Query 023709
Match_columns 278
No_of_seqs 93 out of 95
Neff 3.1
Searched_HMMs 46136
Date Fri Mar 29 06:04:04 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/023709.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/023709hhsearch_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 8.9E-53 1.9E-57 331.4 6.5 84 154-251 1-86 (86)
2 KOG3196 NADH:ubiquinone oxidor 60.7 3 6.5E-05 38.9 0.2 42 120-161 75-116 (233)
3 PF14196 ATC_hydrolase: L-2-am 51.1 43 0.00092 26.9 5.4 58 171-241 88-149 (149)
4 PHA02611 51 baseplate hub asse 44.6 24 0.00052 33.5 3.4 34 90-124 23-56 (249)
5 PRK15031 5-carboxymethyl-2-hyd 38.6 6 0.00013 33.5 -1.4 30 92-121 59-88 (126)
6 TIGR00273 iron-sulfur cluster- 32.5 25 0.00053 35.1 1.5 55 149-212 251-307 (432)
7 PRK13409 putative ATPase RIL; 28.6 28 0.00061 35.6 1.2 30 164-213 35-64 (590)
8 PF11342 DUF3144: Protein of u 24.9 94 0.002 24.7 3.3 40 91-152 6-45 (78)
9 cd03083 TRX_Fd_NuoE_hoxF TRX-l 24.1 41 0.00088 25.5 1.1 12 197-208 43-54 (80)
10 PF14922 FWWh: Protein of unkn 21.0 1.2E+02 0.0027 26.5 3.6 50 108-157 98-149 (161)
11 PF02671 PAH: Paired amphipath 20.1 1.9E+02 0.0042 19.6 3.7 27 90-116 3-30 (47)
No 1
>PF13225 DUF4033: Domain of unknown function (DUF4033)
Probab=100.00 E-value=8.9e-53 Score=331.38 Aligned_cols=84 Identities=74% Similarity=1.380 Sum_probs=82.9
Q ss_pred ccccceeeEEEe--ecCeeeeccEEEeecchhhHHHHhhccccceecccCccccccccccCCchhhhhhhcCCceeeccC
Q 023709 154 WLVGPSEVVEVE--INGEKQRSGVHIKKCSKAEMLIAIFDNRLRYLENSGCVGMCVNMCKFPTQDFFTREFGLPLTMIPN 231 (278)
Q Consensus 154 WLvGP~ev~eve--v~G~~q~sgV~I~KC~~~~~~~~~~~~~~RyLEeSgC~GmCvN~CK~PTQ~FF~~~~GlpLtM~PN 231 (278)
||||||+|+++| .+|.+++|||||||| ||||+|||+|||+|+||+|||+||+++|||||||+||
T Consensus 1 WLvGp~~v~~~e~~~~~~~~~sgV~i~kC--------------RyLEes~C~g~C~N~CK~PtQ~Ff~~~~Glpl~M~PN 66 (86)
T PF13225_consen 1 WLVGPCEVNEVEENGNGRGQKSGVHIEKC--------------RYLEESGCAGMCVNMCKIPTQTFFKEEFGLPLTMEPN 66 (86)
T ss_pred CcccccEeeEeeccCCCccccceEEEEEe--------------EEeecCCceeeeehhcccchHHHHHhccCCceEecCC
Confidence 999999999999 789999999999999 9999999999999999999999999999999999999
Q ss_pred CccceeeEeecCCCCCCCCC
Q 023709 232 FEDMSCEMVYGQVPPSFEDD 251 (278)
Q Consensus 232 FeD~SCem~FG~~PPp~eeD 251 (278)
||||||||+||++|||+|||
T Consensus 67 fed~SC~~~FG~~Ppp~eeD 86 (86)
T PF13225_consen 67 FEDFSCQMIFGQTPPPIEED 86 (86)
T ss_pred CcCcEEEEEcCCCCCCCCCC
Confidence 99999999999999999998
No 2
>KOG3196 consensus NADH:ubiquinone oxidoreductase, NDUFV2/24 kD subunit [Energy production and conversion]
Probab=60.74 E-value=3 Score=38.87 Aligned_cols=42 Identities=21% Similarity=0.180 Sum_probs=23.5
Q ss_pred hcCCCChHHHHHhhcCCchhHHHHHhhhhhhhhhccccceee
Q 023709 120 SMLPPGAPAQFRKLFPPTKWAAEFNAALTVPFFHWLVGPSEV 161 (278)
Q Consensus 120 sl~Pp~~~~~fr~lfpp~k~aae~nA~~T~~~f~WLvGP~ev 161 (278)
.++|+.+..-+.+++--..--.--.|.+-+.||.|=+|---|
T Consensus 75 GWlpiSAM~~VA~~~~v~~mrvyevatfYtmf~r~p~gKy~v 116 (233)
T KOG3196|consen 75 GWLPISAMNEVAEVLEVPPMRVYEVATFYTMFFRKPVGKYHV 116 (233)
T ss_pred CCcCHHHHHHHHHHHcCChHHHHHHHHHHHHhhccCCCCceE
Confidence 355655554454444221111222467778999999986544
No 3
>PF14196 ATC_hydrolase: L-2-amino-thiazoline-4-carboxylic acid hydrolase
Probab=51.13 E-value=43 Score=26.88 Aligned_cols=58 Identities=16% Similarity=0.387 Sum_probs=38.6
Q ss_pred eeccEEEeecchhhHHHHhhccccceecccCccccccccccCCchhhhhhhc--CCceeeccCC--ccceeeEee
Q 023709 171 QRSGVHIKKCSKAEMLIAIFDNRLRYLENSGCVGMCVNMCKFPTQDFFTREF--GLPLTMIPNF--EDMSCEMVY 241 (278)
Q Consensus 171 q~sgV~I~KC~~~~~~~~~~~~~~RyLEeSgC~GmCvN~CK~PTQ~FF~~~~--GlpLtM~PNF--eD~SCem~F 241 (278)
..-.+++.+|+-+ .+..+-||...|.-.|.+ ..-+-+.| |+.|+.+=.- -|--|+|.|
T Consensus 88 ~~~~~~~~~Cp~~-----------~~~k~~G~~e~~~~~C~~--D~~~~~~~~~~~~l~r~~tla~G~~~Cdf~f 149 (149)
T PF14196_consen 88 DEFEFDFTRCPYA-----------EFWKEYGLPELGPIYCDI--DYAMAEGFNPGIRLERTKTLADGDDCCDFRF 149 (149)
T ss_pred CeEEEEEEeChHH-----------HHHHHcCCchHHhHhhhh--hHHHHHhCCCCcEEEEeeEEeCCCCcCccCC
Confidence 4578999999422 456678999999999999 44466667 8877654322 233455543
No 4
>PHA02611 51 baseplate hub assembly protein; Provisional
Probab=44.59 E-value=24 Score=33.51 Aligned_cols=34 Identities=41% Similarity=0.736 Sum_probs=28.7
Q ss_pred ChhhHHHHHHHHhcCCCHHHHHHHHHHHHHhcCCC
Q 023709 90 DYESFVDVSKRVMEGRSRQQQQEVVREVLLSMLPP 124 (278)
Q Consensus 90 gYeglVd~a~~~m~grs~~~q~~~v~~vL~sl~Pp 124 (278)
+|-+|+ +|+.-|+|+++++|++++-+++..++|.
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 4566799999999999999999999855
No 5
>PRK15031 5-carboxymethyl-2-hydroxymuconate delta-isomerase; Provisional
Probab=38.59 E-value=6 Score=33.53 Aligned_cols=30 Identities=27% Similarity=0.390 Sum_probs=25.5
Q ss_pred hhHHHHHHHHhcCCCHHHHHHHHHHHHHhc
Q 023709 92 ESFVDVSKRVMEGRSRQQQQEVVREVLLSM 121 (278)
Q Consensus 92 eglVd~a~~~m~grs~~~q~~~v~~vL~sl 121 (278)
++||.+.-+||.|||.++.+++...++..+
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 389999999999999999998877666554
No 6
>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=32.49 E-value=25 Score=35.13 Aligned_cols=55 Identities=20% Similarity=0.542 Sum_probs=31.9
Q ss_pred hhhhhccccceeeEEEeecCeeeeccEEEeecchhhHHHHhhccccceecccCcc--ccccccccC
Q 023709 149 VPFFHWLVGPSEVVEVEINGEKQRSGVHIKKCSKAEMLIAIFDNRLRYLENSGCV--GMCVNMCKF 212 (278)
Q Consensus 149 ~~~f~WLvGP~ev~evev~G~~q~sgV~I~KC~~~~~~~~~~~~~~RyLEeSgC~--GmCvN~CK~ 212 (278)
+....|.-||+.-.+ ++|.++-..|.++.= ..+||- . +|-|...|+ |.|+|.|++
T Consensus 251 ~~y~~~IsGps~t~D--~~GP~e~hvilldng-r~~~~~----~--~~~e~~~CIrCG~C~~~CPv 307 (432)
T TIGR00273 251 TAYINVLTGPRQEGD--VDGPEEFHLILLDNG-RSNILA----T--EFREVLACIRCGACQNECPV 307 (432)
T ss_pred CcceEEeeCCCCCCC--CCCCcEEEEEEeCCC-cchhhh----h--hhhhHhhCCCCCCccccCcc
Confidence 446678889998655 457665555555431 111110 1 233445554 899999985
No 7
>PRK13409 putative ATPase RIL; Provisional
Probab=28.57 E-value=28 Score=35.64 Aligned_cols=30 Identities=33% Similarity=0.908 Sum_probs=21.6
Q ss_pred EeecCeeeeccEEEeecchhhHHHHhhccccceecccCccccccccccCC
Q 023709 164 VEINGEKQRSGVHIKKCSKAEMLIAIFDNRLRYLENSGCVGMCVNMCKFP 213 (278)
Q Consensus 164 vev~G~~q~sgV~I~KC~~~~~~~~~~~~~~RyLEeSgC~GmCvN~CK~P 213 (278)
+|+++...+..+.=+-| .|| |+||.-|++=
T Consensus 35 ~~~~~~~~~~~~~e~~c-------------------~~c-~~c~~~cp~~ 64 (590)
T PRK13409 35 IEIDEDDGKPVISEELC-------------------IGC-GICVKKCPFD 64 (590)
T ss_pred EEEcCCCCCceeeHhhc-------------------ccc-ccccccCCcc
Confidence 55666555556666677 787 8999999864
No 8
>PF11342 DUF3144: Protein of unknown function (DUF3144); InterPro: IPR021490 This family of proteins with unknown function appears to be restricted to Proteobacteria.
Probab=24.94 E-value=94 Score=24.69 Aligned_cols=40 Identities=23% Similarity=0.356 Sum_probs=25.8
Q ss_pred hhhHHHHHHHHhcCCCHHHHHHHHHHHHHhcCCCChHHHHHhhcCCchhHHHHHhhhhhhhh
Q 023709 91 YESFVDVSKRVMEGRSRQQQQEVVREVLLSMLPPGAPAQFRKLFPPTKWAAEFNAALTVPFF 152 (278)
Q Consensus 91 YeglVd~a~~~m~grs~~~q~~~v~~vL~sl~Pp~~~~~fr~lfpp~k~aae~nA~~T~~~f 152 (278)
-|.||++|++....-.+-+-..+. |+ =++++||++....|
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 378999999988765433333322 11 26888888876654
No 9
>cd03083 TRX_Fd_NuoE_hoxF TRX-like [2Fe-2S] Ferredoxin (Fd) family, NADH:ubiquinone oxidoreductase (Nuo) subunit E subfamily, hoxF; composed of proteins similar to the NAD-reducing hydrogenase (hoxS) alpha subunit of Alcaligenes eutrophus H16. HoxS is a cytoplasmic hydrogenase catalyzing the oxidation of molecular hydrogen accompanied by the reduction of NAD. It is composed of four structural subunits encoded by the genes hoxF, hoxU, hoxY and hoxH. The hoxF protein (or alpha subunit) is a fusion protein containing an N-terminal NuoE-like domain and a C-terminal NuoF domain. NuoE and NuoF are components of Nuo, a multisubunit complex catalyzing the electron transfer of NADH to quinone coupled with the transfer of protons across the membrane. Electrons are transferred from NADH to quinone through a chain of iron-sulfur clusters in Nuo, including the [2Fe-2S] cluster in NuoE and the [4Fe-4S] cluster in NuoF. In addition, NuoF is also the NADH- and FMN-binding subunit. HoxF may be involved
Probab=24.05 E-value=41 Score=25.52 Aligned_cols=12 Identities=33% Similarity=0.808 Sum_probs=10.4
Q ss_pred ecccCccccccc
Q 023709 197 LENSGCVGMCVN 208 (278)
Q Consensus 197 LEeSgC~GmCvN 208 (278)
|+++||.|+|-.
T Consensus 43 l~~~gClG~C~~ 54 (80)
T cd03083 43 LFFTSCTGLCDQ 54 (80)
T ss_pred EEEeceecCcCC
Confidence 889999999954
No 10
>PF14922 FWWh: Protein of unknown function
Probab=21.01 E-value=1.2e+02 Score=26.50 Aligned_cols=50 Identities=20% Similarity=0.363 Sum_probs=42.6
Q ss_pred HHHHHHHHHHHHhcCCCChHHHHHhhcCCch--hHHHHHhhhhhhhhhcccc
Q 023709 108 QQQQEVVREVLLSMLPPGAPAQFRKLFPPTK--WAAEFNAALTVPFFHWLVG 157 (278)
Q Consensus 108 ~~q~~~v~~vL~sl~Pp~~~~~fr~lfpp~k--~aae~nA~~T~~~f~WLvG 157 (278)
.+-++.+.+++-.++.-.+-..|-..||.++ +..++-..+.-.++.|+.|
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 3445678888888888888889999999976 8888999999999999998
No 11
>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=20.05 E-value=1.9e+02 Score=19.61 Aligned_cols=27 Identities=30% Similarity=0.416 Sum_probs=18.9
Q ss_pred ChhhHHHHHHHHhcC-CCHHHHHHHHHH
Q 023709 90 DYESFVDVSKRVMEG-RSRQQQQEVVRE 116 (278)
Q Consensus 90 gYeglVd~a~~~m~g-rs~~~q~~~v~~ 116 (278)
-|+.|+++-+...++ .+..+-.+.|..
T Consensus 3 ~Y~~FL~il~~y~~~~~~~~~v~~~v~~ 30 (47)
T PF02671_consen 3 VYNEFLKILNDYKKGRISRSEVIEEVSE 30 (47)
T ss_dssp HHHHHHHHHHHHHCTCSCHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHhcCCCHHHHHHHHHH
Confidence 589999999888875 466664444433
Done!