Query 047235
Match_columns 276
No_of_seqs 91 out of 93
Neff 3.7
Searched_HMMs 46136
Date Fri Mar 29 09:02:55 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/047235.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/047235hhsearch_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 6.4E-55 1.4E-59 343.2 6.4 85 160-244 1-86 (86)
2 TIGR01958 nuoE_fam NADH-quinon 65.1 28 0.00061 29.5 6.8 12 190-201 110-121 (148)
3 TIGR00273 iron-sulfur cluster- 43.1 12 0.00025 37.5 1.2 44 157-205 253-307 (432)
4 KOG3550 Receptor targeting pro 41.5 1.4E+02 0.0031 27.2 7.5 96 90-186 12-121 (207)
5 COG5201 SKP1 SCF ubiquitin lig 31.7 95 0.0021 27.6 4.8 50 66-116 82-134 (158)
6 PRK05988 formate dehydrogenase 27.5 3.4E+02 0.0073 23.5 7.5 13 189-201 116-128 (156)
7 PF02671 PAH: Paired amphipath 26.2 2E+02 0.0042 19.6 4.7 43 91-138 3-47 (47)
8 PRK12373 NADH dehydrogenase su 24.5 3.9E+02 0.0085 27.1 8.2 12 190-201 132-143 (400)
9 smart00288 VHS Domain present 21.0 3.4E+02 0.0074 22.5 6.1 30 76-105 2-31 (133)
10 PHA03159 hypothetical protein; 20.7 1.4E+02 0.0031 26.4 3.8 39 67-105 94-134 (160)
11 PF11342 DUF3144: Protein of u 20.6 1.8E+02 0.004 23.0 4.1 11 93-103 7-17 (78)
No 1
>PF13225 DUF4033: Domain of unknown function (DUF4033)
Probab=100.00 E-value=6.4e-55 Score=343.15 Aligned_cols=85 Identities=56% Similarity=1.171 Sum_probs=82.7
Q ss_pred ccccceeeeeee-CCCCceeccceEeeccccccccCcccccccccCCchhhhhhhhcCCceeeccCcccceeeeeeCCCC
Q 047235 160 WLMGHCTVNSVD-LPDGTSCQSGVFVERCKYLEESKCVGVCINTCKLPTQTFFKDYMGVPLLMEPNFSDYSCQFKFGILP 238 (276)
Q Consensus 160 WLVGP~eV~~ve-v~dG~~~~sgV~IeKCRyLEeSgC~GmCvN~CKiPTQ~FF~e~~GlPLtM~PNFED~SCqm~FG~~P 238 (276)
||||||+|+++| ..+|++++|||+||||||||||||+|||+|+||+|||+||+|+|||||||+||||||||||+||++|
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 3488889999999999999999999999999999999999999999999999999999999999999
Q ss_pred CCCCCC
Q 047235 239 PLPKDD 244 (276)
Q Consensus 239 Pp~eeD 244 (276)
||+|||
T Consensus 81 pp~eeD 86 (86)
T PF13225_consen 81 PPIEED 86 (86)
T ss_pred CCCCCC
Confidence 999998
No 2
>TIGR01958 nuoE_fam NADH-quinone oxidoreductase, E subunit. This model describes the E chain of complexes that resemble NADH-quinone oxidoreductases. The electron acceptor is a quinone, ubiquinone, in mitochondria and most bacteria, including Escherichia coli, where the recommended gene symbol is nuoB. This model does not identify proteins from chloroplast and cyanobacteria.
Probab=65.12 E-value=28 Score=29.51 Aligned_cols=12 Identities=50% Similarity=1.019 Sum_probs=10.1
Q ss_pred ccccCccccccc
Q 047235 190 LEESKCVGVCIN 201 (276)
Q Consensus 190 LEeSgC~GmCvN 201 (276)
|+.++|.|+|.+
T Consensus 110 l~~~~ClG~C~~ 121 (148)
T TIGR01958 110 LVEVECLGACGN 121 (148)
T ss_pred EEEcCccCccCC
Confidence 778999999963
No 3
>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=43.14 E-value=12 Score=37.54 Aligned_cols=44 Identities=25% Similarity=0.526 Sum_probs=27.4
Q ss_pred cccccccceeeee---------eeCCCCceeccceEeeccccccccCcc--cccccccCC
Q 047235 157 TCQWLMGHCTVNS---------VDLPDGTSCQSGVFVERCKYLEESKCV--GVCINTCKL 205 (276)
Q Consensus 157 ~f~WLVGP~eV~~---------vev~dG~~~~sgV~IeKCRyLEeSgC~--GmCvN~CKi 205 (276)
...|.-||+.-.+ |-|+||+ +.++-.+ |-|...|. |.|+|.|++
T Consensus 253 y~~~IsGps~t~D~~GP~e~hvilldngr---~~~~~~~--~~e~~~CIrCG~C~~~CPv 307 (432)
T TIGR00273 253 YINVLTGPRQEGDVDGPEEFHLILLDNGR---SNILATE--FREVLACIRCGACQNECPV 307 (432)
T ss_pred ceEEeeCCCCCCCCCCCcEEEEEEeCCCc---chhhhhh--hhhHhhCCCCCCccccCcc
Confidence 3467778877554 3345664 3333333 55666665 899999986
No 4
>KOG3550 consensus Receptor targeting protein Lin-7 [Extracellular structures]
Probab=41.55 E-value=1.4e+02 Score=27.22 Aligned_cols=96 Identities=24% Similarity=0.340 Sum_probs=65.4
Q ss_pred CchHHHHHHHHHHHhcCCChHHHHHHHHHHHHHHhCChhhHHHHHHHhcCCC---cchhHHHHHHHHhhhccccccccee
Q 047235 90 PGYDGLIELVNHLMMKGKSSSDARDAAQIRILVSLFPPLVLKLYKILISPLA---GGKIAAMMVARVTALTCQWLMGHCT 166 (276)
Q Consensus 90 ~GYdglVe~a~~lm~kgrs~~eq~~~~~~rVL~sl~Pp~~~~~fr~lf~p~~---~~k~aa~~nA~vT~~~f~WLVGP~e 166 (276)
.+-...||+-.+|...|.-+.+.-++. .+||.|-|=..+...|..+.--+- .-.+-+.-.|..|...|+---|-+-
T Consensus 12 rdv~r~ielleklq~sgevp~~kl~al-q~vlqsef~~avrevye~vyetidi~~s~eira~atakatvaafaaseghah 90 (207)
T KOG3550|consen 12 RDVQRAIELLEKLQRSGEVPPQKLQAL-QKVLQSEFCTAVREVYEHVYETIDIDGSPEIRAAATAKATVAAFAASEGHAH 90 (207)
T ss_pred HHHHHHHHHHHHHHHcCCCCHHHHHHH-HHHHHHHHHHHHHHHHHHHHhhcccCCChHHhhhhhhHHHHHHHHHhccCCC
Confidence 455677888878877787777766666 899999987778888877653210 1145566667778888887788766
Q ss_pred eeeeeCC-----------CCceeccceEeec
Q 047235 167 VNSVDLP-----------DGTSCQSGVFVER 186 (276)
Q Consensus 167 V~~vev~-----------dG~~~~sgV~IeK 186 (276)
-+-||++ +|+.+.|-++|.|
T Consensus 91 prvvelpktdeglgfnvmggkeqnspiyisr 121 (207)
T KOG3550|consen 91 PRVVELPKTDEGLGFNVMGGKEQNSPIYISR 121 (207)
T ss_pred CceeecCccccccceeeccCcccCCceEEEe
Confidence 5556653 4555566666654
No 5
>COG5201 SKP1 SCF ubiquitin ligase, SKP1 component [Posttranslational modification, protein turnover, chaperones]
Probab=31.70 E-value=95 Score=27.55 Aligned_cols=50 Identities=22% Similarity=0.377 Sum_probs=33.0
Q ss_pred hhhHHHHHHHHHHHHHHhCCCCCCCchHHHHHHHHHH---HhcCCChHHHHHHH
Q 047235 66 VLDDLFLSSFRNKLVQEVGLDSEKPGYDGLIELVNHL---MMKGKSSSDARDAA 116 (276)
Q Consensus 66 ~lD~~~l~lF~rkm~~~~G~ds~~~GYdglVe~a~~l---m~kgrs~~eq~~~~ 116 (276)
+-||.||.+=..-|-+.. ..+.-=.|.-|.|++-.+ |+||+|++|.++-.
T Consensus 82 ~wdr~Fm~vDqemL~eI~-laaNYL~ikpLLd~gCKivaemirgkSpeeir~tf 134 (158)
T COG5201 82 FWDRFFMEVDQEMLLEIC-LAANYLEIKPLLDLGCKIVAEMIRGKSPEEIRETF 134 (158)
T ss_pred HHHHHHHHhhHHHHHHHH-HhhccccchHHHHHHHHHHHHHHccCCHHHHHHHh
Confidence 569999998544444443 233334677788876433 78999999976543
No 6
>PRK05988 formate dehydrogenase subunit gamma; Validated
Probab=27.54 E-value=3.4e+02 Score=23.55 Aligned_cols=13 Identities=38% Similarity=0.838 Sum_probs=10.7
Q ss_pred cccccCccccccc
Q 047235 189 YLEESKCVGVCIN 201 (276)
Q Consensus 189 yLEeSgC~GmCvN 201 (276)
-||++.|.|.|.+
T Consensus 116 tL~~~~ClG~C~~ 128 (156)
T PRK05988 116 TLEPVYCLGLCAC 128 (156)
T ss_pred EEEeeeecCccCC
Confidence 4888999999964
No 7
>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=26.18 E-value=2e+02 Score=19.59 Aligned_cols=43 Identities=16% Similarity=0.326 Sum_probs=24.0
Q ss_pred chHHHHHHHHHHHhcCCChHHHHHHHHHHHHHHhCC--hhhHHHHHHHhc
Q 047235 91 GYDGLIELVNHLMMKGKSSSDARDAAQIRILVSLFP--PLVLKLYKILIS 138 (276)
Q Consensus 91 GYdglVe~a~~lm~kgrs~~eq~~~~~~rVL~sl~P--p~~~~~fr~lf~ 138 (276)
-|+.|+++-+....+..+..+..+.+ .+||- |-+..-|+.++|
T Consensus 3 ~Y~~FL~il~~y~~~~~~~~~v~~~v-----~~Ll~~hpdLl~~F~~FlP 47 (47)
T PF02671_consen 3 VYNEFLKILNDYKKGRISRSEVIEEV-----SELLRGHPDLLEEFNRFLP 47 (47)
T ss_dssp HHHHHHHHHHHHHCTCSCHHHHHHHH-----HHHTTT-HHHHHHHHHHSS
T ss_pred HHHHHHHHHHHHHhcCCCHHHHHHHH-----HHHHccCHHHHHHHHhhCc
Confidence 48899998776654445555543333 34442 335555665553
No 8
>PRK12373 NADH dehydrogenase subunit E; Provisional
Probab=24.45 E-value=3.9e+02 Score=27.13 Aligned_cols=12 Identities=50% Similarity=1.251 Sum_probs=10.9
Q ss_pred ccccCccccccc
Q 047235 190 LEESKCVGVCIN 201 (276)
Q Consensus 190 LEeSgC~GmCvN 201 (276)
||+..|.|.|.|
T Consensus 132 Le~veCLGaC~~ 143 (400)
T PRK12373 132 WEEVECLGACVN 143 (400)
T ss_pred EEeeeecCccCC
Confidence 888999999987
No 9
>smart00288 VHS Domain present in VPS-27, Hrs and STAM. Unpublished observations. Domain of unknown function.
Probab=21.04 E-value=3.4e+02 Score=22.47 Aligned_cols=30 Identities=3% Similarity=0.097 Sum_probs=22.3
Q ss_pred HHHHHHHhCCCCCCCchHHHHHHHHHHHhc
Q 047235 76 RNKLVQEVGLDSEKPGYDGLIELVNHLMMK 105 (276)
Q Consensus 76 ~rkm~~~~G~ds~~~GYdglVe~a~~lm~k 105 (276)
.+.+.+++.-....++|+..++++..+..+
T Consensus 2 ~~~i~kATs~~l~~~dw~~~l~icD~i~~~ 31 (133)
T smart00288 2 ERLIDKATSPSLLEEDWELILEICDLINST 31 (133)
T ss_pred hhHHHHHcCcCCCCcCHHHHHHHHHHHhCC
Confidence 355677777777788999999998876543
No 10
>PHA03159 hypothetical protein; Provisional
Probab=20.69 E-value=1.4e+02 Score=26.43 Aligned_cols=39 Identities=21% Similarity=0.324 Sum_probs=30.8
Q ss_pred hhHHHHHHHHHHHHHHhCC--CCCCCchHHHHHHHHHHHhc
Q 047235 67 LDDLFLSSFRNKLVQEVGL--DSEKPGYDGLIELVNHLMMK 105 (276)
Q Consensus 67 lD~~~l~lF~rkm~~~~G~--ds~~~GYdglVe~a~~lm~k 105 (276)
+-.++++.+..-.++++|. =-+..|+.||++-+.+++.+
T Consensus 94 ~r~~AtsvLssYi~esvg~qWF~~hGG~kGL~~fC~~IL~k 134 (160)
T PHA03159 94 YKCVATSMLSSYIAKSVGANWFIDHGGEKGLVEFCDSILPK 134 (160)
T ss_pred HHHHHHHHhHHHHHHHhhhhHHHHcCcHhHHHHHHHHhccC
Confidence 5567788888888888884 35678999999999998743
No 11
>PF11342 DUF3144: Protein of unknown function (DUF3144); InterPro: IPR021490 This family of proteins with unknown function appears to be restricted to Proteobacteria.
Probab=20.56 E-value=1.8e+02 Score=22.99 Aligned_cols=11 Identities=36% Similarity=0.438 Sum_probs=9.4
Q ss_pred HHHHHHHHHHH
Q 047235 93 DGLIELVNHLM 103 (276)
Q Consensus 93 dglVe~a~~lm 103 (276)
|.||++|++..
T Consensus 7 D~fI~lAN~~~ 17 (78)
T PF11342_consen 7 DEFIALANEQN 17 (78)
T ss_pred HHHHHHHHHhh
Confidence 78999999875
Done!