Query 008907
Match_columns 549
No_of_seqs 202 out of 976
Neff 4.4
Searched_HMMs 46136
Date Thu Mar 28 18:04:35 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/008907.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/008907hhsearch_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 2.6E-41 5.7E-46 303.7 5.6 127 10-138 1-129 (129)
2 KOG3238 Chloride ion current i 17.4 1.2E+02 0.0027 30.7 3.1 65 8-72 107-171 (216)
3 smart00265 BH4 BH4 Bcl-2 homol 13.8 1.9E+02 0.004 20.6 2.4 21 19-39 4-24 (27)
4 PF05865 Cypo_polyhedrin: Cypo 12.6 1.8E+02 0.0038 29.0 2.7 28 90-117 140-168 (248)
5 PF11669 WBP-1: WW domain-bind 11.3 1.5E+02 0.0033 26.6 1.7 14 527-540 23-36 (102)
6 PF10954 DUF2755: Protein of u 10.0 2.2E+02 0.0047 25.7 2.2 21 517-537 20-40 (100)
7 PF15281 Consortin_C: Consorti 9.8 3.5E+02 0.0075 25.2 3.5 41 503-547 34-75 (113)
8 PF10856 DUF2678: Protein of u 9.6 2.8E+02 0.006 26.0 2.8 19 522-540 91-109 (118)
9 TIGR03510 XapX XapX domain. Th 9.2 1.2E+02 0.0027 24.2 0.3 9 427-435 22-30 (49)
10 cd06228 Peptidase_M14-like_3 A 9.0 2.4E+02 0.0053 30.4 2.6 39 471-509 274-316 (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=2.6e-41 Score=303.74 Aligned_cols=127 Identities=53% Similarity=1.026 Sum_probs=97.5
Q ss_pred CCCCceeCCChHHHHHHHHHHHhcCCCCCC-CCeeecCCCCCCCCCCCcccccCCCCcceEeeeccccccCCCCcccccc
Q 008907 10 LAPGFRFHPTDEELVRYYLKRKVCHRSLRF-NPICVTDIYKSEPWDLPDKSSLKTRDKEWYFFSMLDKKYGNGSRTNRAT 88 (549)
Q Consensus 10 LPPGfRF~PTDEELV~~YLkrKi~G~plp~-d~I~evDVY~~ePWdLP~~s~~~~~d~eWYFFspr~kKy~nG~R~nRat 88 (549)
|||||||+|||+|||.+||++|+.|.+++. ++|+++|||.+|||+|+... +.++++||||+++++++.+|.|.+|++
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 345779999999999999999999999
Q ss_pred ccceeeecCCceeeec-CCeeEEEEEEEEeecCCCCCCCccCeEEEEEEeC
Q 008907 89 EKGYWKTTGKDRPVHH-NTRTVGMKKTLVYHMGRAPHGERTNWVMHEYRLT 138 (549)
Q Consensus 89 ggGyWKatGk~r~I~~-~g~vVG~KKtLvFy~Grap~G~KT~WvMhEYrL~ 138 (549)
++|+||.+|+.++|.. ++++||+||+|+||.++.+++.+|+|+||||+|.
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 9999999999999997 9999999999999999888999999999999984
No 2
>KOG3238 consensus Chloride ion current inducer protein [Inorganic ion transport and metabolism]
Probab=17.39 E-value=1.2e+02 Score=30.72 Aligned_cols=65 Identities=18% Similarity=0.285 Sum_probs=41.4
Q ss_pred CCCCCCceeCCChHHHHHHHHHHHhcCCCCCCCCeeecCCCCCCCCCCCcccccCCCCcceEeee
Q 008907 8 TSLAPGFRFHPTDEELVRYYLKRKVCHRSLRFNPICVTDIYKSEPWDLPDKSSLKTRDKEWYFFS 72 (549)
Q Consensus 8 ~~LPPGfRF~PTDEELV~~YLkrKi~G~plp~d~I~evDVY~~ePWdLP~~s~~~~~d~eWYFFs 72 (549)
...--+|||+|+|.--+..--......+.+.++...+.+-|.-+=|+.-.....++....||=+.
T Consensus 107 ve~i~e~rfvpsDk~~l~a~f~qfcecqel~p~P~ED~~~~dgee~~mea~d~~~gDs~~~~t~d 171 (216)
T KOG3238|consen 107 VEPITEFRFVPSDKSALEAMFTQFCECQELNPDPDEDEDDYDGEEYDMEAHDAGQGDSPNSYTYD 171 (216)
T ss_pred ccccccceecCCchhHHHHHHHHHHhhhhcCCCccccccccccchhhhhhhhccCCCCccccccc
Confidence 45567899999998777764444445566655556667777777777755444444455565543
No 3
>smart00265 BH4 BH4 Bcl-2 homology region 4.
Probab=13.81 E-value=1.9e+02 Score=20.59 Aligned_cols=21 Identities=24% Similarity=0.441 Sum_probs=16.5
Q ss_pred ChHHHHHHHHHHHhcCCCCCC
Q 008907 19 TDEELVRYYLKRKVCHRSLRF 39 (549)
Q Consensus 19 TDEELV~~YLkrKi~G~plp~ 39 (549)
+-.|||.+|+.-|+.-+..++
T Consensus 4 ~nRelV~~yv~yKLsQrgy~w 24 (27)
T smart00265 4 DNRELVVDYVTYKLSQNGYEW 24 (27)
T ss_pred chHHHHHHHHHHHHhhcCCCC
Confidence 457999999999998665543
No 4
>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=12.57 E-value=1.8e+02 Score=28.98 Aligned_cols=28 Identities=29% Similarity=0.530 Sum_probs=18.4
Q ss_pred cceeeecC-CceeeecCCeeEEEEEEEEe
Q 008907 90 KGYWKTTG-KDRPVHHNTRTVGMKKTLVY 117 (549)
Q Consensus 90 gGyWKatG-k~r~I~~~g~vVG~KKtLvF 117 (549)
.--|.+|| +-|.|..+|++||+...|..
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 35699999 67888899999999988754
No 5
>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=11.25 E-value=1.5e+02 Score=26.58 Aligned_cols=14 Identities=14% Similarity=0.745 Sum_probs=9.2
Q ss_pred HHHHHHHHHHhhee
Q 008907 527 LLLFLWIIILSVGF 540 (549)
Q Consensus 527 ~~~f~~~~~l~~s~ 540 (549)
+|.++|+||+++++
T Consensus 23 ~FWlv~~liill~c 36 (102)
T PF11669_consen 23 YFWLVWVLIILLSC 36 (102)
T ss_pred HHHHHHHHHHHHHH
Confidence 45557787777654
No 6
>PF10954 DUF2755: Protein of unknown function (DUF2755); InterPro: IPR020513 This entry contains membrane proteins with no known function.; GO: 0016021 integral to membrane
Probab=9.95 E-value=2.2e+02 Score=25.70 Aligned_cols=21 Identities=19% Similarity=0.322 Sum_probs=14.8
Q ss_pred ccchhhhHHHHHHHHHHHHHh
Q 008907 517 TGSVVFRSLWLLLFLWIIILS 537 (549)
Q Consensus 517 t~~~v~r~~~~~~f~~~~~l~ 537 (549)
|..-+.-+.|.||||||=--+
T Consensus 20 t~gNiAYAlFVLfcfWaGaQl 40 (100)
T PF10954_consen 20 TPGNIAYALFVLFCFWAGAQL 40 (100)
T ss_pred CcchhHHHHHHHHHHHhhHHH
Confidence 333466789999999985433
No 7
>PF15281 Consortin_C: Consortin C-terminus
Probab=9.82 E-value=3.5e+02 Score=25.20 Aligned_cols=41 Identities=29% Similarity=0.283 Sum_probs=24.1
Q ss_pred CCCC-CCCcccccCcccchhhhHHHHHHHHHHHHHhheeeeeeEEe
Q 008907 503 PTSF-EPAGNIFSGKTGSVVFRSLWLLLFLWIIILSVGFKIGACVS 547 (549)
Q Consensus 503 ~~~~-~~~~~~~~~~t~~~v~r~~~~~~f~~~~~l~~s~k~g~~i~ 547 (549)
-|-| ||+....- --+...+|..|+|+|+--++||+ .|+.+|
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 11223477778887776666655 577766
No 8
>PF10856 DUF2678: Protein of unknown function (DUF2678); InterPro: IPR022564 This family of proteins has no known function.
Probab=9.63 E-value=2.8e+02 Score=26.05 Aligned_cols=19 Identities=26% Similarity=0.347 Sum_probs=16.3
Q ss_pred hhHHHHHHHHHHHHHhhee
Q 008907 522 FRSLWLLLFLWIIILSVGF 540 (549)
Q Consensus 522 ~r~~~~~~f~~~~~l~~s~ 540 (549)
.|-.+|++++++++|.++-
T Consensus 91 fr~li~~~~~~ivllci~a 109 (118)
T PF10856_consen 91 FRYLIYYNCFSIVLLCICA 109 (118)
T ss_pred HHHHHHHHHHHHHHHHHhh
Confidence 7999999999999887763
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=9.17 E-value=1.2e+02 Score=24.20 Aligned_cols=9 Identities=33% Similarity=0.490 Sum_probs=7.1
Q ss_pred CCCCCcccc
Q 008907 427 NVAAAPAFA 435 (549)
Q Consensus 427 ~ipappa~a 435 (549)
-|||||..|
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=9.03 E-value=2.4e+02 Score=30.43 Aligned_cols=39 Identities=21% Similarity=0.378 Sum_probs=31.1
Q ss_pred ecCCCccccccc---CCCeeEEEEEeeccCCCCCC-CCCCCCC
Q 008907 471 LSGSGLDWSVGK---NGDMNIVFSFDLSQNVISPS-PTSFEPA 509 (549)
Q Consensus 471 ~~~~~~~w~~~k---ng~~~~~~s~~~~~~~~~~~-~~~~~~~ 509 (549)
.+|+++||.++. +|...+.+||++|=++..+. ..||.|.
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 5688664
Done!