Query 027916
Match_columns 217
No_of_seqs 158 out of 898
Neff 6.2
Searched_HMMs 46136
Date Fri Mar 29 03:25:38 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/027916.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/027916hhsearch_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 3.6E-41 7.7E-46 266.2 7.6 111 8-118 1-129 (129)
2 PF15480 DUF4640: Domain of un 39.2 12 0.00025 33.7 0.4 16 197-212 232-247 (292)
3 PHA00692 hypothetical protein 29.5 20 0.00043 25.0 0.2 9 7-15 36-44 (74)
4 PF04700 Baculo_gp41: Structur 24.0 73 0.0016 27.0 2.7 23 13-36 3-28 (186)
5 PF07960 CBP4: CBP4; InterPro 23.4 41 0.00088 26.9 1.0 9 15-23 30-38 (128)
6 PF07131 DUF1382: Protein of u 21.7 94 0.002 21.6 2.4 20 10-29 22-48 (61)
7 PF01473 CW_binding_1: Putativ 19.4 75 0.0016 16.3 1.3 8 54-61 7-14 (19)
8 PF06214 SLAM: Signaling lymph 19.3 18 0.0004 28.4 -1.7 37 26-62 75-122 (126)
9 COG5235 RFA2 Single-stranded D 19.2 69 0.0015 28.0 1.6 34 169-202 181-224 (258)
10 smart00707 RPEL Repeat in Dros 19.2 77 0.0017 18.4 1.3 13 11-23 6-18 (26)
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=3.6e-41 Score=266.24 Aligned_cols=111 Identities=39% Similarity=0.796 Sum_probs=92.9
Q ss_pred CCCCeeecCCHHHHHH-HHHHHHcCCCCCC-CceeecCCCCCCCCCCC------CCeEEEeee---------ecCcccCC
Q 027916 8 TPIDVDFASTDENLFG-SLERMIRGSPLPC-NVINDVNPYNHRPSNLP------DGVWYLVCS---------KENTSAQH 70 (217)
Q Consensus 8 LPpGfrF~PTDeELV~-YL~~Ki~g~plp~-~~I~~vDvy~~~Pw~Lp------~~~wYFFs~---------R~~R~t~~ 70 (217)
|||||||+|||+|||. ||++|+.|.+++. ++|+++|||++|||+|+ +.+||||++ |.+|++++
T Consensus 1 LP~G~rF~PtD~ELi~~yL~~k~~g~~~~~~~~i~~~Diy~~~P~~L~~~~~~~~~~~yFF~~~~~~~~~~~r~~R~~~~ 80 (129)
T PF02365_consen 1 LPPGFRFRPTDEELINHYLRPKILGEPLPCEDVIHDVDIYSAHPWELPAKFKGGDEEWYFFSPRKKKYPNGGRPNRVTGG 80 (129)
T ss_dssp --TTEEE---HHHHHHCTHHHHHTT-HHCS-CHSEE--GGGS-GGGCHHHSSS-SSEEEEEEE----------S-EEETT
T ss_pred CCCceEecCChHHHHHHHHHHHhcCCCCCcccceeecccCccChHHhhhhccCCCceEEEEEecccccCCcccccccccc
Confidence 8999999999999999 9999999999986 89999999999999999 679999999 45688999
Q ss_pred ceEEecCcceeEee-CCceeEEEEEeeeeeCCCCCCCCcCeEEEEEEeC
Q 027916 71 GQWRAKGETCEIFS-NSYIIGWRTTLEFFEGQVPNERKTDWVMQEFRIT 118 (217)
Q Consensus 71 G~Wk~~G~~k~I~~-~~~~vG~Kktl~Fy~g~~~~g~kT~WvM~EY~l~ 118 (217)
|+||.+|+.++|.+ ++.+||+|++|+||.++.+++.+|+|+||||+|.
T Consensus 81 G~Wk~~g~~~~i~~~~g~~iG~k~~l~f~~~~~~~~~kt~W~M~EY~L~ 129 (129)
T PF02365_consen 81 GYWKSTGKEKPIKDPGGKVIGFKKTLVFYSGKSPNGKKTGWVMHEYSLE 129 (129)
T ss_dssp EEEEEECEEEEEEE-TTCEEEEEEEEEEEESSTTS-EEEEEEEEEEEE-
T ss_pred eEEeecccccccccccceeeeeEEEEEEEeccCCCCCcCCeEEEEEEeC
Confidence 99999999999999 6778999999999999888899999999999984
No 2
>PF15480 DUF4640: Domain of unknown function (DUF4640)
Probab=39.17 E-value=12 Score=33.65 Aligned_cols=16 Identities=38% Similarity=0.675 Sum_probs=12.5
Q ss_pred eechhhhhhhhheeee
Q 027916 197 VFCLLEWISCLNFVWF 212 (217)
Q Consensus 197 ~~~~~~~~~~~~~~~~ 212 (217)
..+-...++||||-|+
T Consensus 232 t~S~tq~lsClNfgw~ 247 (292)
T PF15480_consen 232 TPSNTQALSCLNFGWV 247 (292)
T ss_pred CCCCccceeeehhHHH
Confidence 3444788999999994
No 3
>PHA00692 hypothetical protein
Probab=29.50 E-value=20 Score=24.97 Aligned_cols=9 Identities=22% Similarity=0.398 Sum_probs=7.4
Q ss_pred CCCCCeeec
Q 027916 7 STPIDVDFA 15 (217)
Q Consensus 7 ~LPpGfrF~ 15 (217)
..||||||-
T Consensus 36 eyppgfrfg 44 (74)
T PHA00692 36 EYPPGFRFG 44 (74)
T ss_pred ecCCCcccc
Confidence 579999995
No 4
>PF04700 Baculo_gp41: Structural glycoprotein p40/gp41 conserved region; InterPro: IPR006790 This is a family of viral structural glycoproteins [] from the baculoviridae.; GO: 0005198 structural molecule activity, 0019012 virion
Probab=23.97 E-value=73 Score=26.99 Aligned_cols=23 Identities=39% Similarity=0.645 Sum_probs=15.9
Q ss_pred eecCCHHHHHH-H--HHHHHcCCCCCC
Q 027916 13 DFASTDENLFG-S--LERMIRGSPLPC 36 (217)
Q Consensus 13 rF~PTDeELV~-Y--L~~Ki~g~plp~ 36 (217)
||. +|||||. | |.+|..|...+.
T Consensus 3 RF~-sDe~Li~yY~~L~K~~g~~~~~~ 28 (186)
T PF04700_consen 3 RFE-SDEELIEYYANLEKKYGGSDVPS 28 (186)
T ss_pred ccc-cHHHHHHHHHHHHHHhCCCCCCc
Confidence 676 8999999 5 345666665544
No 5
>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=23.43 E-value=41 Score=26.91 Aligned_cols=9 Identities=44% Similarity=0.763 Sum_probs=8.2
Q ss_pred cCCHHHHHH
Q 027916 15 ASTDENLFG 23 (217)
Q Consensus 15 ~PTDeELV~ 23 (217)
.||||||+.
T Consensus 30 tPTeEeL~~ 38 (128)
T PF07960_consen 30 TPTEEELFK 38 (128)
T ss_pred CCCHHHHHH
Confidence 699999998
No 6
>PF07131 DUF1382: Protein of unknown function (DUF1382); InterPro: IPR009814 This entry is represented by Bacteriophage lambda, Xis. This entry overlaps with IPR009750, both representing lambda Xis. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. This family consists of several hypothetical Escherichia coli and Bacteriophage lambda-like proteins of around 60 residues in length. The function of this family is unknown.
Probab=21.75 E-value=94 Score=21.64 Aligned_cols=20 Identities=30% Similarity=0.571 Sum_probs=14.4
Q ss_pred CCeeecC----CHHHHHH---HHHHHH
Q 027916 10 IDVDFAS----TDENLFG---SLERMI 29 (217)
Q Consensus 10 pGfrF~P----TDeELV~---YL~~Ki 29 (217)
.|+||.| ||+|... -|.+|+
T Consensus 22 ~GIRFVpiPv~~dee~~~L~s~~~~kL 48 (61)
T PF07131_consen 22 IGIRFVPIPVVTDEEFHTLSSQLSQKL 48 (61)
T ss_pred cCceeeccccccHHHHHHHHHHHHHHH
Confidence 5999998 6777665 555555
No 7
>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=19.42 E-value=75 Score=16.34 Aligned_cols=8 Identities=38% Similarity=1.061 Sum_probs=5.8
Q ss_pred CCeEEEee
Q 027916 54 DGVWYLVC 61 (217)
Q Consensus 54 ~~~wYFFs 61 (217)
++.||||.
T Consensus 7 ~~~wYy~~ 14 (19)
T PF01473_consen 7 NGNWYYFD 14 (19)
T ss_dssp TTEEEEET
T ss_pred CCEEEEeC
Confidence 56788883
No 8
>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=19.33 E-value=18 Score=28.40 Aligned_cols=37 Identities=22% Similarity=0.284 Sum_probs=20.6
Q ss_pred HHHHcCCCCCCCcee--ecCCCCCCCCCCC---------CCeEEEeee
Q 027916 26 ERMIRGSPLPCNVIN--DVNPYNHRPSNLP---------DGVWYLVCS 62 (217)
Q Consensus 26 ~~Ki~g~plp~~~I~--~vDvy~~~Pw~Lp---------~~~wYFFs~ 62 (217)
++||...+++..--+ --|=|.+|+..|. ++.|||.+-
T Consensus 75 kkKIvSldl~eg~sp~yledgY~FhlEnLsL~Il~SrkE~EGWYfmtl 122 (126)
T PF06214_consen 75 KKKIVSLDLSEGGSPRYLEDGYKFHLENLSLEILESRKEDEGWYFMTL 122 (126)
T ss_dssp -EEEEEE-TTS-SS-EESSSSEEEETTTTEEEETT--GGG-EEEEEEE
T ss_pred hheEEEeccccCCCccccccccEEecccceeehhccccccCceEEEEe
Confidence 345555555533222 2377888888886 566999863
No 9
>COG5235 RFA2 Single-stranded DNA-binding replication protein A (RPA), medium (30 kD) subunit [DNA replication, recombination, and repair]
Probab=19.17 E-value=69 Score=27.99 Aligned_cols=34 Identities=29% Similarity=0.201 Sum_probs=22.3
Q ss_pred cccCCCCCCCCCceeeccccc-------CC---Ccccceechhh
Q 027916 169 LSFDKDKDDTRQVSIIRHEVC-------QP---QHSGLVFCLLE 202 (217)
Q Consensus 169 ~~~~~~~~~s~~~s~~~~~~~-------~d---~~~g~~~~~~~ 202 (217)
|...+.+||+|+||.+=++.. +| ..+|++.++++
T Consensus 181 Slf~k~dNdtSsgss~lq~~~~~c~~~~~~~~~~~~~V~I~~ls 224 (258)
T COG5235 181 SLFAKLDNDTSSGSSRLQEDILECYRRNQDENGLHINVVIKMLS 224 (258)
T ss_pred ceeeeccCccccccccccHHHHHHHHHhcCCCCcccceeehHhh
Confidence 445677899999888666542 22 26677777754
No 10
>smart00707 RPEL Repeat in Drosophila CG10860, human KIAA0680 and C. elegans F26H9.2.
Probab=19.17 E-value=77 Score=18.36 Aligned_cols=13 Identities=23% Similarity=0.156 Sum_probs=11.0
Q ss_pred CeeecCCHHHHHH
Q 027916 11 DVDFASTDENLFG 23 (217)
Q Consensus 11 GfrF~PTDeELV~ 23 (217)
....+|+-||||.
T Consensus 6 kl~~RP~~eeLv~ 18 (26)
T smart00707 6 KLSQRPTREELEE 18 (26)
T ss_pred HHHcCCCHHHHHH
Confidence 4568999999997
Done!