Query 007393
Match_columns 605
No_of_seqs 199 out of 969
Neff 4.4
Searched_HMMs 46136
Date Thu Mar 28 22:59:03 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/007393.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/007393hhsearch_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 4.1E-41 8.9E-46 305.8 6.0 127 9-137 1-129 (129)
2 PF15176 LRR19-TM: Leucine-ric 43.9 27 0.00059 32.1 3.5 32 573-605 13-50 (102)
3 PHA02692 hypothetical protein; 34.5 39 0.00085 29.2 2.8 21 558-581 29-49 (70)
4 PHA03054 IMV membrane protein; 33.2 47 0.001 28.8 3.1 34 558-593 29-62 (72)
5 PHA02844 putative transmembran 28.1 65 0.0014 28.3 3.1 6 558-563 29-34 (75)
6 PF12575 DUF3753: Protein of u 26.9 69 0.0015 27.9 3.1 7 559-565 30-36 (72)
7 PF08173 YbgT_YccB: Membrane b 25.2 99 0.0022 22.4 3.1 20 580-599 5-24 (28)
8 PHA02819 hypothetical protein; 23.8 84 0.0018 27.3 3.0 20 572-593 41-60 (71)
9 PF15183 MRAP: Melanocortin-2 21.8 93 0.002 28.0 3.0 37 560-596 20-59 (90)
10 PF10669 Phage_Gp23: Protein g 20.7 1E+02 0.0022 28.5 3.1 17 583-599 23-39 (121)
11 PHA02975 hypothetical protein; 20.4 1E+02 0.0022 26.7 2.8 9 558-566 29-37 (69)
12 PHA00476 hypothetical protein 20.3 93 0.002 28.8 2.8 29 570-600 33-61 (110)
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=4.1e-41 Score=305.81 Aligned_cols=127 Identities=56% Similarity=1.086 Sum_probs=97.2
Q ss_pred CCCCceeCCChHHHHHHHHHHHHCCCCCCC-CCeeeccCCCCCCCCCCcccccccCCceEEEeeccCCCCCCCCCccccc
Q 007393 9 LPLGFRFRPTDEELVDFYLRMKINGHNDEV-SVISEIDVCKREPWDLPDLSVIKTKDREWFFFCPQDRKYPNGHRLNRAT 87 (605)
Q Consensus 9 LPpGFRF~PTDEELI~~YLr~KI~G~plp~-~~I~evDVY~~ePWdLP~~~~~k~~e~eWYFFspr~rKypnG~R~nRat 87 (605)
|||||||+|||+|||.+||++|+.|.+++. .+|+++|||.+|||+||+. .+.++.+||||+++++++++|.|.+|++
T Consensus 1 LP~G~rF~PtD~ELi~~yL~~k~~g~~~~~~~~i~~~Diy~~~P~~L~~~--~~~~~~~~yFF~~~~~~~~~~~r~~R~~ 78 (129)
T PF02365_consen 1 LPPGFRFRPTDEELINHYLRPKILGEPLPCEDVIHDVDIYSAHPWELPAK--FKGGDEEWYFFSPRKKKYPNGGRPNRVT 78 (129)
T ss_dssp --TTEEE---HHHHHHCTHHHHHTT-HHCS-CHSEE--GGGS-GGGCHHH--SSS-SSEEEEEEE----------S-EEE
T ss_pred CCCceEecCChHHHHHHHHHHHhcCCCCCcccceeecccCccChHHhhhh--ccCCCceEEEEEecccccCCcccccccc
Confidence 899999999999999999999999999887 7999999999999999942 2346679999999999999999999999
Q ss_pred ccceeeecCCceeecc-CceeeeeEEEEEEeeCcCCCCCCcCeEEEEEEeC
Q 007393 88 AAGYWKATGKDRKIKS-GNHLIGMKKTLVFHMGRAPKGKRTNWVMHEYRAT 137 (605)
Q Consensus 88 g~GyWKatGkdk~I~s-gg~lIG~KKtLvFy~Grapkg~KT~WvMhEYrL~ 137 (605)
++|+||++|+.++|.. ++.+||+||+|+||.++.+++.+|+|+||||+|.
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 8899999999999999888999999999999983
No 2
>PF15176 LRR19-TM: Leucine-rich repeat family 19 TM domain
Probab=43.90 E-value=27 Score=32.11 Aligned_cols=32 Identities=9% Similarity=0.219 Sum_probs=17.2
Q ss_pred CCcchhHHHHHHHHHHHH---HHHHH---hhhhheeccC
Q 007393 573 HSNRSFAVLFRAAAVVVM---FAILV---STWRCLCLNF 605 (605)
Q Consensus 573 ~s~~~~~~~~~~~~v~vl---~~vl~---~~Wr~l~~~~ 605 (605)
+++.| .++|.+|+++++ +|+|+ -+|+.+.++|
T Consensus 13 ~g~sW-~~LVGVv~~al~~SlLIalaaKC~~~~k~~~SY 50 (102)
T PF15176_consen 13 GGRSW-PFLVGVVVTALVTSLLIALAAKCPVWYKYLASY 50 (102)
T ss_pred CCccc-HhHHHHHHHHHHHHHHHHHHHHhHHHHHHHhcc
Confidence 35557 566555554443 33333 3687777654
No 3
>PHA02692 hypothetical protein; Provisional
Probab=34.55 E-value=39 Score=29.21 Aligned_cols=21 Identities=19% Similarity=0.191 Sum_probs=12.3
Q ss_pred eeeeccccCccccCCCCcchhHHH
Q 007393 558 TVLMDKDTSNTFRAGHSNRSFAVL 581 (605)
Q Consensus 558 ~~~~~kv~s~~~ka~~s~~~~~~~ 581 (605)
+++.+|.++ +++++..|...+
T Consensus 29 sVLtDk~~~---~~~~~~~~~~~i 49 (70)
T PHA02692 29 TVMTEKPAC---DRSKGVPWTTVF 49 (70)
T ss_pred HHHcCCCcc---cccCCcchHHHH
Confidence 467778555 566666663333
No 4
>PHA03054 IMV membrane protein; Provisional
Probab=33.16 E-value=47 Score=28.83 Aligned_cols=34 Identities=15% Similarity=0.108 Sum_probs=15.0
Q ss_pred eeeeccccCccccCCCCcchhHHHHHHHHHHHHHHH
Q 007393 558 TVLMDKDTSNTFRAGHSNRSFAVLFRAAAVVVMFAI 593 (605)
Q Consensus 558 ~~~~~kv~s~~~ka~~s~~~~~~~~~~~~v~vl~~v 593 (605)
+++.+|-+.+.-+-+++..| +++..+++++++++
T Consensus 29 sVl~dk~~~~~~~~~~~~~~--~~~ii~l~~v~~~~ 62 (72)
T PHA03054 29 SVLSDEKTVTSTNNTGCWGW--YWLIIIFFIVLILL 62 (72)
T ss_pred HHHcCCCCcccccccCCchH--HHHHHHHHHHHHHH
Confidence 45667755522122445555 33333344444333
No 5
>PHA02844 putative transmembrane protein; Provisional
Probab=28.14 E-value=65 Score=28.25 Aligned_cols=6 Identities=50% Similarity=0.706 Sum_probs=3.4
Q ss_pred eeeecc
Q 007393 558 TVLMDK 563 (605)
Q Consensus 558 ~~~~~k 563 (605)
+++.+|
T Consensus 29 sVLtd~ 34 (75)
T PHA02844 29 SVLSDD 34 (75)
T ss_pred HHHcCC
Confidence 346666
No 6
>PF12575 DUF3753: Protein of unknown function (DUF3753); InterPro: IPR009175 This group represents an uncharacterised conserved protein belonging to poxvirus family I2.
Probab=26.88 E-value=69 Score=27.91 Aligned_cols=7 Identities=57% Similarity=0.729 Sum_probs=3.4
Q ss_pred eeecccc
Q 007393 559 VLMDKDT 565 (605)
Q Consensus 559 ~~~~kv~ 565 (605)
++.+|-+
T Consensus 30 Vltdk~~ 36 (72)
T PF12575_consen 30 VLTDKKK 36 (72)
T ss_pred HHcCCcc
Confidence 4555554
No 7
>PF08173 YbgT_YccB: Membrane bound YbgT-like protein; InterPro: IPR012994 This family contains a set of membrane proteins, typically 33 amino acids long. The family has no known function, but the protein is found in the operon CydAB in Escherichia coli. Members have a consensus motif (MWYFXW), which is rich in aromatic residues. The protein forms a single membrane-spanning helix. This family seems to be restricted to proteobacteria [].
Probab=25.19 E-value=99 Score=22.44 Aligned_cols=20 Identities=20% Similarity=0.411 Sum_probs=16.9
Q ss_pred HHHHHHHHHHHHHHHHhhhh
Q 007393 580 VLFRAAAVVVMFAILVSTWR 599 (605)
Q Consensus 580 ~~~~~~~v~vl~~vl~~~Wr 599 (605)
.-+..+.++++|.|+..+|-
T Consensus 5 aWilG~~lA~~~~i~~a~wl 24 (28)
T PF08173_consen 5 AWILGVLLACAFGILNAMWL 24 (28)
T ss_pred HHHHHHHHHHHHHHHHHHHh
Confidence 34678889999999999995
No 8
>PHA02819 hypothetical protein; Provisional
Probab=23.81 E-value=84 Score=27.33 Aligned_cols=20 Identities=20% Similarity=0.208 Sum_probs=8.4
Q ss_pred CCCcchhHHHHHHHHHHHHHHH
Q 007393 572 GHSNRSFAVLFRAAAVVVMFAI 593 (605)
Q Consensus 572 ~~s~~~~~~~~~~~~v~vl~~v 593 (605)
+++..| +++..+++++++++
T Consensus 41 ~~~~~~--~~~ii~l~~~~~~~ 60 (71)
T PHA02819 41 KKSFLR--YYLIIGLVTIVFVI 60 (71)
T ss_pred cCChhH--HHHHHHHHHHHHHH
Confidence 444445 33333344444333
No 9
>PF15183 MRAP: Melanocortin-2 receptor accessory protein family
Probab=21.85 E-value=93 Score=28.01 Aligned_cols=37 Identities=24% Similarity=0.249 Sum_probs=20.3
Q ss_pred eeccccCccccCCCCcchhHH---HHHHHHHHHHHHHHHh
Q 007393 560 LMDKDTSNTFRAGHSNRSFAV---LFRAAAVVVMFAILVS 596 (605)
Q Consensus 560 ~~~kv~s~~~ka~~s~~~~~~---~~~~~~v~vl~~vl~~ 596 (605)
|+|.+|+...|-+-.+.+.+. +-.+|+|+.||+||+-
T Consensus 20 ylD~~pVd~~~Lka~kysIVI~FWv~LA~FV~~lF~iL~~ 59 (90)
T PF15183_consen 20 YLDLIPVDEEKLKANKYSIVIAFWVSLAAFVVFLFLILLY 59 (90)
T ss_pred hcccCccCHHHhcccceeeehhHHHHHHHHHHHHHHHHHH
Confidence 556777766555544442221 1234566677777753
No 10
>PF10669 Phage_Gp23: Protein gp23 (Bacteriophage A118); InterPro: IPR018926 This entry is represented by the major tail subunit protein, Gp23 of Listeria phage A118 and prophage found in Bacilli. The function is currently unknown.
Probab=20.73 E-value=1e+02 Score=28.52 Aligned_cols=17 Identities=18% Similarity=0.470 Sum_probs=12.4
Q ss_pred HHHHHHHHHHHHHhhhh
Q 007393 583 RAAAVVVMFAILVSTWR 599 (605)
Q Consensus 583 ~~~~v~vl~~vl~~~Wr 599 (605)
.+|+++.|++|..+||-
T Consensus 23 ~i~~FiILLIi~~~IW~ 39 (121)
T PF10669_consen 23 FIVVFIILLIITKSIWH 39 (121)
T ss_pred HHHHHHHHHHHHHHHhh
Confidence 34566677788889995
No 11
>PHA02975 hypothetical protein; Provisional
Probab=20.44 E-value=1e+02 Score=26.70 Aligned_cols=9 Identities=33% Similarity=0.394 Sum_probs=5.3
Q ss_pred eeeeccccC
Q 007393 558 TVLMDKDTS 566 (605)
Q Consensus 558 ~~~~~kv~s 566 (605)
+++.+|-+.
T Consensus 29 sVLtdk~~~ 37 (69)
T PHA02975 29 HVLTGKKEP 37 (69)
T ss_pred HHHcCCCCC
Confidence 456777544
No 12
>PHA00476 hypothetical protein
Probab=20.33 E-value=93 Score=28.84 Aligned_cols=29 Identities=21% Similarity=0.450 Sum_probs=20.9
Q ss_pred cCCCCcchhHHHHHHHHHHHHHHHHHhhhhh
Q 007393 570 RAGHSNRSFAVLFRAAAVVVMFAILVSTWRC 600 (605)
Q Consensus 570 ka~~s~~~~~~~~~~~~v~vl~~vl~~~Wr~ 600 (605)
|.-|=. |+.+.|.+|+.+|+++.| ++|-.
T Consensus 33 K~icl~-lssfvfsSvallvil~~L-~TW~T 61 (110)
T PHA00476 33 KGICLT-LSSFVFSSVALLVILVLL-GTWST 61 (110)
T ss_pred HHHHHH-HHHHHHHHHHHHHHHHHH-hcccc
Confidence 444434 556788888888888877 99964
Done!