Query 025631
Match_columns 250
No_of_seqs 13 out of 15
Neff 1.8
Searched_HMMs 46136
Date Fri Mar 29 07:50:37 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/025631.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/025631hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 TIGR01848 PHA_reg_PhaR polyhyd 88.9 0.26 5.6E-06 40.3 1.8 34 147-180 2-48 (107)
2 PF07879 PHB_acc_N: PHB/PHA ac 88.4 0.3 6.5E-06 36.9 1.8 34 147-180 2-48 (64)
3 KOG2820 FAD-dependent oxidored 65.2 13 0.00028 36.3 5.3 83 60-151 227-315 (399)
4 PF12893 Lumazine_bd_2: Putati 36.2 82 0.0018 23.3 4.5 44 166-212 70-113 (116)
5 PF11035 SnAPC_2_like: Small n 33.8 8.7 0.00019 36.9 -1.3 12 159-170 206-217 (344)
6 PRK00044 psd phosphatidylserin 31.9 30 0.00065 31.0 1.8 24 51-74 44-71 (288)
7 PF11456 DUF3019: Protein of u 29.5 95 0.0021 24.4 4.0 27 168-194 67-96 (102)
8 PRK03934 phosphatidylserine de 27.1 51 0.0011 29.3 2.4 24 51-74 34-59 (265)
9 COG1293 Predicted RNA-binding 24.4 1.1E+02 0.0024 30.2 4.3 60 108-174 48-107 (564)
10 smart00294 4.1m putative band 23.7 33 0.00072 22.3 0.4 20 111-130 2-21 (26)
11 TIGR02976 phageshock_pspB phag 21.9 32 0.0007 26.2 0.2 16 144-159 19-34 (75)
12 smart00135 LY Low-density lipo 20.9 1.1E+02 0.0023 18.0 2.3 28 156-183 8-38 (43)
No 1
>TIGR01848 PHA_reg_PhaR polyhydroxyalkanoate synthesis repressor PhaR. Poly-B-hydroxyalkanoates are lipidlike carbon/energy storage polymers found in granular inclusions. PhaR is a regulatory protein found in general near other proteins associated with polyhydroxyalkanoate (PHA) granule biosynthesis and utilization. It is found to be a DNA-binding homotetramer that is also capable of binding short chain hydroxyalkanoic acids and PHA granules. PhaR may regulate the expression of itself, of the phasins that coat granules, and of enzymes that direct carbon flux into polymers stored in granules.
Probab=88.88 E-value=0.26 Score=40.27 Aligned_cols=34 Identities=47% Similarity=0.683 Sum_probs=27.4
Q ss_pred eehhcccccCCCCc------------ceeecceEEEeecCcce-eee
Q 025631 147 LVKHYRNRRLGDPE------------FVLDFEEIYVIDSKTKS-ITR 180 (250)
Q Consensus 147 L~KHYrNrR~~dp~------------FvLdfeeiyViDsktkS-Itr 180 (250)
++|-|-|||+=|++ +|.+=+++-|+|+||+. |||
T Consensus 2 ~IKKY~NRRLYDT~tS~YITLedi~~lV~~g~~f~V~DakTgeDiT~ 48 (107)
T TIGR01848 2 IIKKYPNRRLYDTETSSYVTLEDIRDLVREGREFQVVDSKSGDDLTR 48 (107)
T ss_pred cccccCCCcccCCCccceeeHHHHHHHHHCCCeEEEEECCCCchhHH
Confidence 68999999999875 67788888888888764 554
No 2
>PF07879 PHB_acc_N: PHB/PHA accumulation regulator DNA-binding domain; InterPro: IPR012909 This domain is found at the N terminus of the polyhydroxyalkanoate (PHA) synthesis regulators. These regulators have been shown to directly bind DNA and PHA []. The invariant nature of this domain compared to the C-terminal IPR007897 from INTERPRO domain(s) suggests that it contains the DNA-binding function.
Probab=88.39 E-value=0.3 Score=36.91 Aligned_cols=34 Identities=50% Similarity=0.710 Sum_probs=26.5
Q ss_pred eehhcccccCCCCc------------ceeecceEEEeecCcce-eee
Q 025631 147 LVKHYRNRRLGDPE------------FVLDFEEIYVIDSKTKS-ITR 180 (250)
Q Consensus 147 L~KHYrNrR~~dp~------------FvLdfeeiyViDsktkS-Itr 180 (250)
++|-|-|||+=|++ +|.+=+++-|+|++|+. |||
T Consensus 2 iIKKY~NRRLYDT~~s~YiTL~di~~lV~~g~~~~V~D~ktgeDiT~ 48 (64)
T PF07879_consen 2 IIKKYPNRRLYDTETSSYITLEDIAQLVREGEDFKVVDAKTGEDITR 48 (64)
T ss_pred cccccCCCccccCCCceeEeHHHHHHHHHCCCeEEEEECCCCcccHH
Confidence 58999999999875 56777888888888764 444
No 3
>KOG2820 consensus FAD-dependent oxidoreductase [General function prediction only]
Probab=65.24 E-value=13 Score=36.33 Aligned_cols=83 Identities=27% Similarity=0.372 Sum_probs=54.2
Q ss_pred ceeecccccccccCCCCCCCCcccceeeeecCCCCce----eecccccCCCchhhhhhhcccCCccc--ccCCCCCCCCC
Q 025631 60 HKISLMECDFFIRKPPDPDNDVYDFREMYVTPPDTDI----YAIPKVLAPMPQKYIRCAVSDYGCYN--VTEPPIDAPRD 133 (250)
Q Consensus 60 HKisL~~CDFfIRK~PDpD~dVyDFREMYVTpPdTDv----YsiPrVl~pMPqky~rC~~~~yg~yn--vtePPid~pRd 133 (250)
--|+|-.|- |++|.+-|-- ..+=-+-|+-||.-|. ||.|- --|.+-++-.|+.=+ ++.+|--+|--
T Consensus 227 ~~i~ltvcy-wk~~~~~~~~-l~~d~~f~~F~~~~~~~~~~ya~p~------~eYpg~~k~~yh~g~~v~~~~~~~p~~~ 298 (399)
T KOG2820|consen 227 APIQLTVCY-WKTKKNMPVY-LFDDDCFYAFPPYPDTKLIKYALPG------YEYPGLMKVDYHEGSKVVPIDPDGPPKR 298 (399)
T ss_pred ceeEeehhh-heeecCCcee-ecCCCCceeccCCCCcceEEeccCC------CCCcceEEEeecCCCcCCCCCCCCCccc
Confidence 347888885 5777776632 2222355777777665 88887 677776666665442 56666666666
Q ss_pred cCchhhHHhhhhheehhc
Q 025631 134 PMYKSEREIHKVFLVKHY 151 (250)
Q Consensus 134 p~yk~E~ei~KVfL~KHY 151 (250)
|.-+ +-++|.-|+.+|-
T Consensus 299 s~~~-~idl~~~f~~~~~ 315 (399)
T KOG2820|consen 299 SLPK-AIDLMRRFLRTFG 315 (399)
T ss_pred Ccch-HHHHHHHHHHHhC
Confidence 6666 6778888887763
No 4
>PF12893 Lumazine_bd_2: Putative lumazine-binding; PDB: 3BLZ_C 3DUK_F 3FKA_C.
Probab=36.23 E-value=82 Score=23.34 Aligned_cols=44 Identities=27% Similarity=0.370 Sum_probs=29.0
Q ss_pred ceEEEeecCcceeeeeeEEEeecCCccCCCceEEEeeCCeeeEEEeC
Q 025631 166 EEIYVIDSKTKSITRAKVLVTLPRNRDRKSDLLIVRDNGNSFKIIHA 212 (250)
Q Consensus 166 eeiyViDsktkSItrAkV~v~vpr~RDR~~dlL~irD~G~sFkIi~~ 212 (250)
.+|..||-.- .+.-|+|.++.+ +....+-+.+++.+| ..||+++
T Consensus 70 ~~i~~i~i~g-~~A~a~v~~~~~-~~~~~d~~~L~K~dg-~WkIv~k 113 (116)
T PF12893_consen 70 ESILSIDIDG-DVASAKVEYEFP-GFWFVDYFTLVKTDG-GWKIVSK 113 (116)
T ss_dssp EEEEEEEEET-TEEEEEEEEEEE-TEEEEEEEEEEEETT-EEEEEEE
T ss_pred eEEEEEEEEC-CEEEEEEEEEEC-CCceEEEEEEEEECC-EEEEEEE
Confidence 4555666544 777778877777 444455566677665 6899875
No 5
>PF11035 SnAPC_2_like: Small nuclear RNA activating complex subunit 2-like; InterPro: IPR021281 This family of proteins is SnAPC subunit 2-like. SnAPC allows the transcription of human small nuclear RNA genes to occur by recognition of the proximal sequence element [].
Probab=33.82 E-value=8.7 Score=36.85 Aligned_cols=12 Identities=58% Similarity=1.107 Sum_probs=10.5
Q ss_pred CcceeecceEEE
Q 025631 159 PEFVLDFEEIYV 170 (250)
Q Consensus 159 p~FvLdfeeiyV 170 (250)
-+|++|||+||=
T Consensus 206 ~d~~VDFEKIYK 217 (344)
T PF11035_consen 206 GDFVVDFEKIYK 217 (344)
T ss_pred cceeeeHHHHHH
Confidence 579999999993
No 6
>PRK00044 psd phosphatidylserine decarboxylase; Reviewed
Probab=31.89 E-value=30 Score=30.99 Aligned_cols=24 Identities=33% Similarity=0.551 Sum_probs=18.1
Q ss_pred EeecCccccce--eeccc--ccccccCC
Q 025631 51 DYRIDEDEFHK--ISLME--CDFFIRKP 74 (250)
Q Consensus 51 dY~i~EDEFHK--isL~~--CDFfIRK~ 74 (250)
.|.||-+|+.+ ++=+. .|||+||.
T Consensus 44 ~~~i~~~E~~~~~~~~y~s~~~FF~R~l 71 (288)
T PRK00044 44 KYKVDMSEAQKPDPAAYKTFNDFFTRAL 71 (288)
T ss_pred HhCCCHHHHccCChhhCCCHHHhceecc
Confidence 58899999886 44444 49999994
No 7
>PF11456 DUF3019: Protein of unknown function (DUF3019); InterPro: IPR021559 This is a bacterial family of uncharacterised proteins.
Probab=29.45 E-value=95 Score=24.36 Aligned_cols=27 Identities=37% Similarity=0.551 Sum_probs=19.6
Q ss_pred EEEeecCcce-eeeeeEEEe-e-cCCccCC
Q 025631 168 IYVIDSKTKS-ITRAKVLVT-L-PRNRDRK 194 (250)
Q Consensus 168 iyViDsktkS-ItrAkV~v~-v-pr~RDR~ 194 (250)
..+||+.|.. +..|+|+|+ + |++|-|+
T Consensus 67 f~L~~~~~~~~la~~~v~V~~~~~k~Rrr~ 96 (102)
T PF11456_consen 67 FSLRDSDTGQPLAQVKVKVTWVSPKVRRRR 96 (102)
T ss_pred EEEEeCCCCcEEEEEEEEEEEeccCcCCcc
Confidence 3468999988 888898875 4 6555554
No 8
>PRK03934 phosphatidylserine decarboxylase; Provisional
Probab=27.07 E-value=51 Score=29.26 Aligned_cols=24 Identities=25% Similarity=0.391 Sum_probs=20.1
Q ss_pred EeecCccccceeecccc--cccccCC
Q 025631 51 DYRIDEDEFHKISLMEC--DFFIRKP 74 (250)
Q Consensus 51 dY~i~EDEFHKisL~~C--DFfIRK~ 74 (250)
.|+||.+|+..++=+.| |||+||.
T Consensus 34 ~~~i~~~e~~~~~~y~sfn~FF~R~l 59 (265)
T PRK03934 34 IFKIDMSEFKPPENYKSLNALFTRSL 59 (265)
T ss_pred HHCCCHHHhcCcccCCCHHHhccccC
Confidence 68999999976666666 9999996
No 9
>COG1293 Predicted RNA-binding protein homologous to eukaryotic snRNP [Transcription]
Probab=24.39 E-value=1.1e+02 Score=30.23 Aligned_cols=60 Identities=22% Similarity=0.291 Sum_probs=46.3
Q ss_pred hhhhhhhcccCCcccccCCCCCCCCCcCchhhHHhhhhheehhcccccCCCCcceeecceEEEeecC
Q 025631 108 QKYIRCAVSDYGCYNVTEPPIDAPRDPMYKSEREIHKVFLVKHYRNRRLGDPEFVLDFEEIYVIDSK 174 (250)
Q Consensus 108 qky~rC~~~~yg~ynvtePPid~pRdp~yk~E~ei~KVfL~KHYrNrR~~dp~FvLdfeeiyViDsk 174 (250)
.+.+=|....+++.++|.++...|..|..-. ..|.||-++.|...- ..++|+.|.+|.-+
T Consensus 48 ~~~li~~~~~~~~i~lT~~~~~~p~~p~~F~------~~LRK~l~g~~i~~i-~Q~~~DRIl~~~f~ 107 (564)
T COG1293 48 RKLLLSEHPVRSRIHLTKKPKENPALPSSFA------MLLRKHLKGARIEKI-EQLGFDRILELKFK 107 (564)
T ss_pred ceEEEEecCCcceEEeCCCCcCCCCCCChHH------HHHHHHhccCceEeE-EecCCceEEEEEEe
Confidence 3445566678888999999888888876543 357899999988764 46889999999887
No 10
>smart00294 4.1m putative band 4.1 homologues' binding motif.
Probab=23.65 E-value=33 Score=22.33 Aligned_cols=20 Identities=30% Similarity=0.406 Sum_probs=16.7
Q ss_pred hhhhcccCCcccccCCCCCC
Q 025631 111 IRCAVSDYGCYNVTEPPIDA 130 (250)
Q Consensus 111 ~rC~~~~yg~ynvtePPid~ 130 (250)
.||..++.|.|++.|||...
T Consensus 2 yry~~R~kGSY~t~E~kg~~ 21 (26)
T smart00294 2 YRYKHRDEGSYHTHEPKGXX 21 (26)
T ss_pred cEEEecccCceEcCCCCCcc
Confidence 37889999999999998543
No 11
>TIGR02976 phageshock_pspB phage shock protein B. This model describes the PspB protein of the psp (phage shock protein) operon, as found in Escherichia coli and many related species. Expression of a phage protein called secretin protein IV, and a number of other stresses including ethanol, heat shock, and defects in protein secretion trigger sigma-54-dependent expression of the phage shock regulon. PspB is both a regulator and an effector protein of the phage shock response.
Probab=21.94 E-value=32 Score=26.21 Aligned_cols=16 Identities=31% Similarity=0.696 Sum_probs=11.8
Q ss_pred hhheehhcccccCCCC
Q 025631 144 KVFLVKHYRNRRLGDP 159 (250)
Q Consensus 144 KVfL~KHYrNrR~~dp 159 (250)
-.+|.+|||+++....
T Consensus 19 p~wl~lHY~~k~~~~~ 34 (75)
T TIGR02976 19 PLWLILHYRSKRKTAA 34 (75)
T ss_pred HHHHHHHHHhhhccCC
Confidence 3568999998876543
No 12
>smart00135 LY Low-density lipoprotein-receptor YWTD domain. Type "B" repeats in low-density lipoprotein (LDL) receptor that plays a central role in mammalian cholesterol metabolism. Also present in a variety of molecules similar to gp300/megalin.
Probab=20.94 E-value=1.1e+02 Score=18.03 Aligned_cols=28 Identities=29% Similarity=0.526 Sum_probs=20.7
Q ss_pred CCCCc-ceeec--ceEEEeecCcceeeeeeE
Q 025631 156 LGDPE-FVLDF--EEIYVIDSKTKSITRAKV 183 (250)
Q Consensus 156 ~~dp~-FvLdf--eeiyViDsktkSItrAkV 183 (250)
...|+ +.+|. ..+|-.|+....|.+++.
T Consensus 8 ~~~~~~la~d~~~~~lYw~D~~~~~I~~~~~ 38 (43)
T smart00135 8 LGHPNGLAVDWIEGRLYWTDWGLDVIEVANL 38 (43)
T ss_pred CCCcCEEEEeecCCEEEEEeCCCCEEEEEeC
Confidence 34444 55555 579999999999999874
Done!