Query 009389
Match_columns 536
No_of_seqs 198 out of 972
Neff 4.8
Searched_HMMs 46136
Date Thu Mar 28 12:31:44 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/009389.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/009389hhsearch_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 7E-41 1.5E-45 301.5 5.4 127 10-138 1-129 (129)
2 KOG3238 Chloride ion current i 17.5 1.2E+02 0.0027 30.5 3.1 66 7-72 106-171 (216)
3 PF11669 WBP-1: WW domain-bind 12.5 1.3E+02 0.0028 26.8 1.7 14 514-527 23-36 (102)
4 PF10954 DUF2755: Protein of u 11.0 1.9E+02 0.0041 25.8 2.2 20 504-523 20-39 (100)
5 PF10856 DUF2678: Protein of u 10.6 2.4E+02 0.0053 26.2 2.8 19 509-527 91-109 (118)
6 PF05865 Cypo_polyhedrin: Cypo 10.3 2.3E+02 0.005 27.9 2.7 28 90-117 140-168 (248)
7 smart00265 BH4 BH4 Bcl-2 homol 10.1 2.9E+02 0.0063 19.4 2.4 20 19-38 4-23 (27)
8 PF15281 Consortin_C: Consorti 10.0 3.4E+02 0.0074 25.0 3.5 41 490-534 34-75 (113)
9 TIGR03510 XapX XapX domain. Th 9.9 1.1E+02 0.0024 24.2 0.3 9 414-422 22-30 (49)
10 cd06228 Peptidase_M14-like_3 A 9.4 2.3E+02 0.005 30.5 2.6 39 458-496 274-316 (332)
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=7e-41 Score=301.46 Aligned_cols=127 Identities=53% Similarity=1.026 Sum_probs=97.2
Q ss_pred CCCCceeCCChHHHHHHHHHHHhcCCCCCC-CCeeeccCCCCCCCCCCcccccCCCCcceeeeeccccccCCCCcccccC
Q 009389 10 LAPGFRFHPTDEELVRYYLKRKVCHRSLRF-NPICVTDIYKSEPWDLPDKSSLKTRDKEWYFFSMLDKKYGNGSRTNRAT 88 (536)
Q Consensus 10 LPPGfRF~PTDEELI~~YL~rKi~G~pl~~-~~I~evDVY~~dPWdLp~~~~~~~~d~eWYFFs~r~rK~~nG~R~nR~t 88 (536)
|||||||+|||+|||.+||++|+.|.+++. ++|+++|||.+|||+|++.. .+++.+||||+++++++.++.|.+|++
T Consensus 1 LP~G~rF~PtD~ELi~~yL~~k~~g~~~~~~~~i~~~Diy~~~P~~L~~~~--~~~~~~~yFF~~~~~~~~~~~r~~R~~ 78 (129)
T PF02365_consen 1 LPPGFRFRPTDEELINHYLRPKILGEPLPCEDVIHDVDIYSAHPWELPAKF--KGGDEEWYFFSPRKKKYPNGGRPNRVT 78 (129)
T ss_dssp --TTEEE---HHHHHHCTHHHHHTT-HHCS-CHSEE--GGGS-GGGCHHHS--SS-SSEEEEEEE----------S-EEE
T ss_pred CCCceEecCChHHHHHHHHHHHhcCCCCCcccceeecccCccChHHhhhhc--cCCCceEEEEEecccccCCcccccccc
Confidence 899999999999999999999999999887 68999999999999999532 335679999999999999999999999
Q ss_pred ccceeeecCCCceeec-CCeeEEEEEEEEeecCCCCCCCCcCeEEEEEEeC
Q 009389 89 EKGYWKTTGKDRPVHH-NTRTVGMKKTLVYHMGRAPHGERTNWVMHEYRLT 138 (536)
Q Consensus 89 ggGyWK~tG~~k~I~~-~g~vVG~KKtLvFy~Gr~p~G~kT~WvMhEY~L~ 138 (536)
++|+||.+|+.++|.. ++.+||+||+|+||.++.+++.+|+|+||||+|.
T Consensus 79 ~~G~Wk~~g~~~~i~~~~g~~iG~k~~l~f~~~~~~~~~kt~W~M~EY~L~ 129 (129)
T PF02365_consen 79 GGGYWKSTGKEKPIKDPGGKVIGFKKTLVFYSGKSPNGKKTGWVMHEYSLE 129 (129)
T ss_dssp TTEEEEEECEEEEEEE-TTCEEEEEEEEEEEESSTTS-EEEEEEEEEEEE-
T ss_pred cceEEeecccccccccccceeeeeEEEEEEEeccCCCCCcCCeEEEEEEeC
Confidence 9999999999999987 8999999999999998888899999999999984
No 2
>KOG3238 consensus Chloride ion current inducer protein [Inorganic ion transport and metabolism]
Probab=17.46 E-value=1.2e+02 Score=30.55 Aligned_cols=66 Identities=18% Similarity=0.283 Sum_probs=41.9
Q ss_pred CCCCCCCceeCCChHHHHHHHHHHHhcCCCCCCCCeeeccCCCCCCCCCCcccccCCCCcceeeee
Q 009389 7 STSLAPGFRFHPTDEELVRYYLKRKVCHRSLRFNPICVTDIYKSEPWDLPDKSSLKTRDKEWYFFS 72 (536)
Q Consensus 7 ~~~LPPGfRF~PTDEELI~~YL~rKi~G~pl~~~~I~evDVY~~dPWdLp~~~~~~~~d~eWYFFs 72 (536)
.+..--+|||+|+|.--+...-.......-+.+....+.+-|.-+=|+.-......+....||=+.
T Consensus 106 dve~i~e~rfvpsDk~~l~a~f~qfcecqel~p~P~ED~~~~dgee~~mea~d~~~gDs~~~~t~d 171 (216)
T KOG3238|consen 106 DVEPITEFRFVPSDKSALEAMFTQFCECQELNPDPDEDEDDYDGEEYDMEAHDAGQGDSPNSYTYD 171 (216)
T ss_pred cccccccceecCCchhHHHHHHHHHHhhhhcCCCccccccccccchhhhhhhhccCCCCccccccc
Confidence 455677999999998777764344444555555446666777766677655444445555565553
No 3
>PF11669 WBP-1: WW domain-binding protein 1; InterPro: IPR021684 This family of proteins represents WBP-1, a ligand of the WW domain of Yes-associated protein. This protein has a proline-rich domain. WBP-1 does not bind to the SH3 domain [].
Probab=12.50 E-value=1.3e+02 Score=26.84 Aligned_cols=14 Identities=14% Similarity=0.745 Sum_probs=9.4
Q ss_pred HHHHHHHHHHhhee
Q 009389 514 LLLFLWIIILSVGF 527 (536)
Q Consensus 514 ~~~f~~~~~l~~s~ 527 (536)
+|.++|+||+++++
T Consensus 23 ~FWlv~~liill~c 36 (102)
T PF11669_consen 23 YFWLVWVLIILLSC 36 (102)
T ss_pred HHHHHHHHHHHHHH
Confidence 45557888877664
No 4
>PF10954 DUF2755: Protein of unknown function (DUF2755); InterPro: IPR020513 This entry contains membrane proteins with no known function.; GO: 0016021 integral to membrane
Probab=11.00 E-value=1.9e+02 Score=25.82 Aligned_cols=20 Identities=20% Similarity=0.373 Sum_probs=14.4
Q ss_pred ccchhhhHHHHHHHHHHHHH
Q 009389 504 TGSVVFRSLWLLLFLWIIIL 523 (536)
Q Consensus 504 t~~~v~r~~~~~~f~~~~~l 523 (536)
|..-+.-+.|.||||||=--
T Consensus 20 t~gNiAYAlFVLfcfWaGaQ 39 (100)
T PF10954_consen 20 TPGNIAYALFVLFCFWAGAQ 39 (100)
T ss_pred CcchhHHHHHHHHHHHhhHH
Confidence 33346678999999998543
No 5
>PF10856 DUF2678: Protein of unknown function (DUF2678); InterPro: IPR022564 This family of proteins has no known function.
Probab=10.64 E-value=2.4e+02 Score=26.21 Aligned_cols=19 Identities=26% Similarity=0.347 Sum_probs=16.3
Q ss_pred hhHHHHHHHHHHHHHhhee
Q 009389 509 FRSLWLLLFLWIIILSVGF 527 (536)
Q Consensus 509 ~r~~~~~~f~~~~~l~~s~ 527 (536)
.|-.+|++++++++|.++-
T Consensus 91 fr~li~~~~~~ivllci~a 109 (118)
T PF10856_consen 91 FRYLIYYNCFSIVLLCICA 109 (118)
T ss_pred HHHHHHHHHHHHHHHHHhh
Confidence 7999999999999987763
No 6
>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=10.32 E-value=2.3e+02 Score=27.95 Aligned_cols=28 Identities=29% Similarity=0.530 Sum_probs=18.1
Q ss_pred cceeeecC-CCceeecCCeeEEEEEEEEe
Q 009389 90 KGYWKTTG-KDRPVHHNTRTVGMKKTLVY 117 (536)
Q Consensus 90 gGyWK~tG-~~k~I~~~g~vVG~KKtLvF 117 (536)
.--|.+|| +-|.|+..|++||+...|..
T Consensus 140 shpweatgikyrki~~dgeivgyshyfel 168 (248)
T PF05865_consen 140 SHPWEATGIKYRKIHRDGEIVGYSHYFEL 168 (248)
T ss_dssp --S-B--GGG-EEEEETTEEEEEEEEEE-
T ss_pred cCCccccCceEEEeeccceEeeeeeeeec
Confidence 34699999 56788889999999988865
No 7
>smart00265 BH4 BH4 Bcl-2 homology region 4.
Probab=10.11 E-value=2.9e+02 Score=19.42 Aligned_cols=20 Identities=25% Similarity=0.403 Sum_probs=15.8
Q ss_pred ChHHHHHHHHHHHhcCCCCC
Q 009389 19 TDEELVRYYLKRKVCHRSLR 38 (536)
Q Consensus 19 TDEELI~~YL~rKi~G~pl~ 38 (536)
+-.|||.+|+.-|+.-+..+
T Consensus 4 ~nRelV~~yv~yKLsQrgy~ 23 (27)
T smart00265 4 DNRELVVDYVTYKLSQNGYE 23 (27)
T ss_pred chHHHHHHHHHHHHhhcCCC
Confidence 45799999999999865443
No 8
>PF15281 Consortin_C: Consortin C-terminus
Probab=9.97 E-value=3.4e+02 Score=25.04 Aligned_cols=41 Identities=29% Similarity=0.283 Sum_probs=23.8
Q ss_pred CCCC-CCCcccccCcccchhhhHHHHHHHHHHHHHhheeeeeeEEe
Q 009389 490 PTSF-EPAGNIFSGKTGSVVFRSLWLLLFLWIIILSVGFKIGACVS 534 (536)
Q Consensus 490 ~~~~-~~~~~~~~~~t~~~v~r~~~~~~f~~~~~l~~s~k~g~~i~ 534 (536)
-|-| ||+....- --+...+|..|+|+|+--++||+ .|+.+|
T Consensus 34 rVRF~eped~~dq-d~~~g~Scl~L~LlclvTv~lS~---gGTALY 75 (113)
T PF15281_consen 34 RVRFQEPEDTLDQ-DEVGGDSCLLLLLLCLVTVVLSV---GGTALY 75 (113)
T ss_pred eeeeeCccccccc-cccCCCccHHHHHHHHHHHHHhc---cceEEE
Confidence 5666 66655330 11223467778887776666655 677776
No 9
>TIGR03510 XapX XapX domain. This model describes an uncharacterized small, hydrophobic protein of about 50 amino acids, found between the xapB and xapR genes of the E. coli xanthosine utilization system, and homologous regions in other small proteins, such as the N-terminal region of DUF1427 (Pfam model pfam07235). We name this domain XapX, as it comprises the full length of the protein encoded between the genes for the well-studied XapB and XapR proteins.
Probab=9.86 E-value=1.1e+02 Score=24.22 Aligned_cols=9 Identities=33% Similarity=0.490 Sum_probs=7.1
Q ss_pred CCCCCcccc
Q 009389 414 NVAAAPAFA 422 (536)
Q Consensus 414 ~ipappa~a 422 (536)
-|||||..|
T Consensus 22 p~PAPP~la 30 (49)
T TIGR03510 22 PSPAPPVLA 30 (49)
T ss_pred CCCCCchHH
Confidence 479999876
No 10
>cd06228 Peptidase_M14-like_3 A functionally uncharacterized subgroup of the M14 family of metallocarboxypeptidases (MCPs). The M14 family are zinc-binding carboxypeptidases (CPs) which hydrolyze single, C-terminal amino acids from polypeptide chains, and have a recognition site for the free C-terminal carboxyl group, which is a key determinant of specificity. Two major subfamilies of the M14 family, defined based on sequence and structural homology, are the A/B and N/E subfamilies. Enzymes belonging to the A/B subfamily are normally synthesized as inactive precursors containing preceding signal peptide, followed by an N-terminal pro-region linked to the enzyme; these proenzymes are called procarboxypeptidases. The A/B enzymes can be further divided based on their substrate specificity; Carboxypeptidase A-like (CPA-like) enzymes favor hydrophobic residues while carboxypeptidase B-like (CPB-like) enzymes only cleave the basic residues lysine or arginine. The A forms have slightly differe
Probab=9.42 E-value=2.3e+02 Score=30.50 Aligned_cols=39 Identities=21% Similarity=0.378 Sum_probs=31.1
Q ss_pred ecCCCccccccc---CCCeeEEEEEeeccCCCCCC-CCCCCCC
Q 009389 458 LSGSGLDWSVGK---NGDMNIVFSFDLSQNVISPS-PTSFEPA 496 (536)
Q Consensus 458 ~~~~~~~w~~~k---~g~~~~~~s~~~~~~~~~~~-~~~~~~~ 496 (536)
.+|+++||.++. +|...+.+||++|=++..+. ..||.|.
T Consensus 274 ~sG~s~D~ay~~~~~~~~~~~~~s~t~El~~~~~~~~~gF~~p 316 (332)
T cd06228 274 TSGASDDYAFSRHFADAVKRKVFSYTIEFGETNSEAECPFYPT 316 (332)
T ss_pred CCCChhhhhhhccccccccCceEEEEEEeCCCCCCCCcCCCCC
Confidence 469999999984 78888999999998877643 5578664
Done!