Query 030909
Match_columns 169
No_of_seqs 110 out of 989
Neff 6.6
Searched_HMMs 46136
Date Fri Mar 29 06:24:56 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/030909.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/030909hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF02365 NAM: No apical merist 100.0 1.5E-39 3.2E-44 244.3 5.9 104 18-121 1-129 (129)
2 PHA00692 hypothetical protein 55.6 4.4 9.5E-05 26.7 0.3 10 16-25 35-44 (74)
3 PF07960 CBP4: CBP4; InterPro 35.8 20 0.00044 27.1 1.2 12 24-35 29-40 (128)
4 smart00707 RPEL Repeat in Dros 34.5 28 0.0006 19.1 1.3 14 20-33 5-18 (26)
5 PF05865 Cypo_polyhedrin: Cypo 29.2 75 0.0016 25.4 3.4 26 75-100 142-168 (248)
6 PF13822 ACC_epsilon: Acyl-CoA 27.3 32 0.0007 22.4 0.9 7 25-31 10-16 (62)
7 smart00265 BH4 BH4 Bcl-2 homol 25.2 72 0.0016 17.6 1.9 17 27-43 4-20 (27)
8 PF15374 CCDC71L: Coiled-coil 24.5 74 0.0016 28.3 2.9 37 19-57 29-66 (376)
9 PF09497 Med12: Transcription 23.3 29 0.00063 23.0 0.2 31 2-36 20-50 (64)
10 PF07131 DUF1382: Protein of u 22.4 59 0.0013 21.4 1.4 14 20-33 22-39 (61)
11 cd00954 NAL N-Acetylneuraminic 22.4 54 0.0012 27.4 1.7 19 18-37 103-121 (288)
12 PLN02417 dihydrodipicolinate s 22.3 56 0.0012 27.3 1.7 18 18-36 103-120 (280)
13 TIGR02313 HpaI-NOT-DapA 2,4-di 20.4 67 0.0015 27.0 1.8 19 18-37 102-120 (294)
No 1
>PF02365 NAM: No apical meristem (NAM) protein; InterPro: IPR003441 The NAC domain (for Petunia hybrida (Petunia) NAM and for Arabidopsis ATAF1, ATAF2, and CUC2) is an N-terminal module of ~160 amino acids, which is found in proteins of the NAC family of plant-specific transcriptional regulators (no apical meristem (NAM) proteins) []. NAC proteins are involved in developmental processes, including formation of the shoot apical meristem, floral organs and lateral shoots, as well as in plant hormonal control and defence. The NAC domain is accompanied by diverse C-terminal transcriptional activation domains. The NAC domain has been shown to be a DNA-binding domain (DBD) and a dimerization domain [,]. The NAC domain can be subdivided into five subdomains (A-E). Each subdomain is distinguishable by blocks of heterogeneous amino acids or gaps. While the NAC domains were rich in basic amino acids (R, K and H) as a whole, the distribution of positive and negative amino acids in each subdomain were unequal. Subdomains C and D are rich in basic amino acids but poor in acidic amino acids, while subdomain B contains a high proportion of acidic amino acids. Putative nuclear localization signals (NLS) have been detected in subdomains C and D []. The DBD is contained within a 60 amino acid region located within subdomains D and E []. The overall structure of the NAC domain monomer consists of a very twisted antiparallel beta-sheet, which packs against an N-terminal alpha-helix on one side and one shorter helix on the other side surrounded by a few helical elements. The structure suggests that the NAC domain mediates dimerization through conserved interactions including a salt bridge, and DNA binding through the NAC dimer face rich in positive charges [].; GO: 0003677 DNA binding, 0006355 regulation of transcription, DNA-dependent; PDB: 1UT4_A 3SWM_B 4DUL_B 3SWP_D 1UT7_B 3ULX_A.
Probab=100.00 E-value=1.5e-39 Score=244.30 Aligned_cols=104 Identities=51% Similarity=1.031 Sum_probs=84.6
Q ss_pred CCCceEECCChHHHHHHHHhhhhcCCCCC--ceeeeccCCCCCCCCCC----------------------CcccccccCC
Q 030909 18 LPPGFRFHPRDDELVCDYLMKKVTHTNES--ILLAAVDLNKCEPWDIP----------------------GLRTNRATAS 73 (169)
Q Consensus 18 LP~G~RF~PTDeELI~~YL~~ki~g~~~~--~~I~~~Dvy~~~Pw~L~----------------------g~R~~R~~~~ 73 (169)
|||||||+|||+|||.+||++|+.|.+++ .+|.++|||+.+||+|+ |.|.+|++++
T Consensus 1 LP~G~rF~PtD~ELi~~yL~~k~~g~~~~~~~~i~~~Diy~~~P~~L~~~~~~~~~~~yFF~~~~~~~~~~~r~~R~~~~ 80 (129)
T PF02365_consen 1 LPPGFRFRPTDEELINHYLRPKILGEPLPCEDVIHDVDIYSAHPWELPAKFKGGDEEWYFFSPRKKKYPNGGRPNRVTGG 80 (129)
T ss_dssp --TTEEE---HHHHHHCTHHHHHTT-HHCS-CHSEE--GGGS-GGGCHHHSSS-SSEEEEEEE----------S-EEETT
T ss_pred CCCceEecCChHHHHHHHHHHHhcCCCCCcccceeecccCccChHHhhhhccCCCceEEEEEecccccCCcccccccccc
Confidence 89999999999999999999999997765 68999999999999998 3567788999
Q ss_pred ceEeecCCceEEee-CCeEeEEEEEeeeeecCCCCCCccCeEEEEEEeC
Q 030909 74 GYWKATGKDRAILR-KGSLVGMRKTLVFYRGRAPKGKKTEWVMHEFRLE 121 (169)
Q Consensus 74 G~Wk~~g~~~~I~~-~g~~iG~kr~l~F~~~~~~~~~kt~W~M~EY~l~ 121 (169)
|+||.+|+.+.|.+ +|.+||+|++|+||.++.+++.+|+|+||||+|.
T Consensus 81 G~Wk~~g~~~~i~~~~g~~iG~k~~l~f~~~~~~~~~kt~W~M~EY~L~ 129 (129)
T PF02365_consen 81 GYWKSTGKEKPIKDPGGKVIGFKKTLVFYSGKSPNGKKTGWVMHEYSLE 129 (129)
T ss_dssp EEEEEECEEEEEEE-TTCEEEEEEEEEEEESSTTS-EEEEEEEEEEEE-
T ss_pred eEEeecccccccccccceeeeeEEEEEEEeccCCCCCcCCeEEEEEEeC
Confidence 99999999999998 9999999999999998888889999999999984
No 2
>PHA00692 hypothetical protein
Probab=55.56 E-value=4.4 Score=26.73 Aligned_cols=10 Identities=60% Similarity=1.361 Sum_probs=8.4
Q ss_pred CCCCCceEEC
Q 030909 16 AQLPPGFRFH 25 (169)
Q Consensus 16 ~~LP~G~RF~ 25 (169)
..+||||||-
T Consensus 35 veyppgfrfg 44 (74)
T PHA00692 35 VEYPPGFRFG 44 (74)
T ss_pred EecCCCcccc
Confidence 5689999995
No 3
>PF07960 CBP4: CBP4; InterPro: IPR012420 The CBP4 gene in Saccharomyces cerevisiae is essential for the expression and activity of ubiquinol-cytochrome c reductase [, ]. This family appears to be fungal specific.
Probab=35.82 E-value=20 Score=27.10 Aligned_cols=12 Identities=33% Similarity=0.631 Sum_probs=9.9
Q ss_pred ECCChHHHHHHH
Q 030909 24 FHPRDDELVCDY 35 (169)
Q Consensus 24 F~PTDeELI~~Y 35 (169)
-.||||||+..|
T Consensus 29 ~tPTeEeL~~r~ 40 (128)
T PF07960_consen 29 TTPTEEELFKRY 40 (128)
T ss_pred cCCCHHHHHHhc
Confidence 369999999865
No 4
>smart00707 RPEL Repeat in Drosophila CG10860, human KIAA0680 and C. elegans F26H9.2.
Probab=34.53 E-value=28 Score=19.10 Aligned_cols=14 Identities=21% Similarity=0.247 Sum_probs=11.4
Q ss_pred CceEECCChHHHHH
Q 030909 20 PGFRFHPRDDELVC 33 (169)
Q Consensus 20 ~G~RF~PTDeELI~ 33 (169)
....++||.+|||.
T Consensus 5 ~kl~~RP~~eeLv~ 18 (26)
T smart00707 5 RKLSQRPTREELEE 18 (26)
T ss_pred HHHHcCCCHHHHHH
Confidence 34568999999987
No 5
>PF05865 Cypo_polyhedrin: Cypovirus polyhedrin protein; InterPro: IPR008464 This family consists of several Cypovirus polyhedrin proteins. Polyhedrin is known to form a crystalline matrix (polyhedra) in infected insect cells [].; PDB: 2OH7_A 2OH5_A 2OH6_A.
Probab=29.17 E-value=75 Score=25.38 Aligned_cols=26 Identities=38% Similarity=0.648 Sum_probs=17.7
Q ss_pred eEeecCC-ceEEeeCCeEeEEEEEeee
Q 030909 75 YWKATGK-DRAILRKGSLVGMRKTLVF 100 (169)
Q Consensus 75 ~Wk~~g~-~~~I~~~g~~iG~kr~l~F 100 (169)
-|.++|- -++|..+|++||+...|..
T Consensus 142 pweatgikyrki~~dgeivgyshyfel 168 (248)
T PF05865_consen 142 PWEATGIKYRKIHRDGEIVGYSHYFEL 168 (248)
T ss_dssp S-B--GGG-EEEEETTEEEEEEEEEE-
T ss_pred CccccCceEEEeeccceEeeeeeeeec
Confidence 3778876 4778889999999988876
No 6
>PF13822 ACC_epsilon: Acyl-CoA carboxylase epsilon subunit
Probab=27.32 E-value=32 Score=22.42 Aligned_cols=7 Identities=57% Similarity=1.123 Sum_probs=6.6
Q ss_pred CCChHHH
Q 030909 25 HPRDDEL 31 (169)
Q Consensus 25 ~PTDeEL 31 (169)
+||||||
T Consensus 10 nPt~eEl 16 (62)
T PF13822_consen 10 NPTDEEL 16 (62)
T ss_pred CCCHHHH
Confidence 7999999
No 7
>smart00265 BH4 BH4 Bcl-2 homology region 4.
Probab=25.18 E-value=72 Score=17.63 Aligned_cols=17 Identities=35% Similarity=0.636 Sum_probs=14.2
Q ss_pred ChHHHHHHHHhhhhcCC
Q 030909 27 RDDELVCDYLMKKVTHT 43 (169)
Q Consensus 27 TDeELI~~YL~~ki~g~ 43 (169)
+-.|||.+|+.-|+...
T Consensus 4 ~nRelV~~yv~yKLsQr 20 (27)
T smart00265 4 DNRELVVDYVTYKLSQN 20 (27)
T ss_pred chHHHHHHHHHHHHhhc
Confidence 46799999999998763
No 8
>PF15374 CCDC71L: Coiled-coil domain-containing protein 71L
Probab=24.46 E-value=74 Score=28.29 Aligned_cols=37 Identities=16% Similarity=0.259 Sum_probs=27.0
Q ss_pred CCceEECCChHHHHHHHHhh-hhcCCCCCceeeeccCCCC
Q 030909 19 PPGFRFHPRDDELVCDYLMK-KVTHTNESILLAAVDLNKC 57 (169)
Q Consensus 19 P~G~RF~PTDeELI~~YL~~-ki~g~~~~~~I~~~Dvy~~ 57 (169)
|.--.|--||.|||. ||.- |-.| ..|.++..-|||+|
T Consensus 29 PmS~dl~~te~qLv~-Flq~Lr~eG-fqP~ILrSkDVYGY 66 (376)
T PF15374_consen 29 PMSKDLSDTEAQLVA-FLQGLRHEG-FQPTILRSKDVYGY 66 (376)
T ss_pred ccccccchhHHHHHH-HHHHHhhcC-CCceeecccccccc
Confidence 555667789999999 6764 2222 45678888999986
No 9
>PF09497 Med12: Transcription mediator complex subunit Med12; InterPro: IPR019035 The Mediator complex is a coactivator involved in the regulated transcription of nearly all RNA polymerase II-dependent genes. Mediator functions as a bridge to convey information from gene-specific regulatory proteins to the basal RNA polymerase II transcription machinery. The Mediator complex, having a compact conformation in its free form, is recruited to promoters by direct interactions with regulatory proteins and serves for the assembly of a functional preinitiation complex with RNA polymerase II and the general transcription factors. On recruitment the Mediator complex unfolds to an extended conformation and partially surrounds RNA polymerase II, specifically interacting with the unphosphorylated form of the C-terminal domain (CTD) of RNA polymerase II. The Mediator complex dissociates from the RNA polymerase II holoenzyme and stays at the promoter when transcriptional elongation begins. The Mediator complex is composed of at least 31 subunits: MED1, MED4, MED6, MED7, MED8, MED9, MED10, MED11, MED12, MED13, MED13L, MED14, MED15, MED16, MED17, MED18, MED19, MED20, MED21, MED22, MED23, MED24, MED25, MED26, MED27, MED29, MED30, MED31, CCNC, CDK8 and CDC2L6/CDK11. The subunits form at least three structurally distinct submodules. The head and the middle modules interact directly with RNA polymerase II, whereas the elongated tail module interacts with gene-specific regulatory proteins. Mediator containing the CDK8 module is less active than Mediator lacking this module in supporting transcriptional activation. The head module contains: MED6, MED8, MED11, SRB4/MED17, SRB5/MED18, ROX3/MED19, SRB2/MED20 and SRB6/MED22. The middle module contains: MED1, MED4, NUT1/MED5, MED7, CSE2/MED9, NUT2/MED10, SRB7/MED21 and SOH1/MED31. CSE2/MED9 interacts directly with MED4. The tail module contains: MED2, PGD1/MED3, RGR1/MED14, GAL11/MED15 and SIN4/MED16. The CDK8 module contains: MED12, MED13, CCNC and CDK8. Individual preparations of the Mediator complex lacking one or more distinct subunits have been variously termed ARC, CRSP, DRIP, PC2, SMCC and TRAP. Med12 is a component of the evolutionarily conserved Mediator complex []. The Med12 subunit may specifically regulate transcription of targets of the Wnt signaling pathway and SHH signaling pathway. Med12 is a negative regulator of the Gli3-dependent sonic hedgehog signaling pathway via its interaction with Gli3 within the Mediator. A complex is formed between Med12, Med13, CDK8 and CycC which is responsible for suppression of transcription []. ; GO: 0001104 RNA polymerase II transcription cofactor activity, 0006357 regulation of transcription from RNA polymerase II promoter, 0016592 mediator complex
Probab=23.34 E-value=29 Score=23.03 Aligned_cols=31 Identities=23% Similarity=0.441 Sum_probs=24.4
Q ss_pred CCCCCCCCccccccCCCCCceEECCChHHHHHHHH
Q 030909 2 SSSNNSNNNIRMVEAQLPPGFRFHPRDDELVCDYL 36 (169)
Q Consensus 2 ~~~~~~~~~~~~~~~~LP~G~RF~PTDeELI~~YL 36 (169)
+++++++-+++...-..|.|+| -++|+....
T Consensus 20 ~dLa~~~~pL~~Lsk~iPhg~k----~~~ll~~l~ 50 (64)
T PF09497_consen 20 KDLANPNVPLRKLSKKIPHGIK----KEELLEQLC 50 (64)
T ss_pred HHHcCCCCCHHHHHHHCCCccc----HHHHHHHHH
Confidence 3567777888888888999998 888888444
No 10
>PF07131 DUF1382: Protein of unknown function (DUF1382); InterPro: IPR009814 This entry is represented by Bacteriophage lambda, Xis. This entry overlaps with IPR009750, both representing lambda Xis. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. This family consists of several hypothetical Escherichia coli and Bacteriophage lambda-like proteins of around 60 residues in length. The function of this family is unknown.
Probab=22.45 E-value=59 Score=21.41 Aligned_cols=14 Identities=43% Similarity=0.776 Sum_probs=10.8
Q ss_pred CceEECC----ChHHHHH
Q 030909 20 PGFRFHP----RDDELVC 33 (169)
Q Consensus 20 ~G~RF~P----TDeELI~ 33 (169)
.|+||.| ||+|+..
T Consensus 22 ~GIRFVpiPv~~dee~~~ 39 (61)
T PF07131_consen 22 IGIRFVPIPVVTDEEFHT 39 (61)
T ss_pred cCceeeccccccHHHHHH
Confidence 5999999 6777643
No 11
>cd00954 NAL N-Acetylneuraminic acid aldolase, also called N-acetylneuraminate lyase (NAL), which catalyses the reversible aldol reaction of N-acetyl-D-mannosamine and pyruvate to give N-acetyl-D-neuraminic acid (D-sialic acid). It has a widespread application as biocatalyst for the synthesis of sialic acid and its derivatives. This enzyme has been shown to be quite specific for pyruvate as the donor, but flexible to a variety of D- and, to some extent, L-hexoses and pentoses as acceptor substrates. NAL is member of dihydrodipicolinate synthase family that comprises several pyruvate-dependent class I aldolases.
Probab=22.38 E-value=54 Score=27.35 Aligned_cols=19 Identities=16% Similarity=0.102 Sum_probs=13.6
Q ss_pred CCCceEECCChHHHHHHHHh
Q 030909 18 LPPGFRFHPRDDELVCDYLM 37 (169)
Q Consensus 18 LP~G~RF~PTDeELI~~YL~ 37 (169)
+||- -|.||++||+.||..
T Consensus 103 ~~P~-y~~~~~~~i~~~~~~ 121 (288)
T cd00954 103 ITPF-YYKFSFEEIKDYYRE 121 (288)
T ss_pred eCCC-CCCCCHHHHHHHHHH
Confidence 3554 478999999996543
No 12
>PLN02417 dihydrodipicolinate synthase
Probab=22.33 E-value=56 Score=27.27 Aligned_cols=18 Identities=11% Similarity=0.333 Sum_probs=14.1
Q ss_pred CCCceEECCChHHHHHHHH
Q 030909 18 LPPGFRFHPRDDELVCDYL 36 (169)
Q Consensus 18 LP~G~RF~PTDeELI~~YL 36 (169)
+|| +-|.||++||+.||-
T Consensus 103 ~~P-~y~~~~~~~i~~~f~ 120 (280)
T PLN02417 103 INP-YYGKTSQEGLIKHFE 120 (280)
T ss_pred cCC-ccCCCCHHHHHHHHH
Confidence 455 568999999999763
No 13
>TIGR02313 HpaI-NOT-DapA 2,4-dihydroxyhept-2-ene-1,7-dioic acid aldolase. This model represents a subset of the DapA (dihydrodipicolinate synthase) family which has apparently evolved a separate function. The product of DapA, dihydrodipicolinate, results from the non-enzymatic cyclization and dehydration of 6-amino-2,4-dihydroxyhept-2-ene-1,7-dioic acid, which is different from the substrate of this reaction only in the presence of the amino group. In the absence of this amino group, and running the reaction in the opposite direction, the reaction corresponds to the HpaI aldolase component of the 4-hydroxyphenylacetic acid catabolism pathway (see TIGR02311). At present, this variant of DapA is found only in Oceanobacillus iheyensis HTE831 and Thermus thermophilus HB27. In both of these cases, one or more other DapA genes can be found and the one identified by this model is part of an operon for 4-hydroxyphenylacetic acid catabolism.
Probab=20.40 E-value=67 Score=27.03 Aligned_cols=19 Identities=16% Similarity=0.244 Sum_probs=13.9
Q ss_pred CCCceEECCChHHHHHHHHh
Q 030909 18 LPPGFRFHPRDDELVCDYLM 37 (169)
Q Consensus 18 LP~G~RF~PTDeELI~~YL~ 37 (169)
+||- .|.|++++|+.||-.
T Consensus 102 ~pP~-y~~~~~~~l~~~f~~ 120 (294)
T TIGR02313 102 IVPY-YNKPNQEALYDHFAE 120 (294)
T ss_pred cCcc-CCCCCHHHHHHHHHH
Confidence 3444 489999999996643
Done!