligase I (P18858 from SWISSPROT), and in Saccharomyces cerevisiae (Baker's yeast) (P04819 from SWISSPROT), this region was necessary for catalysis, and separated from the amino terminus by targeting elements. In Vaccinia virus (P16272 from SWISSPROT) this region was not essential for catalysis, but deletion decreases the affinity for nicked DNA and decreased the rate of strand joining at a step subsequent to enzyme-adenylate formation []. ; GO: 0003677 DNA binding, 0003910 DNA ligase (ATP) activity, 0006281 DNA repair, 0006310 DNA recombination; PDB: 2CFM_A 3RR5_A 2HIX_A 2HIV_A 3L2P_A 1X9N_A 4EQ5_A 3GDE_A.
Probab=18.85 E-value=1.8e+02 Score=24.35 Aligned_cols=47 Identities=15% Similarity=0.257 Sum_probs=34.7
Q ss_pred hhHHHHHHHHHhcCCCHHHHHHHHHHHHHhcCCC----ChHHHHHhhcCCc
Q 024686 91 YESFVDVSKRVMEGRSRQQQQEVVREVLLSMLPP----GAPAQFRKLFPPT 137 (264)
Q Consensus 91 YdglVe~a~~lm~grs~~~q~~~v~~vL~sl~Pp----~~~~~fr~lfpp~ 137 (264)
|..|+++..++..-.+..+-.+++.+.|.++.+. .+-.+++.+||+.
T Consensus 3 F~~l~~l~~~l~~~~~~~~k~~~l~~~~~~~~~~~~~~~~~~~~~~l~P~~ 53 (177)
T PF04675_consen 3 FSDLCELFEKLESTSSRLEKIAILSNFFRSWREEDLGPDLYLLLRLLFPEY 53 (177)
T ss_dssp HHHHHHHHHHHHT---HHHHHHHHHHHHHTSHCCGHHCHHHHHHTHSSTTT
T ss_pred HHHHHHHHHHHHhccCHHHHHHHHHHHHHHcccchhhhHHHHHhcccccch
Confidence 6678888888887777778888999999998766 3556778888874
Done!