Query 046001
Match_columns 256
No_of_seqs 111 out of 120
Neff 3.6
Searched_HMMs 46136
Date Fri Mar 29 07:41:51 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/046001.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/046001hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF04927 SMP: Seed maturation 99.8 6.5E-20 1.4E-24 135.9 6.6 61 129-189 1-61 (62)
2 PF04927 SMP: Seed maturation 99.8 2.6E-19 5.6E-24 132.7 3.3 58 9-66 1-61 (62)
3 PF09018 Phage_Capsid_P3: P3 m 57.1 4.1 8.9E-05 38.7 0.4 11 9-19 137-147 (394)
4 PF03061 4HBT: Thioesterase su 19.8 54 0.0012 22.6 0.9 17 7-23 41-57 (79)
5 TIGR00051 acyl-CoA thioester h 17.4 68 0.0015 23.9 1.1 15 8-22 60-74 (117)
6 cd07046 BMC_PduU-EutS 1,2-prop 16.5 1.1E+02 0.0024 25.3 2.2 22 92-113 1-23 (110)
7 TIGR00388 glyQ glycyl-tRNA syn 15.5 53 0.0011 31.6 0.1 9 9-17 186-194 (293)
8 PF13279 4HBT_2: Thioesterase- 11.8 1.1E+02 0.0024 23.2 0.9 15 8-22 55-69 (121)
9 cd03442 BFIT_BACH Brown fat-in 11.3 1.2E+02 0.0026 22.6 1.0 17 7-23 61-77 (123)
10 TIGR02799 thio_ybgC tol-pal sy 11.3 1.3E+02 0.0027 23.0 1.1 15 8-22 64-78 (126)
No 1
>PF04927 SMP: Seed maturation protein; InterPro: IPR007011 Late embryogenesis abundant (LEA) proteins accumulate to high levels during the last stage of seed formation (when a natural desiccation of the seed tissues takes place) and during periods of water deficit in vegetative organs. LEA proteins have been grouped into at least six families on the basis of sequence similarity. Although significant similarity has not been detected between the members of the different classes, a unifying and outstanding feature of these proteins is their high hydrophilicity and high percentage of glycines. Amino acid sequence analysis allows one to predict that these proteins exist primarily as random coils. This property has been confirmed in few cases with purified proteins and is supported by the fact that proteins of this type do not coagulate upon heating. LEA protein families have been identified in a wide range of different plant species to the extent that they can be considered ubiquitous in plants. Moreover, it has been shown that members of at least one of the LEA protein families, the so-called dehydrins, are present in a range of photosynthetic organisms, including lower plants, algae, and cyanobacteria. In addition similar proteins, the hydrophilins are induced in a variety of different taxons, of non-photosynthetic organsims, in response to osmotic stress. All of these proteins have a high hydrophilicity index, generally greater than 1.0 []. This conserved region identifies a set of plant seed maturation proteins described as LEA D34.
Probab=99.80 E-value=6.5e-20 Score=135.90 Aligned_cols=61 Identities=61% Similarity=0.719 Sum_probs=58.2
Q ss_pred ccchhHHHHHhhhhhCCCCCChhhHHHHHHHHHHhcCCCCCCCCcHHHHHHHHHHHccccc
Q 046001 129 GITIGEALEATALTAGKKPVEWSDAAAIQAAEVRATGRINITPGGVAAAAQSAATINARTT 189 (256)
Q Consensus 129 ~itiGealeaaa~~~g~kPV~~~DAAaiQaAE~ratG~~~~~~GG~AA~aQSAA~~N~r~~ 189 (256)
+|||||+|++++..+++|||+++||++||+||+|++|.+.+.|||++++|||||++|++..
T Consensus 1 ~vt~gdvl~A~a~~~~~kpVt~eDAa~iqsAE~r~~g~~~~~~GGvAa~~qsAA~~N~~~~ 61 (62)
T PF04927_consen 1 KVTIGDVLEAAAGLPGDKPVTPEDAAAIQSAEARATGGAQTQPGGVAAAAQSAADKNERAG 61 (62)
T ss_pred CccHHHHHHHHhcccccCCCCHHHHHHHHHHHHhhCCCCCCCCCCHHHHHHHHHHHhhhcc
Confidence 5999999999989999999999999999999999999988999999999999999999863
No 2
>PF04927 SMP: Seed maturation protein; InterPro: IPR007011 Late embryogenesis abundant (LEA) proteins accumulate to high levels during the last stage of seed formation (when a natural desiccation of the seed tissues takes place) and during periods of water deficit in vegetative organs. LEA proteins have been grouped into at least six families on the basis of sequence similarity. Although significant similarity has not been detected between the members of the different classes, a unifying and outstanding feature of these proteins is their high hydrophilicity and high percentage of glycines. Amino acid sequence analysis allows one to predict that these proteins exist primarily as random coils. This property has been confirmed in few cases with purified proteins and is supported by the fact that proteins of this type do not coagulate upon heating. LEA protein families have been identified in a wide range of different plant species to the extent that they can be considered ubiquitous in plants. Moreover, it has been shown that members of at least one of the LEA protein families, the so-called dehydrins, are present in a range of photosynthetic organisms, including lower plants, algae, and cyanobacteria. In addition similar proteins, the hydrophilins are induced in a variety of different taxons, of non-photosynthetic organsims, in response to osmotic stress. All of these proteins have a high hydrophilicity index, generally greater than 1.0 []. This conserved region identifies a set of plant seed maturation proteins described as LEA D34.
Probab=99.76 E-value=2.6e-19 Score=132.71 Aligned_cols=58 Identities=41% Similarity=0.593 Sum_probs=56.2
Q ss_pred CCccCceee-cccccccCcCCchhHHHHHHHHHhhhc--cccCCchHHHHHHHHHHhhhcC
Q 046001 9 PIKYGDVFS-VEGEIAEMAVAPRDAALMQTAENAMLG--QIQKGTAASMMQSAAERNEKGG 66 (256)
Q Consensus 9 pi~Ygdvf~-v~g~la~~piap~dAa~MqsAE~~v~G--~tqkgg~Aa~MqsAA~~NeraG 66 (256)
||||||||+ +.+.+++|||+|+||+.|||||.+.+| +++|||.++.|||||.+|++.|
T Consensus 1 ~vt~gdvl~A~a~~~~~kpVt~eDAa~iqsAE~r~~g~~~~~~GGvAa~~qsAA~~N~~~~ 61 (62)
T PF04927_consen 1 KVTIGDVLEAAAGLPGDKPVTPEDAAAIQSAEARATGGAQTQPGGVAAAAQSAADKNERAG 61 (62)
T ss_pred CccHHHHHHHHhcccccCCCCHHHHHHHHHHHHhhCCCCCCCCCCHHHHHHHHHHHhhhcc
Confidence 799999999 999999999999999999999999999 7999999999999999999876
No 3
>PF09018 Phage_Capsid_P3: P3 major capsid protein; InterPro: IPR015108 The major capsid protein p3 from Bacteriophage PRD1 adopts a double-barrel structure comprising two eight-stranded viral beta-barrels or jelly rolls, each of which contains a 12-residue alpha-helix. This protein then trimerises through a 'trimerisation loop' sequence, and is incorporated within the viral capsid []. ; PDB: 1HX6_A 1HQN_C 1GW8_K 1GW7_J 1HB7_L 1HB5_B 1HB9_L 1W8X_B 1CJD_C.
Probab=57.12 E-value=4.1 Score=38.67 Aligned_cols=11 Identities=73% Similarity=1.226 Sum_probs=7.3
Q ss_pred CCccCceeecc
Q 046001 9 PIKYGDVFSVE 19 (256)
Q Consensus 9 pi~Ygdvf~v~ 19 (256)
|||||||.||-
T Consensus 137 pikygdvmnvi 147 (394)
T PF09018_consen 137 PIKYGDVMNVI 147 (394)
T ss_dssp SS--BSSS-SS
T ss_pred Cccccceeeec
Confidence 99999999985
No 4
>PF03061 4HBT: Thioesterase superfamily; InterPro: IPR006683 This family contains a wide variety of enzymes, principally thioesterases. This family includes 4HBT (3.1.2.23 from EC) which catalyses the final step in the biosynthesis of 4-hydroxybenzoate from 4-chlorobenzoate in the soil dwelling microbe Pseudomonas CBS-3. This family includes various cytosolic long-chain acyl-CoA thioester hydrolases. Long-chain acyl-CoA hydrolases hydrolyse palmitoyl-CoA to CoA and palmitate, they also catalyse the hydrolysis of other long chain fatty acyl-CoA thioesters. ; PDB: 3F5O_F 2F0X_D 2H4U_C 2PRX_A 2OV9_D 1YLI_B 3BJK_F 1IXL_A 3DKZ_B 2EIS_B ....
Probab=19.81 E-value=54 Score=22.63 Aligned_cols=17 Identities=35% Similarity=0.725 Sum_probs=12.5
Q ss_pred CCCCccCceeecccccc
Q 046001 7 RRPIKYGDVFSVEGEIA 23 (256)
Q Consensus 7 ~rpi~Ygdvf~v~g~la 23 (256)
.||+++||.+-+.+.+-
T Consensus 41 ~~p~~~gd~l~~~~~v~ 57 (79)
T PF03061_consen 41 LRPVRPGDTLRVEARVV 57 (79)
T ss_dssp SS-BBTTSEEEEEEEEE
T ss_pred ccccCCCeEEEEEEEEE
Confidence 35999999998877653
No 5
>TIGR00051 acyl-CoA thioester hydrolase, YbgC/YbaW family. This model describes a subset of related acyl-CoA thioesterases that include several at least partially characterized proteins. YbgC is an acyl-CoA thioesterase associated with the Tol-Pal system. YbaW is part of the FadM regulon.
Probab=17.43 E-value=68 Score=23.87 Aligned_cols=15 Identities=27% Similarity=0.682 Sum_probs=11.1
Q ss_pred CCCccCceeeccccc
Q 046001 8 RPIKYGDVFSVEGEI 22 (256)
Q Consensus 8 rpi~Ygdvf~v~g~l 22 (256)
||++|||.+.|+-.+
T Consensus 60 ~~~~~gd~v~v~~~~ 74 (117)
T TIGR00051 60 KPARLDDVLEIRTQI 74 (117)
T ss_pred CcccCCCEEEEEEEE
Confidence 488888888776544
No 6
>cd07046 BMC_PduU-EutS 1,2-propanediol utilization protein U (PduU)/ethanolamine utilization protein S (EutS), Bacterial Micro-Compartment (BMC) domain. PduU encapsulates several related enzymes within a shell composed of a few thousand protein subunits. PduU exists as a hexamer which might further assemble into the flat facets of the polyhedral outer shell of the pdu organelle. This proteinaceous noncarboxysome microcompartment is involved in coenzyme B12-dependent degradation of 1,2-propanediol. The core of PduU is related to the typical BMC domain and its natural oligomeric state is a cyclic hexamer. Unlike other typical BMC domain proteins, the 3D topology of PduU reveals a circular permuted variation on the typical BMC fold which leads to several unique features. The exact functions related to those unique features are still not clear. Another difference is the presence of a deep cavity on one side of the hexamer as well as an intermolecular six-stranded beta barrel that seems to
Probab=16.51 E-value=1.1e+02 Score=25.28 Aligned_cols=22 Identities=27% Similarity=0.241 Sum_probs=18.8
Q ss_pred ceeEeeeecc-eeeeeeecCCCc
Q 046001 92 RRIITEEIGG-QVVGQYSQPSSL 113 (256)
Q Consensus 92 ~RivTE~VaG-Qvvgq~~~p~~~ 113 (256)
.|||-|+|-| |++..|+-|.+.
T Consensus 1 ~r~~~~~v~gk~i~~~~vI~~v~ 23 (110)
T cd07046 1 QRIIQEYVPGKQITLAHLIANPD 23 (110)
T ss_pred CcceEEecCcceEEEEEEecCCC
Confidence 3899999988 899999998774
No 7
>TIGR00388 glyQ glycyl-tRNA synthetase, tetrameric type, alpha subunit. This tetrameric form of glycyl-tRNA synthetase (2 alpha, 2 beta) is found in the majority of completed eubacterial genomes, with the two genes fused in a few species. A substantially different homodimeric form (not recognized by this model) replaces this form in the Archaea, animals, yeasts, and some eubacteria.
Probab=15.50 E-value=53 Score=31.61 Aligned_cols=9 Identities=56% Similarity=1.043 Sum_probs=7.7
Q ss_pred CCccCceee
Q 046001 9 PIKYGDVFS 17 (256)
Q Consensus 9 pi~Ygdvf~ 17 (256)
||+|||||-
T Consensus 186 ~vtYgdv~~ 194 (293)
T TIGR00388 186 KTTYGDVFH 194 (293)
T ss_pred ccchhhccc
Confidence 599999994
No 8
>PF13279 4HBT_2: Thioesterase-like superfamily; PDB: 2W3X_E 3CK1_A 2GF6_C 2NUJ_A 2HLJ_A 2XFL_B 2XEM_B 2OIW_B 2HX5_A 2FUJ_A ....
Probab=11.81 E-value=1.1e+02 Score=23.24 Aligned_cols=15 Identities=40% Similarity=0.973 Sum_probs=9.1
Q ss_pred CCCccCceeeccccc
Q 046001 8 RPIKYGDVFSVEGEI 22 (256)
Q Consensus 8 rpi~Ygdvf~v~g~l 22 (256)
||++|||.|.|.-.+
T Consensus 55 ~~~~~~d~~~v~~~~ 69 (121)
T PF13279_consen 55 RPLRFGDRLEVETRV 69 (121)
T ss_dssp S--BTTSEEEEEEEE
T ss_pred ccccCCCEEEEEEEE
Confidence 488888888776544
No 9
>cd03442 BFIT_BACH Brown fat-inducible thioesterase (BFIT). Brain acyl-CoA hydrolase (BACH). These enzymes deacylate long-chain fatty acids by hydrolyzing acyl-CoA thioesters to free fatty acids and CoA-SH. Eukaryotic members of this family are expressed in brain, testis, and brown adipose tissues. The archeal and eukaryotic members of this family have two tandem copies of the conserved hot dog fold, while most bacterial members have only one copy.
Probab=11.31 E-value=1.2e+02 Score=22.62 Aligned_cols=17 Identities=24% Similarity=0.665 Sum_probs=12.7
Q ss_pred CCCCccCceeecccccc
Q 046001 7 RRPIKYGDVFSVEGEIA 23 (256)
Q Consensus 7 ~rpi~Ygdvf~v~g~la 23 (256)
++|+++||+..+.+.+-
T Consensus 61 ~~p~~~gd~l~i~~~v~ 77 (123)
T cd03442 61 LKPVRVGDVVELSARVV 77 (123)
T ss_pred cCccccCcEEEEEEEEE
Confidence 35888888887777664
No 10
>TIGR02799 thio_ybgC tol-pal system-associated acyl-CoA thioesterase. The tol-pal system consists of five critical genes. Inner membrane proteins TolQ and TolR convert protomotive force to energy that is transduced through TolA to an outer membrane complex of TolB and Pal. The system is known to be required to maintain outer membrane integrity. In a system with several homologous parts, ExbB and ExbD transduces energy through TonB to a variety of outer membrane proteins, many of which are siderophore receptors. The tol-pal system therefore may also be involved in transport. This family consists of a protein nearly always found in operons with the genes of the tol-pal system. The significance of this thioesterase to the tol-pal system is unclear, but either of two observations may be relevant. First, Pal, or peptidoglycan-associated lipoprotein, has a conserved N-terminal cleavage and acylation that makes it a lipoprotein. Second, the tol-pal system is implicated not only in the import o
Probab=11.29 E-value=1.3e+02 Score=23.03 Aligned_cols=15 Identities=20% Similarity=0.623 Sum_probs=10.4
Q ss_pred CCCccCceeeccccc
Q 046001 8 RPIKYGDVFSVEGEI 22 (256)
Q Consensus 8 rpi~Ygdvf~v~g~l 22 (256)
||++|||.+.|+-.+
T Consensus 64 ~~~~~gd~v~v~~~v 78 (126)
T TIGR02799 64 KPARLDDLLTVTTRV 78 (126)
T ss_pred CcccCCCEEEEEEEE
Confidence 477888877776554
Done!