Query 030079
Match_columns 183
No_of_seqs 131 out of 795
Neff 5.5
Searched_HMMs 46136
Date Fri Mar 29 08:11:37 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/030079.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/030079hhsearch_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 99.9 1.3E-27 2.8E-32 184.4 6.3 82 3-84 32-129 (129)
2 PF15480 DUF4640: Domain of un 50.6 4.9 0.00011 35.5 -0.2 28 147-178 220-247 (292)
3 KOG4286 Dystrophin-like protei 34.5 14 0.00031 37.1 0.2 52 53-108 613-677 (966)
4 PF01473 CW_binding_1: Putativ 27.2 44 0.00096 17.1 1.3 8 20-27 7-14 (19)
5 PF03002 Somatostatin: Somatos 11.9 92 0.002 16.5 0.3 9 171-179 6-14 (18)
6 PF05865 Cypo_polyhedrin: Cypo 10.4 3.7E+02 0.008 22.5 3.6 28 36-63 140-168 (248)
7 COG4311 SoxD Sarcosine oxidase 10.0 93 0.002 23.5 -0.1 41 7-47 22-65 (97)
8 cd01785 PDZ_GEF_RA Ubiquitin-l 8.5 1.2E+02 0.0025 22.4 -0.1 27 74-108 29-55 (85)
9 COG5235 RFA2 Single-stranded D 8.1 2.5E+02 0.0055 24.4 1.8 19 136-154 182-200 (258)
10 COG3100 Uncharacterized protei 8.1 2.4E+02 0.0052 21.3 1.5 15 96-110 8-22 (103)
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=99.94 E-value=1.3e-27 Score=184.39 Aligned_cols=82 Identities=28% Similarity=0.658 Sum_probs=70.8
Q ss_pred CcceecCCCCCCCCCCC------CCeEEEeee---------ecCCcccCCceeeeCcceEEee-CCeeEEEEEEEEEeeC
Q 030079 3 SILTTIGPQIYLNCNVP------DGVWYLVCS---------KENTSAQHGQWRAKGETCEIFS-NSYIIGWRTTLEFFEG 66 (183)
Q Consensus 3 ~vI~evDvy~~dPwdLp------~~~wYFFs~---------R~~R~t~~G~Wk~~G~~k~I~~-~g~~VG~KktL~Fy~G 66 (183)
++|.++|||.+|||+|+ +++||||++ |.+|++++|+||++|+.++|.+ ++.+||+|++|+||.|
T Consensus 32 ~~i~~~Diy~~~P~~L~~~~~~~~~~~yFF~~~~~~~~~~~r~~R~~~~G~Wk~~g~~~~i~~~~g~~iG~k~~l~f~~~ 111 (129)
T PF02365_consen 32 DVIHDVDIYSAHPWELPAKFKGGDEEWYFFSPRKKKYPNGGRPNRVTGGGYWKSTGKEKPIKDPGGKVIGFKKTLVFYSG 111 (129)
T ss_dssp CHSEE--GGGS-GGGCHHHSSS-SSEEEEEEE----------S-EEETTEEEEEECEEEEEEE-TTCEEEEEEEEEEEES
T ss_pred cceeecccCccChHHhhhhccCCCceEEEEEecccccCCcccccccccceEEeecccccccccccceeeeeEEEEEEEec
Confidence 68999999999999998 679999999 3568899999999999999998 7899999999999999
Q ss_pred cCCCCCccCeEEEeEEeC
Q 030079 67 QVPNERKTDWVMQEFRIT 84 (183)
Q Consensus 67 ~~p~g~kT~WvMhEY~l~ 84 (183)
+.+++.+|+|+||||+|.
T Consensus 112 ~~~~~~kt~W~M~EY~L~ 129 (129)
T PF02365_consen 112 KSPNGKKTGWVMHEYSLE 129 (129)
T ss_dssp STTS-EEEEEEEEEEEE-
T ss_pred cCCCCCcCCeEEEEEEeC
Confidence 889999999999999984
No 2
>PF15480 DUF4640: Domain of unknown function (DUF4640)
Probab=50.58 E-value=4.9 Score=35.54 Aligned_cols=28 Identities=25% Similarity=0.383 Sum_probs=17.3
Q ss_pred ceeeccccccCCccceeeehhhhhhhhheeee
Q 030079 147 VSIIRHEVCQPQHSGLVFCLLEWISCLNFVWF 178 (183)
Q Consensus 147 ~s~~~~~~~~~~~~g~~~~~~~~~~~~~~~~~ 178 (183)
+|+++..-++++ ..+-.++++||||-|+
T Consensus 220 SS~Ss~qpE~~d----t~S~tq~lsClNfgw~ 247 (292)
T PF15480_consen 220 SSVSSGQPEKED----TPSNTQALSCLNFGWV 247 (292)
T ss_pred eccccCCcccCC----CCCCccceeeehhHHH
Confidence 444444444333 3344789999999994
No 3
>KOG4286 consensus Dystrophin-like protein [Cell motility; Signal transduction mechanisms; Cytoskeleton]
Probab=34.48 E-value=14 Score=37.13 Aligned_cols=52 Identities=25% Similarity=0.395 Sum_probs=36.7
Q ss_pred eeEEEE-EEEE----------EeeCcCCCCCccCeEEEeEEeCCccccCCCCCCCCe--EEEEEEEcCC
Q 030079 53 YIIGWR-TTLE----------FFEGQVPNERKTDWVMQEFRITQKRLYGDKKEEDSS--SLCRVFLSGK 108 (183)
Q Consensus 53 ~~VG~K-ktL~----------Fy~G~~p~g~kT~WvMhEY~l~~~~~~~~~~~~~~~--VLCrIy~K~~ 108 (183)
.|||+| |.|+ |+.|++.++.|++--|.||........ ...++ +||-=|+.++
T Consensus 613 pIvG~RyR~l~~fn~dlCq~CF~sgraak~hk~~~pM~Ey~~~tts~~----d~rdfak~L~nkfr~~~ 677 (966)
T KOG4286|consen 613 PIIGFRYRSLKHFNYDICQSCFFSGRAAKGHKMHYPMVEYCTPTTSGE----DVRDFAKVLKNKFRTKR 677 (966)
T ss_pred ccceeeeeehhhcChhHHhhHhhhcccccCCCCCCCceeeeCCCCChh----hHHHHHHHHHhhhccch
Confidence 479998 5665 678999999999999999999875321 11222 6776666444
No 4
>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=27.21 E-value=44 Score=17.14 Aligned_cols=8 Identities=38% Similarity=1.061 Sum_probs=6.2
Q ss_pred CCeEEEee
Q 030079 20 DGVWYLVC 27 (183)
Q Consensus 20 ~~~wYFFs 27 (183)
++.||||.
T Consensus 7 ~~~wYy~~ 14 (19)
T PF01473_consen 7 NGNWYYFD 14 (19)
T ss_dssp TTEEEEET
T ss_pred CCEEEEeC
Confidence 57899984
No 5
>PF03002 Somatostatin: Somatostatin/Cortistatin family; InterPro: IPR018142 Somatostatin inhibits the release of the pituitary growth hormone, somatotropin and inhibits the release of glucagon and insulin from the pancreas of fasted animals. Cortistatin is a cortical neuropeptide with neuronal depressant and sleep-modulating properties [].; GO: 0005179 hormone activity, 0005576 extracellular region
Probab=11.93 E-value=92 Score=16.53 Aligned_cols=9 Identities=44% Similarity=1.224 Sum_probs=7.0
Q ss_pred hhhheeeee
Q 030079 171 SCLNFVWFS 179 (183)
Q Consensus 171 ~~~~~~~~~ 179 (183)
.|-||.|=+
T Consensus 6 ~CknffWK~ 14 (18)
T PF03002_consen 6 GCKNFFWKT 14 (18)
T ss_pred cccceeecc
Confidence 588999954
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=10.42 E-value=3.7e+02 Score=22.54 Aligned_cols=28 Identities=25% Similarity=0.535 Sum_probs=17.9
Q ss_pred CCceeeeCcc-eEEeeCCeeEEEEEEEEE
Q 030079 36 HGQWRAKGET-CEIFSNSYIIGWRTTLEF 63 (183)
Q Consensus 36 ~G~Wk~~G~~-k~I~~~g~~VG~KktL~F 63 (183)
.--|.++|-. +.|...|++||+--.|..
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 3569999954 889899999999876653
No 7
>COG4311 SoxD Sarcosine oxidase delta subunit [Amino acid transport and metabolism]
Probab=9.96 E-value=93 Score=23.46 Aligned_cols=41 Identities=12% Similarity=0.234 Sum_probs=27.8
Q ss_pred ecCCCC-CCCCCCCCCeE--EEeeeecCCcccCCceeeeCcceE
Q 030079 7 TIGPQI-YLNCNVPDGVW--YLVCSKENTSAQHGQWRAKGETCE 47 (183)
Q Consensus 7 evDvy~-~dPwdLp~~~w--YFFs~R~~R~t~~G~Wk~~G~~k~ 47 (183)
+++|-. .||.++.+.+| |+|-+-..|.+-.-+|..++..+.
T Consensus 22 ~A~i~RP~d~a~~sde~w~dY~flR~NprG~~~E~W~H~~GCrr 65 (97)
T COG4311 22 DAHIARPADPADASDEEWGDYVFLRDNPRGLHRERWRHTHGCRR 65 (97)
T ss_pred cccccCCCCcccCCHHHHhhheeeccCCCcchhHHhhhccchhh
Confidence 344444 47888888888 888764557777778888765443
No 8
>cd01785 PDZ_GEF_RA Ubiquitin-like domain of PDZ_GEF_RA. PDZ_GEF_RA PDZ-GEF is a guanine nucleotide exchange factor (GEF) characterised by the presence of a PSD-95/DlgA/ZO-1 (PDZ) domain, a Ras-association (RA) domain and a region related to a cyclic nucleotide binding domain (RCBD). RA-GEF exchanges nucleotides of both Rap1 and Rap2, but is also thought to mediate cAMP-induced Ras activation. The RA domain interacts with Rap1 and also contributes to the membrane localization of RA-GEF. This domain may function in a positive feedback loop.
Probab=8.50 E-value=1.2e+02 Score=22.36 Aligned_cols=27 Identities=33% Similarity=0.437 Sum_probs=21.0
Q ss_pred cCeEEEeEEeCCccccCCCCCCCCeEEEEEEEcCC
Q 030079 74 TDWVMQEFRITQKRLYGDKKEEDSSSLCRVFLSGK 108 (183)
Q Consensus 74 T~WvMhEY~l~~~~~~~~~~~~~~~VLCrIy~K~~ 108 (183)
+.-.|+||.|... ...|.||-|-....
T Consensus 29 v~lal~eFgi~~~--------s~~~sLceVtV~~~ 55 (85)
T cd01785 29 VMLALQEFGITAP--------SSNFSLCEVSVTPG 55 (85)
T ss_pred HHHHHHHhCCCCC--------ccceEEEEEEecCC
Confidence 4567889999875 57999999987643
No 9
>COG5235 RFA2 Single-stranded DNA-binding replication protein A (RPA), medium (30 kD) subunit [DNA replication, recombination, and repair]
Probab=8.14 E-value=2.5e+02 Score=24.37 Aligned_cols=19 Identities=32% Similarity=0.144 Sum_probs=12.6
Q ss_pred cCCCCCCCCCcceeecccc
Q 030079 136 SFDKDKDDTRQVSIIRHEV 154 (183)
Q Consensus 136 ~~~~~~~~~~~~s~~~~~~ 154 (183)
...+.+||||+||..=.+.
T Consensus 182 lf~k~dNdtSsgss~lq~~ 200 (258)
T COG5235 182 LFAKLDNDTSSGSSRLQED 200 (258)
T ss_pred eeeeccCccccccccccHH
Confidence 3467888888887744433
No 10
>COG3100 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=8.06 E-value=2.4e+02 Score=21.35 Aligned_cols=15 Identities=33% Similarity=0.627 Sum_probs=11.2
Q ss_pred CCeEEEEEEEcCCCC
Q 030079 96 DSSSLCRVFLSGKQS 110 (183)
Q Consensus 96 ~~~VLCrIy~K~~~~ 110 (183)
.---||-||+++++.
T Consensus 8 ~~~mlCaIYkS~kk~ 22 (103)
T COG3100 8 SKSMLCAIYKSPKKD 22 (103)
T ss_pred ceeeeeeeeecCcCC
Confidence 345799999987753
Done!