Query 021353
Match_columns 313
No_of_seqs 180 out of 791
Neff 5.1
Searched_HMMs 46136
Date Fri Mar 29 09:34:37 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/021353.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/021353hhsearch_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 8.5E-27 1.8E-31 195.8 5.7 97 4-114 31-129 (129)
2 PF05865 Cypo_polyhedrin: Cypo 18.3 1.2E+02 0.0027 27.7 3.1 26 66-91 142-168 (248)
3 PF10534 CRIC_ras_sig: Connect 12.6 69 0.0015 26.3 0.0 23 290-312 37-61 (95)
4 PF06214 SLAM: Signaling lymph 10.6 1.2E+02 0.0026 26.1 0.7 27 14-40 93-123 (126)
5 PF01473 CW_binding_1: Putativ 9.7 2.1E+02 0.0045 16.1 1.3 8 31-38 7-14 (19)
6 PF07045 DUF1330: Protein of u 9.3 2E+02 0.0043 21.2 1.5 17 296-312 41-58 (65)
7 PF12043 DUF3527: Domain of un 9.3 6.4E+02 0.014 25.4 5.4 84 9-117 23-109 (346)
8 TIGR03116 cas_csf3 CRISPR-asso 9.1 2.2E+02 0.0047 26.6 1.9 22 51-76 94-115 (214)
9 PRK10154 hypothetical protein; 8.5 3.5E+02 0.0076 23.6 2.8 21 86-109 80-100 (134)
10 KOG4286 Dystrophin-like protei 8.0 89 0.0019 34.6 -1.2 50 81-132 613-675 (966)
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=99.93 E-value=8.5e-27 Score=195.77 Aligned_cols=97 Identities=32% Similarity=0.622 Sum_probs=69.5
Q ss_pred cccccccccCCCCCCCCCCCCCCC-CCCCCeEEEeeecccccccCCcccccccCCCCCCCCCceEeecCCcceEEe-CCe
Q 021353 4 DEFIPTIEGDQGICYTHPENLPGA-KKDGSSVHFFHRTTNAYATGQRKRRKIQSEHSLNEEHVRWHKTGKTKPVIE-NGI 81 (313)
Q Consensus 4 d~fIptvd~d~dIy~~~PwdLPg~-~~~G~~wYFFs~~~~ky~~G~R~~R~t~~G~~~~~~~G~Wk~tGk~k~I~~-~g~ 81 (313)
.++|+++| ||.+|||+||.. ...++.||||+++.+++.+|.|++|++++ |+||++|+.++|.. +|.
T Consensus 31 ~~~i~~~D----iy~~~P~~L~~~~~~~~~~~yFF~~~~~~~~~~~r~~R~~~~--------G~Wk~~g~~~~i~~~~g~ 98 (129)
T PF02365_consen 31 EDVIHDVD----IYSAHPWELPAKFKGGDEEWYFFSPRKKKYPNGGRPNRVTGG--------GYWKSTGKEKPIKDPGGK 98 (129)
T ss_dssp -CHSEE------GGGS-GGGCHHHSSS-SSEEEEEEE----------S-EEETT--------EEEEEECEEEEEEE-TTC
T ss_pred ccceeecc----cCccChHHhhhhccCCCceEEEEEecccccCCcccccccccc--------eEEeecccccccccccce
Confidence 35677776 999999999942 33456999999999999999999998765 59999999999998 899
Q ss_pred eeEEEEEEEEEeccCCCCCCCCCCeEEEEEEeC
Q 021353 82 QKGCRKIMVLYKSTKKGTKPDKSNWVMHQYHLG 114 (313)
Q Consensus 82 ~VG~KK~LvFY~g~~~g~kg~KT~WvMHEY~L~ 114 (313)
+||+||+|+||.++ ++++.+|+|+||||+|.
T Consensus 99 ~iG~k~~l~f~~~~--~~~~~kt~W~M~EY~L~ 129 (129)
T PF02365_consen 99 VIGFKKTLVFYSGK--SPNGKKTGWVMHEYSLE 129 (129)
T ss_dssp EEEEEEEEEEEESS--TTS-EEEEEEEEEEEE-
T ss_pred eeeeEEEEEEEecc--CCCCCcCCeEEEEEEeC
Confidence 99999999999876 56789999999999984
No 2
>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=18.32 E-value=1.2e+02 Score=27.67 Aligned_cols=26 Identities=27% Similarity=0.502 Sum_probs=17.2
Q ss_pred eEeecC-CcceEEeCCeeeEEEEEEEE
Q 021353 66 RWHKTG-KTKPVIENGIQKGCRKIMVL 91 (313)
Q Consensus 66 ~Wk~tG-k~k~I~~~g~~VG~KK~LvF 91 (313)
-|.+|| +-+.|..+|.+||.-..|.+
T Consensus 142 pweatgikyrki~~dgeivgyshyfel 168 (248)
T PF05865_consen 142 PWEATGIKYRKIHRDGEIVGYSHYFEL 168 (248)
T ss_dssp S-B--GGG-EEEEETTEEEEEEEEEE-
T ss_pred CccccCceEEEeeccceEeeeeeeeec
Confidence 599999 56778889999999776653
No 3
>PF10534 CRIC_ras_sig: Connector enhancer of kinase suppressor of ras; InterPro: IPR019555 The multi-domain protein Connector enhancer of kinase suppressor of ras (Connector enhancer of KSR) (CNK) functions as a scaffold in several signal cascades and acts on proliferation, differentiation and apoptosis. CNK connects upstream activators and downstream targets of Ras- and Rho-dependent signalling pathways and may allow cross-talk between these pathways. In invertebrates, CNK is expressed as one isoform, whereas in mammals there exists CNK1, CNK2A, and its splice variant CNK2B. CNK proteins consist of one sterile alpha motif (SAM) domain (see PDOC50105 from PROSITEDOC, IPR001660 from INTERPRO) one conserved region in CNK (CRIC) domain, one PSD-96/Dlg-A/ZO-1 (PDZ) domain (see PDOC50106 from PROSITEDOC, IPR001478 from INTERPRO) and one pleckstrin homology (PH) domain (see PDOC50003 from PROSITEDOC, IPR001849 from INTERPRO. The CRIC domain is enriched in leucine residues and functions as a protein-protein interaction domain [, ].; PDB: 1WWV_A.
Probab=12.64 E-value=69 Score=26.27 Aligned_cols=23 Identities=35% Similarity=0.728 Sum_probs=0.0
Q ss_pred CCCCccccceee--chhhHhhhhhc
Q 021353 290 TPPDSHLADLQF--SDESILGWLDR 312 (313)
Q Consensus 290 Tppdf~Ls~~~f--sq~s~~~~~~~ 312 (313)
+|.+|.=+-++- .-.++++||||
T Consensus 37 ~p~~vL~aVveLi~aAK~Ll~WLdR 61 (95)
T PF10534_consen 37 PPNDVLTAVVELIGAAKALLSWLDR 61 (95)
T ss_dssp -------------------------
T ss_pred CcHHHHHHHHHHHHHHHhhcccccC
Confidence 466776666666 78889999988
No 4
>PF06214 SLAM: Signaling lymphocytic activation molecule (SLAM) protein; InterPro: IPR010407 This entry is found in several mammalian signalling lymphocytic activation molecule (SLAM) proteins. Optimal T cell activation and expansion require engagement of the TCR plus co-stimulatory signals delivered through accessory molecules. SLAM, a 70 kDa co-stimulatory molecule belonging to the Ig superfamily, is defined as a human cell surface molecule that mediates CD28-independent proliferation of human T cells and IFN-gamma production by human Th1 and Th2 clones []. SLAM has also been recognised as a receptor for Measles virus [].; GO: 0004872 receptor activity, 0046649 lymphocyte activation, 0009986 cell surface, 0016021 integral to membrane; PDB: 3ALX_D 3ALZ_B 3ALW_A.
Probab=10.58 E-value=1.2e+02 Score=26.06 Aligned_cols=27 Identities=22% Similarity=0.234 Sum_probs=16.7
Q ss_pred CCCCCCCCCCCC----CCCCCCCeEEEeeec
Q 021353 14 QGICYTHPENLP----GAKKDGSSVHFFHRT 40 (313)
Q Consensus 14 ~dIy~~~PwdLP----g~~~~G~~wYFFs~~ 40 (313)
.|=|.+|+.+|. +-++..+-|||-+-.
T Consensus 93 edgY~FhlEnLsL~Il~SrkE~EGWYfmtlE 123 (126)
T PF06214_consen 93 EDGYKFHLENLSLEILESRKEDEGWYFMTLE 123 (126)
T ss_dssp SSSEEEETTTTEEEETT--GGG-EEEEEEEE
T ss_pred ccccEEecccceeehhccccccCceEEEEee
Confidence 356889999984 333444678887653
No 5
>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=9.72 E-value=2.1e+02 Score=16.12 Aligned_cols=8 Identities=13% Similarity=0.393 Sum_probs=6.2
Q ss_pred CCeEEEee
Q 021353 31 GSSVHFFH 38 (313)
Q Consensus 31 G~~wYFFs 38 (313)
+..||||.
T Consensus 7 ~~~wYy~~ 14 (19)
T PF01473_consen 7 NGNWYYFD 14 (19)
T ss_dssp TTEEEEET
T ss_pred CCEEEEeC
Confidence 46899994
No 6
>PF07045 DUF1330: Protein of unknown function (DUF1330); InterPro: IPR010753 This family consists of several hypothetical bacterial proteins of around 90 residues in length. The function of this family is unknown.; PDB: 2FIU_B 3HHL_A 3DCA_D 3LO3_I.
Probab=9.27 E-value=2e+02 Score=21.15 Aligned_cols=17 Identities=24% Similarity=0.536 Sum_probs=13.0
Q ss_pred ccceee-chhhHhhhhhc
Q 021353 296 LADLQF-SDESILGWLDR 312 (313)
Q Consensus 296 Ls~~~f-sq~s~~~~~~~ 312 (313)
+.=++| |.+.+.+|.++
T Consensus 41 ~viieFPs~~aa~~~~~s 58 (65)
T PF07045_consen 41 VVIIEFPSMEAAKAWYNS 58 (65)
T ss_dssp EEEEEESSHHHHHHHHCS
T ss_pred EEEEECCCHHHHHHHHCC
Confidence 445789 99999998753
No 7
>PF12043 DUF3527: Domain of unknown function (DUF3527); InterPro: IPR021916 This presumed domain is functionally uncharacterised. This domain is found in eukaryotes. This domain is about 120 amino acids in length. This domain has a conserved CDCGGWD sequence motif.
Probab=9.27 E-value=6.4e+02 Score=25.38 Aligned_cols=84 Identities=15% Similarity=0.135 Sum_probs=43.1
Q ss_pred ccccCCCCCCCCCCCCCCCCCCCC-eEEEe-eecccccccCCcccccccCCCCCCCCCceEeecC-CcceEEeCCeeeEE
Q 021353 9 TIEGDQGICYTHPENLPGAKKDGS-SVHFF-HRTTNAYATGQRKRRKIQSEHSLNEEHVRWHKTG-KTKPVIENGIQKGC 85 (313)
Q Consensus 9 tvd~d~dIy~~~PwdLPg~~~~G~-~wYFF-s~~~~ky~~G~R~~R~t~~G~~~~~~~G~Wk~tG-k~k~I~~~g~~VG~ 85 (313)
-|+...+||..-.|.+--..+++- ..|=| +....| |+ .|.|...+ +.|.. +.+||-
T Consensus 23 svd~~~~VlaAt~~k~~~~~~~~~~~vYTFhs~~e~K--------Kk----------s~~w~~~~~k~k~~---~~iVGQ 81 (346)
T PF12043_consen 23 SVDNPEEVLAATMWKSGSSDKNDLNWVYTFHSIKEVK--------KK----------SGSWINSGDKNKSS---SNIVGQ 81 (346)
T ss_pred EeCCcccEEEEEEeecccccccccceEEEEEeecccc--------cc----------ccccccccccccCC---cceEEE
Confidence 456667889888888753333333 34644 433221 11 12455443 23322 268888
Q ss_pred EEEEEEEeccCCCCCCCCCCeEEEEEEeCCCC
Q 021353 86 RKIMVLYKSTKKGTKPDKSNWVMHQYHLGTDE 117 (313)
Q Consensus 86 KK~LvFY~g~~~g~kg~KT~WvMHEY~L~~~~ 117 (313)
.|.=..+.... ...+. =+..||.|-..+
T Consensus 82 MkVSss~~~~~---~~~~~-s~~~EFVLf~~~ 109 (346)
T PF12043_consen 82 MKVSSSLSSEP---SKQGS-SMVTEFVLFGVD 109 (346)
T ss_pred EEeeeeeeecc---cCCcc-eeEEEEEEEecc
Confidence 88765554442 11222 455677776654
No 8
>TIGR03116 cas_csf3 CRISPR-associated protein, Csf3 family. Members of this family show up near CRISPR repeats in Acidithiobacillus ferrooxidans ATCC 23270, Azoarcus sp. EbN1, and Rhodoferax ferrireducens DSM 15236. In the latter two species, the CRISPR/cas locus is found on a plasmid. This family is one of several characteristic of a type of CRISPR-associated (cas) gene cluster we designate Aferr after A. ferrooxidans, where it is both chromosomal and the only type of cas gene cluster found. The gene is designated csf3 (CRISPR/cas Subtype as in A. ferrooxidans protein 3), as it lies third closest to the repeats.
Probab=9.13 E-value=2.2e+02 Score=26.61 Aligned_cols=22 Identities=27% Similarity=0.508 Sum_probs=16.3
Q ss_pred cccccCCCCCCCCCceEeecCCcceE
Q 021353 51 RRKIQSEHSLNEEHVRWHKTGKTKPV 76 (313)
Q Consensus 51 ~R~t~~G~~~~~~~G~Wk~tGk~k~I 76 (313)
+|.++.+ ...|.|.+.|+.++-
T Consensus 94 ~r~i~d~----~~~g~~~a~g~~~p~ 115 (214)
T TIGR03116 94 SRFIGDD----LDRGLWQARGKVNPE 115 (214)
T ss_pred hhhhccc----hhhhhhhhcccCCCc
Confidence 4666554 678899999988763
No 9
>PRK10154 hypothetical protein; Provisional
Probab=8.48 E-value=3.5e+02 Score=23.58 Aligned_cols=21 Identities=5% Similarity=0.268 Sum_probs=15.4
Q ss_pred EEEEEEEeccCCCCCCCCCCeEEE
Q 021353 86 RKIMVLYKSTKKGTKPDKSNWVMH 109 (313)
Q Consensus 86 KK~LvFY~g~~~g~kg~KT~WvMH 109 (313)
.++|.||+.= .++..|+|+--
T Consensus 80 s~tl~f~~~l---k~~q~T~W~~~ 100 (134)
T PRK10154 80 SQSLNIPSEI---KEGQTTDWINI 100 (134)
T ss_pred ceEEecchhh---ccCCccccEEc
Confidence 3788888765 45689999853
No 10
>KOG4286 consensus Dystrophin-like protein [Cell motility; Signal transduction mechanisms; Cytoskeleton]
Probab=7.97 E-value=89 Score=34.62 Aligned_cols=50 Identities=20% Similarity=0.313 Sum_probs=35.2
Q ss_pred eeeEEEEE-E----------EEEeccCCCCCCCCCCeEEEEEEeCCCCCCCCCCe--EEEEEEEe
Q 021353 81 IQKGCRKI-M----------VLYKSTKKGTKPDKSNWVMHQYHLGTDEDEKDDEY--VVSKVFYQ 132 (313)
Q Consensus 81 ~~VG~KK~-L----------vFY~g~~~g~kg~KT~WvMHEY~L~~~~~~~~~e~--VLCKIf~k 132 (313)
.+||+|-. | .|+.|+ ..++.|++.-|.||...+...+...+| |||--|+.
T Consensus 613 pIvG~RyR~l~~fn~dlCq~CF~sgr--aak~hk~~~pM~Ey~~~tts~~d~rdfak~L~nkfr~ 675 (966)
T KOG4286|consen 613 PIIGFRYRSLKHFNYDICQSCFFSGR--AAKGHKMHYPMVEYCTPTTSGEDVRDFAKVLKNKFRT 675 (966)
T ss_pred ccceeeeeehhhcChhHHhhHhhhcc--cccCCCCCCCceeeeCCCCChhhHHHHHHHHHhhhcc
Confidence 47787743 3 366777 567899999999999999875543444 56665554
Done!