Query 016337
Match_columns 391
No_of_seqs 168 out of 889
Neff 4.4
Searched_HMMs 46136
Date Fri Mar 29 05:56:43 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/016337.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/016337hhsearch_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 8.3E-42 1.8E-46 294.1 7.7 127 28-161 1-129 (129)
2 MTH00213 ND6 NADH dehydrogenas 19.4 76 0.0017 31.2 2.1 57 261-324 123-183 (239)
3 KOG4286 Dystrophin-like protei 17.9 36 0.00078 38.8 -0.5 87 125-216 613-719 (966)
4 PHA00692 hypothetical protein 15.5 58 0.0012 26.0 0.3 10 26-35 35-44 (74)
5 smart00265 BH4 BH4 Bcl-2 homol 13.1 2E+02 0.0044 19.4 2.3 19 37-55 4-22 (27)
6 PF07960 CBP4: CBP4; InterPro 11.6 1.2E+02 0.0026 27.5 1.1 11 35-45 30-40 (128)
7 PF08260 Kinin: Insect kinin p 11.0 1.1E+02 0.0024 15.4 0.4 6 271-276 3-8 (8)
8 cd00265 MADS_MEF2_like MEF2 (m 10.8 1.8E+02 0.0038 23.5 1.8 22 352-373 49-70 (77)
9 PRK11560 phosphoethanolamine t 10.4 1.6E+02 0.0034 32.3 1.8 30 304-336 525-554 (558)
10 PF01473 CW_binding_1: Putativ 9.9 1.9E+02 0.0042 17.1 1.3 8 84-91 7-14 (19)
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=8.3e-42 Score=294.07 Aligned_cols=127 Identities=38% Similarity=0.663 Sum_probs=94.3
Q ss_pred CCCcceecCChHHHHHHHHHHhhcCCCCCCCCCceeeccCCCCCccccccccccCCCceEEEEecccccccCCCcceecc
Q 016337 28 KVDGIKFKPTAEVLIFVYLAGMVSGSTDGPIFPLIQEVDVYQYEPSKLKSKAHDFGDGNMYFFSRVQKKYKKGSIRERKA 107 (391)
Q Consensus 28 LPPGfRF~PTDEELV~~YL~rKv~G~pl~~~~~~I~evDVY~~ePWdLP~~~~~~gd~eWYFFs~r~rKy~nG~R~nRat 107 (391)
|||||||+|||||||.+||++|+.|.+++ ...+|+++|||++|||+|++.... ++++||||+++++++.++.|.+|++
T Consensus 1 LP~G~rF~PtD~ELi~~yL~~k~~g~~~~-~~~~i~~~Diy~~~P~~L~~~~~~-~~~~~yFF~~~~~~~~~~~r~~R~~ 78 (129)
T PF02365_consen 1 LPPGFRFRPTDEELINHYLRPKILGEPLP-CEDVIHDVDIYSAHPWELPAKFKG-GDEEWYFFSPRKKKYPNGGRPNRVT 78 (129)
T ss_dssp --TTEEE---HHHHHHCTHHHHHTT-HHC-S-CHSEE--GGGS-GGGCHHHSSS--SSEEEEEEE----------S-EEE
T ss_pred CCCceEecCChHHHHHHHHHHHhcCCCCC-cccceeecccCccChHHhhhhccC-CCceEEEEEecccccCCcccccccc
Confidence 89999999999999999999999999972 337899999999999999953333 6679999999999999999999999
Q ss_pred CCceEe-cCCceeeec-CCCeEEEEEEeeeecccCCCCCCCCCcccCeEEEEEEeC
Q 016337 108 KGGFWK-TGKCNTVRG-KDGGTGTERSLTYYSYRHDPKPGEKPIKTHWLMREYMLK 161 (391)
Q Consensus 108 ggGyWK-tG~~K~I~~-~G~vIG~KKtLvFY~gr~~pk~G~~~~KTgWvMhEYrL~ 161 (391)
++|+|| +|+++.|.+ +|.+||+|++|+||.++. + ++ .+|+|+||||+|.
T Consensus 79 ~~G~Wk~~g~~~~i~~~~g~~iG~k~~l~f~~~~~-~-~~---~kt~W~M~EY~L~ 129 (129)
T PF02365_consen 79 GGGYWKSTGKEKPIKDPGGKVIGFKKTLVFYSGKS-P-NG---KKTGWVMHEYSLE 129 (129)
T ss_dssp TTEEEEEECEEEEEEE-TTCEEEEEEEEEEEESST-T-S----EEEEEEEEEEEE-
T ss_pred cceEEeecccccccccccceeeeeEEEEEEEeccC-C-CC---CcCCeEEEEEEeC
Confidence 999999 999999999 999999999999998766 4 67 8999999999984
No 2
>MTH00213 ND6 NADH dehydrogenase subunit 6; Provisional
Probab=19.43 E-value=76 Score=31.21 Aligned_cols=57 Identities=26% Similarity=0.182 Sum_probs=34.0
Q ss_pred CCCCCCCccccccccccccCCCCCCCc----cccCCCCCCCCCCCCCCChhhhhhhhhcCCCCCCccc
Q 016337 261 PNSFQNTTDITFASWGSISPAPNNNFP----LYSSNLNPAASTPERPSSNSFQNMINMMGVSSAAPAD 324 (391)
Q Consensus 261 ~~~~~~~~~~~~~~~~~~~~~~~~~~~----~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 324 (391)
|+||-|.. -.-=|..|-+|..++- -|+|-|.+.- ...++-|||.|+|++-.+++|+-
T Consensus 123 p~sf~n~~---~~~~g~~~~~~~~~~~~~~~~v~~~~~~~~----~~~~~~~qn~~~~~~~~~~~~~~ 183 (239)
T MTH00213 123 PDSFLNNP---SGRGGAERYELTNILSDRNRGVSSLLGSDK----ESITTGIQNNIYMRVGATGAPYL 183 (239)
T ss_pred CHHHhcCC---CCCCCccccCcchhccccCCChhhhcccch----hcccHHhhhhhcccccccCCccc
Confidence 46676664 3334455555554442 3445444322 23567899999999888888764
No 3
>KOG4286 consensus Dystrophin-like protein [Cell motility; Signal transduction mechanisms; Cytoskeleton]
Probab=17.91 E-value=36 Score=38.82 Aligned_cols=87 Identities=21% Similarity=0.202 Sum_probs=52.7
Q ss_pred CeEEEEE-Eee----------eecccCCCCCCCCCcccCeEEEEEEeCCCCC-CCCC--eEEEEEEEecCCCCccccCCC
Q 016337 125 GGTGTER-SLT----------YYSYRHDPKPGEKPIKTHWLMREYMLKRPKN-DKES--MALCVVYFHGQRDNEDKQNSH 190 (391)
Q Consensus 125 ~vIG~KK-tLv----------FY~gr~~pk~G~~~~KTgWvMhEYrL~~~~~-~~~d--~VLCRIykK~r~~~~~k~~~~ 190 (391)
-+||+|- .|+ |..|+. . +| .|++.-|.||....... ...+ -|||--|+.++.-.+..+..+
T Consensus 613 pIvG~RyR~l~~fn~dlCq~CF~sgra-a-k~---hk~~~pM~Ey~~~tts~~d~rdfak~L~nkfr~~~~~a~~~rrGy 687 (966)
T KOG4286|consen 613 PIIGFRYRSLKHFNYDICQSCFFSGRA-A-KG---HKMHYPMVEYCTPTTSGEDVRDFAKVLKNKFRTKRYFAKHPRRGY 687 (966)
T ss_pred ccceeeeeehhhcChhHHhhHhhhccc-c-cC---CCCCCCceeeeCCCCChhhHHHHHHHHHhhhccchhhhcccccCC
Confidence 4678773 332 456888 4 78 89999999999887654 1122 288888887766555544443
Q ss_pred CCcccC----CC--CCCCCCCccccCCchhhh
Q 016337 191 PDVEAE----GS--PTRNNPALIHWDSNLEAI 216 (391)
Q Consensus 191 ~~~~~e----~s--~s~~~p~~~h~~s~~~~~ 216 (391)
..+... +. .+..-|+..|.++.+..|
T Consensus 688 lpvq~~~e~~~~et~pa~sP~~~~t~t~s~~~ 719 (966)
T KOG4286|consen 688 LPVQTVLEGDNMETQPASSPQLSHTDTHSRIE 719 (966)
T ss_pred ccchhcccccccccCccCCCCCcccchHHHHH
Confidence 322211 11 123457777777666554
No 4
>PHA00692 hypothetical protein
Probab=15.51 E-value=58 Score=26.02 Aligned_cols=10 Identities=20% Similarity=0.341 Sum_probs=8.3
Q ss_pred CCCCCcceec
Q 016337 26 WKKVDGIKFK 35 (391)
Q Consensus 26 ~~LPPGfRF~ 35 (391)
+..||||||-
T Consensus 35 veyppgfrfg 44 (74)
T PHA00692 35 VEYPPGFRFG 44 (74)
T ss_pred EecCCCcccc
Confidence 4689999995
No 5
>smart00265 BH4 BH4 Bcl-2 homology region 4.
Probab=13.06 E-value=2e+02 Score=19.44 Aligned_cols=19 Identities=16% Similarity=0.130 Sum_probs=15.7
Q ss_pred ChHHHHHHHHHHhhcCCCC
Q 016337 37 TAEVLIFVYLAGMVSGSTD 55 (391)
Q Consensus 37 TDEELV~~YL~rKv~G~pl 55 (391)
+-.|||.+|+.-|+.-+..
T Consensus 4 ~nRelV~~yv~yKLsQrgy 22 (27)
T smart00265 4 DNRELVVDYVTYKLSQNGY 22 (27)
T ss_pred chHHHHHHHHHHHHhhcCC
Confidence 4579999999999987655
No 6
>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=11.56 E-value=1.2e+02 Score=27.46 Aligned_cols=11 Identities=45% Similarity=0.588 Sum_probs=9.2
Q ss_pred cCChHHHHHHH
Q 016337 35 KPTAEVLIFVY 45 (391)
Q Consensus 35 ~PTDEELV~~Y 45 (391)
.||||||+..|
T Consensus 30 tPTeEeL~~r~ 40 (128)
T PF07960_consen 30 TPTEEELFKRY 40 (128)
T ss_pred CCCHHHHHHhc
Confidence 49999999764
No 7
>PF08260 Kinin: Insect kinin peptide; InterPro: IPR013202 This entry represents neuropeptides that are the first members of the insect kinin-family isolated from the American cockroach. Their occurrence in the retrocerebral complex suggests a physiological role as a neurohormone. The C-terminal sequence Phe-X-Ser-Trp-Gly-NH2 characterised the peptides as members of the insect kinin family. Data suggest a possible involvement of insect kinins in water-balance by regulating the osmoregulation. Insect kinins also mediate visceral muscle contractile activity (myotropic activity) []. These peptides have lengths ranging from 6 to 14 amino acids [].
Probab=11.01 E-value=1.1e+02 Score=15.38 Aligned_cols=6 Identities=67% Similarity=1.680 Sum_probs=3.7
Q ss_pred cccccc
Q 016337 271 TFASWG 276 (391)
Q Consensus 271 ~~~~~~ 276 (391)
.|.|||
T Consensus 3 afnswg 8 (8)
T PF08260_consen 3 AFNSWG 8 (8)
T ss_pred cccccC
Confidence 466775
No 8
>cd00265 MADS_MEF2_like MEF2 (myocyte enhancer factor 2)-like/Type II subfamily of MADS ( MCM1, Agamous, Deficiens, and SRF (serum response factor) box family of eukaryotic transcriptional regulators. Binds DNA and exists as hetero and homo-dimers. Differs from SRF-like/Type I subgroup mainly in position of the alpha helix responsible for the dimerization interface. Important in homeotic regulation in plants and in immediate-early development in animals. Also found in fungi.
Probab=10.77 E-value=1.8e+02 Score=23.51 Aligned_cols=22 Identities=27% Similarity=0.516 Sum_probs=18.5
Q ss_pred cCCCCccccCchhHHHHHHHhh
Q 016337 352 ADGSPYQYSSNDDIQLLEQYLF 373 (391)
Q Consensus 352 ~~~~~~~~~~~~~~~~~~~~~~ 373 (391)
.+|.+|.|++...-+.|+.|+=
T Consensus 49 p~gk~~~f~s~s~~~vl~ry~~ 70 (77)
T cd00265 49 SSGKLYEFSSPSMEKIIERYQK 70 (77)
T ss_pred CCCceEEecCCCHHHHHHHHHh
Confidence 3589999999888889999873
No 9
>PRK11560 phosphoethanolamine transferase; Provisional
Probab=10.39 E-value=1.6e+02 Score=32.34 Aligned_cols=30 Identities=30% Similarity=0.680 Sum_probs=24.3
Q ss_pred CChhhhhhhhhcCCCCCCccccccCCCCccccc
Q 016337 304 SSNSFQNMINMMGVSSAAPADSIINTPNNWCST 336 (391)
Q Consensus 304 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 336 (391)
.-+=|.-++.++||. ..|.++|--||||+.
T Consensus 525 ~~dlf~TlL~~~gv~---~p~~~~~~~~~~~~~ 554 (558)
T PRK11560 525 HVELFDTILGCLGYT---SPDGGINENNNWCHI 554 (558)
T ss_pred ehhHHHHHHHHcCCC---CChhhccccCCcccC
Confidence 346688899999997 567888877999974
No 10
>PF01473 CW_binding_1: Putative cell wall binding repeat; InterPro: IPR018337 The cell wall-binding repeat (CW) is an about 20 amino acid residue module, essentially found in two bacterial Gram-positive protein families; the choline binding proteins and glucosyltransferases (2.4.1.5 from EC). In choline-binding proteins cell wall binding repeats bind to choline moieties of both teichoic and lipoteichoic acids, two components peculiar to the cell surface of Gram-positive bacteria [, ]. In glucosyltransferases the region spanning the CW repeats is a glucan binding domain []. Several crystal structures of CW have been solved [, ]. In the choline binding protein LytA, the repeats adopt a solenoid fold consisting exclusively of beta-hairpins that stack to form a left-handed superhelix with a boomerang-like shape. The choline groups bind between beta-hairpin 'steps' of the superhelix []. In Cpl-1 CW repeats assemble in two sub-domains: an N-terminal superhelical moiety similar to the LytA one and a C-terminal beta-sheet involved in interactions with the lysozyme domain. Choline is bound between repeats 1 and 2, and, 2 and 3 of the superhelical sub-domain []. Some proteins known to contain cell-wall binding repeats include: Pneumococcal N-acetylmuramoyl-L-alanine amidase (autolysin, lytA) (3.5.1.28 from EC). It is a surface-exposed enzyme that rules the self-destruction of pneumococcal cells through degradation of their peptidoglycan backbone. It mediates the release of toxic substances that damage the host tissues. Pneumococcal endo-beta-N-acetylglucosaminidase (lytB) (3.2.1.96 from EC). It plays an important role in cell wall degradation and cell separation. Pneumococcal teichoic acid phosphorylcholine esterase (pce or cbpE), a cell wall hydrolase important for cellular adhesion and colonisation. Lactobacillales glucosyltransferase. It catalyses the transfer of glucosyl units from the cleavage of sucrose to a growing chain of glucan. Clostridium difficile toxin A (tcdA) and toxin B (tcdb). They are the causative agents of the antibiotic-associated pseudomembranous colitis. They are intracellular acting toxins that reach their targets after receptor-mediated endocytosis. Clostridium acetobutylicum cspA protein. Siphoviridae bacteriophages N-acetylmuramoyl-L-alanine amidase. It lyses the bacterial host cell wall. Podoviridae lysozyme protein (cpl-1). It is capable of digesting the pneumococcal cell wall. The cell wall binding repeats are also known as the choline-binding repeats (ChBr) or the choline-binding domain (ChBD). ; PDB: 1GVM_C 2BML_B 1HCX_A 1OBA_A 1H09_A 2J8F_A 2IXU_A 2J8G_A 2IXV_A 2X8O_A ....
Probab=9.86 E-value=1.9e+02 Score=17.07 Aligned_cols=8 Identities=50% Similarity=1.331 Sum_probs=6.3
Q ss_pred CceEEEEe
Q 016337 84 DGNMYFFS 91 (391)
Q Consensus 84 d~eWYFFs 91 (391)
++.||||.
T Consensus 7 ~~~wYy~~ 14 (19)
T PF01473_consen 7 NGNWYYFD 14 (19)
T ss_dssp TTEEEEET
T ss_pred CCEEEEeC
Confidence 47899994
Done!