Query 046632
Match_columns 225
No_of_seqs 167 out of 953
Neff 6.6
Searched_HMMs 46136
Date Fri Mar 29 02:51:38 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/046632.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/046632hhsearch_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 1.3E-46 2.8E-51 297.6 6.9 129 9-148 1-129 (129)
2 cd00490 Met_repressor_MetJ Met 45.7 16 0.00036 27.2 2.0 39 16-59 50-88 (103)
3 COG3060 MetJ Transcriptional r 45.0 11 0.00025 27.8 1.1 39 16-59 51-89 (105)
4 PRK05264 transcriptional repre 42.9 18 0.00039 27.1 1.8 39 16-59 51-89 (105)
5 smart00265 BH4 BH4 Bcl-2 homol 40.0 32 0.00069 20.0 2.2 21 18-38 4-24 (27)
6 PHA00692 hypothetical protein 37.6 14 0.0003 25.5 0.5 10 7-16 35-44 (74)
7 PF01340 MetJ: Met Apo-repress 35.8 34 0.00073 25.6 2.3 39 16-59 50-88 (104)
8 PF07960 CBP4: CBP4; InterPro 30.5 27 0.00058 27.8 1.2 14 13-26 26-40 (128)
9 PLN02417 dihydrodipicolinate s 26.4 33 0.00072 30.3 1.1 21 6-27 100-120 (280)
10 cd00952 CHBPH_aldolase Trans-o 25.4 35 0.00076 30.6 1.1 21 5-26 106-126 (309)
11 cd00954 NAL N-Acetylneuraminic 24.9 35 0.00075 30.1 1.0 20 7-27 101-120 (288)
12 KOG4286 Dystrophin-like protei 24.1 24 0.00052 35.9 -0.2 40 129-173 636-677 (966)
13 PF02180 BH4: Bcl-2 homology r 23.9 65 0.0014 18.7 1.7 20 19-38 5-24 (27)
14 TIGR02313 HpaI-NOT-DapA 2,4-di 23.6 41 0.00089 29.9 1.2 21 6-27 99-119 (294)
15 smart00707 RPEL Repeat in Dros 23.3 57 0.0012 18.7 1.3 13 12-24 6-18 (26)
16 PF01473 CW_binding_1: Putativ 22.8 59 0.0013 16.6 1.3 8 63-70 7-14 (19)
17 PF13822 ACC_epsilon: Acyl-CoA 21.1 50 0.0011 22.6 1.0 9 16-24 10-18 (62)
18 PF08338 DUF1731: Domain of un 20.9 69 0.0015 20.8 1.6 16 11-26 31-47 (48)
19 TIGR00674 dapA dihydrodipicoli 20.7 57 0.0012 28.7 1.5 23 5-28 96-118 (285)
20 cd00950 DHDPS Dihydrodipicolin 20.3 52 0.0011 28.7 1.2 32 5-38 98-129 (284)
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=1.3e-46 Score=297.61 Aligned_cols=129 Identities=36% Similarity=0.664 Sum_probs=96.7
Q ss_pred CCCcceeCCChHHHHHHHHHhhhcCCCCCCCceeeccCCCCCCCccccceeecCcceEEEEEcccccccCCcccccccCC
Q 046632 9 LPPGYRFAPTDEEIVAHYLYNKVHGRPVSTSAVIDNIDVYRDENVWIRIFERTGENALYFFTTLKKKTENGVQVERETNC 88 (225)
Q Consensus 9 LPpGfRF~PTDeELv~~YL~~ki~g~~l~~~~~I~~~Dvy~~~Pw~Lp~~~~~g~~~wyFF~~~~~k~~~g~R~~R~~~~ 88 (225)
|||||||+|||+|||.+||++|+.|.+++...+|+++|||++|||+|+.....++.+||||+++++++.++.|.+|++++
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 89999999999999999999999999998878999999999999999954334578999999999999999999999999
Q ss_pred ceeeecCCceeEEcccCCCCcccccceeEEEEEeeeeeccCCCCCCCcccCeEEEEEEeC
Q 046632 89 GTWRSQKNTRIYRHRYNKTGDKIIKKQHIGSRRNFTYVPKEGSRGGVIKGTWVMHEYRLD 148 (225)
Q Consensus 89 G~Wk~~g~~k~I~~~~~~~g~~~~~g~~vG~kk~l~Fy~~~g~~~~~~kT~WvMhEY~l~ 148 (225)
|+||++|+.++|.... |.+||+|++|+|| .++.+++.+|+|+||||+|.
T Consensus 81 G~Wk~~g~~~~i~~~~---------g~~iG~k~~l~f~--~~~~~~~~kt~W~M~EY~L~ 129 (129)
T PF02365_consen 81 GYWKSTGKEKPIKDPG---------GKVIGFKKTLVFY--SGKSPNGKKTGWVMHEYSLE 129 (129)
T ss_dssp EEEEEECEEEEEEE-T---------TCEEEEEEEEEEE--ESSTTS-EEEEEEEEEEEE-
T ss_pred eEEeeccccccccccc---------ceeeeeEEEEEEE--eccCCCCCcCCeEEEEEEeC
Confidence 9999999999999853 5789999999999 88888899999999999984
No 2
>cd00490 Met_repressor_MetJ Met Repressor, MetJ. MetJ is a bacterial regulatory protein that uses S-adenosylmethionine (SAM) as a corepressor to regulate the production of Methionine. MetJ binds arrays of two to five adjacent copies of an eight base-pair 'metbox' sequence. MetJ forms sufficiently strong interactions with the sugar-phosphate backbone to accomodate sequence variation in natural operators. However, it is very sensitive to particular base changes in the operator. MetJ exists as a homodimer.
Probab=45.68 E-value=16 Score=27.18 Aligned_cols=39 Identities=15% Similarity=0.305 Sum_probs=32.8
Q ss_pred CCChHHHHHHHHHhhhcCCCCCCCceeeccCCCCCCCcccccee
Q 046632 16 APTDEEIVAHYLYNKVHGRPVSTSAVIDNIDVYRDENVWIRIFE 59 (225)
Q Consensus 16 ~PTDeELv~~YL~~ki~g~~l~~~~~I~~~Dvy~~~Pw~Lp~~~ 59 (225)
|-|-.||++.-...-..|+|||. +.|+-+..|..||...
T Consensus 50 HATNSELLCEAFLHAfTGQPLP~-----D~Dl~K~~~d~iP~~a 88 (103)
T cd00490 50 HATNSELLCEAFLHAFTGQPLPD-----DADLRKERSDEIPEAA 88 (103)
T ss_pred hcccHHHHHHHHHHHhcCCCCCC-----hhhhhhcCcccccHHH
Confidence 56788888887778889999998 5788899999998764
No 3
>COG3060 MetJ Transcriptional regulator of met regulon [Transcription / Amino acid transport and metabolism]
Probab=44.99 E-value=11 Score=27.82 Aligned_cols=39 Identities=18% Similarity=0.326 Sum_probs=32.7
Q ss_pred CCChHHHHHHHHHhhhcCCCCCCCceeeccCCCCCCCcccccee
Q 046632 16 APTDEEIVAHYLYNKVHGRPVSTSAVIDNIDVYRDENVWIRIFE 59 (225)
Q Consensus 16 ~PTDeELv~~YL~~ki~g~~l~~~~~I~~~Dvy~~~Pw~Lp~~~ 59 (225)
|-|..||++.-...-..|+|||. +.|+.+.-|.+||..+
T Consensus 51 hatnsellceaflhaftgqplpt-----d~dl~ker~deipe~a 89 (105)
T COG3060 51 HATNSELLCEAFLHAFTGQPLPT-----DADLRKERSDEIPEAA 89 (105)
T ss_pred hhhhHHHHHHHHHHHHcCCCCCC-----cHHHHHhccccchHHH
Confidence 56778888887777889999998 6788888999998865
No 4
>PRK05264 transcriptional repressor protein MetJ; Provisional
Probab=42.89 E-value=18 Score=27.14 Aligned_cols=39 Identities=15% Similarity=0.289 Sum_probs=32.7
Q ss_pred CCChHHHHHHHHHhhhcCCCCCCCceeeccCCCCCCCcccccee
Q 046632 16 APTDEEIVAHYLYNKVHGRPVSTSAVIDNIDVYRDENVWIRIFE 59 (225)
Q Consensus 16 ~PTDeELv~~YL~~ki~g~~l~~~~~I~~~Dvy~~~Pw~Lp~~~ 59 (225)
|-|-.||++.-...-..|+|||. +-|+-+..|..+|...
T Consensus 51 HATNSELLCEAFLHA~TGQPLP~-----D~Dl~Kd~~d~ip~~a 89 (105)
T PRK05264 51 HATNSELLCEAFLHAFTGQPLPD-----DEDLRKERSDEIPEAA 89 (105)
T ss_pred hcccHHHHHHHHHHHHcCCCCCC-----hhhhhhcCcccchHHH
Confidence 56788898887778889999998 5688899999998754
No 5
>smart00265 BH4 BH4 Bcl-2 homology region 4.
Probab=39.96 E-value=32 Score=19.96 Aligned_cols=21 Identities=19% Similarity=0.276 Sum_probs=16.7
Q ss_pred ChHHHHHHHHHhhhcCCCCCC
Q 046632 18 TDEEIVAHYLYNKVHGRPVST 38 (225)
Q Consensus 18 TDeELv~~YL~~ki~g~~l~~ 38 (225)
+-.|||.+|+.-|+.....++
T Consensus 4 ~nRelV~~yv~yKLsQrgy~w 24 (27)
T smart00265 4 DNRELVVDYVTYKLSQNGYEW 24 (27)
T ss_pred chHHHHHHHHHHHHhhcCCCC
Confidence 457999999999997665544
No 6
>PHA00692 hypothetical protein
Probab=37.62 E-value=14 Score=25.50 Aligned_cols=10 Identities=50% Similarity=1.241 Sum_probs=8.2
Q ss_pred CCCCCcceeC
Q 046632 7 PALPPGYRFA 16 (225)
Q Consensus 7 ~~LPpGfRF~ 16 (225)
...||||||-
T Consensus 35 veyppgfrfg 44 (74)
T PHA00692 35 VEYPPGFRFG 44 (74)
T ss_pred EecCCCcccc
Confidence 4689999995
No 7
>PF01340 MetJ: Met Apo-repressor, MetJ; InterPro: IPR002084 Binding of a specific DNA fragment and S-adenosyl methionine (SAM) co-repressor molecules to the Escherichia coli methionine repressor (MetJ) leads to a significant reduction in dynamic flexibility of the ternary complex, with considerable entropy-enthalpy compensation, not necessarily involving any overall conformational change []. MetJ is a regulatory protein which when combined with S-adenosylmethionine (SAM) represses the expression of the methionine regulon and of enzymes involved in SAM synthesis. It is also autoregulated. The crystal structure of the met repressor-operator complex shows two dimeric repressor molecules bound to adjacent sites 8 base pairs apart on an 18-base-pair DNA fragment. Sequence specificity is achieved by insertion of double-stranded antiparallel protein beta-ribbons into the major groove of B-form DNA, with direct hydrogen-bonding between amino-acid side chains and the base pairs. The repressor also recognises sequence-dependent distortion or flexibility of the operator phosphate backbone, conferring specificity even for inaccessible base pairs [].; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0006555 methionine metabolic process; PDB: 1MJO_D 1CMB_A 1MJQ_C 1CMC_B 1MJK_A 1MJ2_A 1MJP_A 1MJM_B 1CMA_B 1MJL_A ....
Probab=35.78 E-value=34 Score=25.60 Aligned_cols=39 Identities=21% Similarity=0.305 Sum_probs=25.6
Q ss_pred CCChHHHHHHHHHhhhcCCCCCCCceeeccCCCCCCCcccccee
Q 046632 16 APTDEEIVAHYLYNKVHGRPVSTSAVIDNIDVYRDENVWIRIFE 59 (225)
Q Consensus 16 ~PTDeELv~~YL~~ki~g~~l~~~~~I~~~Dvy~~~Pw~Lp~~~ 59 (225)
|-|..||++.-...-..|+|||. +.|+-+..|..+|...
T Consensus 50 HATNSeLLcEAFLHAfTGQPLP~-----D~dl~kd~~d~ip~~~ 88 (104)
T PF01340_consen 50 HATNSELLCEAFLHAFTGQPLPT-----DDDLRKDRPDEIPAEA 88 (104)
T ss_dssp S-SHHHHHHHHHHHHHH-----------TTGGGSTSGSSS-HHH
T ss_pred hcccHHHHHHHHHHHhcCCCCCC-----hhhhhhcCCccchHHH
Confidence 56888998887777889999998 6788899999998754
No 8
>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=30.54 E-value=27 Score=27.78 Aligned_cols=14 Identities=36% Similarity=0.909 Sum_probs=10.8
Q ss_pred cee-CCChHHHHHHH
Q 046632 13 YRF-APTDEEIVAHY 26 (225)
Q Consensus 13 fRF-~PTDeELv~~Y 26 (225)
|.+ .||||||+..|
T Consensus 26 ~~y~tPTeEeL~~r~ 40 (128)
T PF07960_consen 26 VKYTTPTEEELFKRY 40 (128)
T ss_pred heecCCCHHHHHHhc
Confidence 444 59999999865
No 9
>PLN02417 dihydrodipicolinate synthase
Probab=26.36 E-value=33 Score=30.26 Aligned_cols=21 Identities=19% Similarity=0.393 Sum_probs=16.1
Q ss_pred CCCCCCcceeCCChHHHHHHHH
Q 046632 6 LPALPPGYRFAPTDEEIVAHYL 27 (225)
Q Consensus 6 ~~~LPpGfRF~PTDeELv~~YL 27 (225)
.+-+|| |-|.||++||+.||-
T Consensus 100 v~~~~P-~y~~~~~~~i~~~f~ 120 (280)
T PLN02417 100 ALHINP-YYGKTSQEGLIKHFE 120 (280)
T ss_pred EEEcCC-ccCCCCHHHHHHHHH
Confidence 345666 558999999999774
No 10
>cd00952 CHBPH_aldolase Trans-o-hydroxybenzylidenepyruvate hydratase-aldolase (HBPHA) and trans-2'-carboxybenzalpyruvate hydratase-aldolase (CBPHA). HBPHA catalyzes HBP to salicyaldehyde and pyruvate. This reaction is part of the degradative pathways for naphthalene and naphthalenesulfonates by bacteria. CBPHA is homologous to HBPHA and catalyzes the cleavage of CBP to 2-carboxylbenzaldehyde and pyruvate during the degradation of phenanthrene. They are member of the DHDPS family of Schiff-base-dependent class I aldolases.
Probab=25.43 E-value=35 Score=30.62 Aligned_cols=21 Identities=14% Similarity=0.072 Sum_probs=16.5
Q ss_pred CCCCCCCcceeCCChHHHHHHH
Q 046632 5 QLPALPPGYRFAPTDEEIVAHY 26 (225)
Q Consensus 5 ~~~~LPpGfRF~PTDeELv~~Y 26 (225)
+.+-+|| |.|.||+++|+.||
T Consensus 106 ~vlv~~P-~y~~~~~~~l~~yf 126 (309)
T cd00952 106 GTMLGRP-MWLPLDVDTAVQFY 126 (309)
T ss_pred EEEECCC-cCCCCCHHHHHHHH
Confidence 4466777 56899999999876
No 11
>cd00954 NAL N-Acetylneuraminic acid aldolase, also called N-acetylneuraminate lyase (NAL), which catalyses the reversible aldol reaction of N-acetyl-D-mannosamine and pyruvate to give N-acetyl-D-neuraminic acid (D-sialic acid). It has a widespread application as biocatalyst for the synthesis of sialic acid and its derivatives. This enzyme has been shown to be quite specific for pyruvate as the donor, but flexible to a variety of D- and, to some extent, L-hexoses and pentoses as acceptor substrates. NAL is member of dihydrodipicolinate synthase family that comprises several pyruvate-dependent class I aldolases.
Probab=24.90 E-value=35 Score=30.14 Aligned_cols=20 Identities=35% Similarity=0.441 Sum_probs=14.7
Q ss_pred CCCCCcceeCCChHHHHHHHH
Q 046632 7 PALPPGYRFAPTDEEIVAHYL 27 (225)
Q Consensus 7 ~~LPpGfRF~PTDeELv~~YL 27 (225)
+-+||-| |.||++||+.||.
T Consensus 101 ~~~~P~y-~~~~~~~i~~~~~ 120 (288)
T cd00954 101 SAITPFY-YKFSFEEIKDYYR 120 (288)
T ss_pred EEeCCCC-CCCCHHHHHHHHH
Confidence 4456644 7899999998664
No 12
>KOG4286 consensus Dystrophin-like protein [Cell motility; Signal transduction mechanisms; Cytoskeleton]
Probab=24.09 E-value=24 Score=35.92 Aligned_cols=40 Identities=20% Similarity=0.135 Sum_probs=28.3
Q ss_pred CCCCCCCcccCeEEEEEEeCCCCccccccCCCCc--EEEEEEEEcCC
Q 046632 129 EGSRGGVIKGTWVMHEYRLDGISISNARINNIGD--YVICRIKKKQP 173 (225)
Q Consensus 129 ~g~~~~~~kT~WvMhEY~l~~~~~~~~~~~~~~~--~VLCrI~~k~~ 173 (225)
.|++.++.+++.-|.||-....+... ..+ -+||--|+.++
T Consensus 636 sgraak~hk~~~pM~Ey~~~tts~~d-----~rdfak~L~nkfr~~~ 677 (966)
T KOG4286|consen 636 SGRAAKGHKMHYPMVEYCTPTTSGED-----VRDFAKVLKNKFRTKR 677 (966)
T ss_pred hcccccCCCCCCCceeeeCCCCChhh-----HHHHHHHHHhhhccch
Confidence 68889999999999999987765431 112 26776666444
No 13
>PF02180 BH4: Bcl-2 homology region 4; InterPro: IPR003093 Apoptosis, or programmed cell death (PCD), is a common and evolutionarily conserved property of all metazoans []. In many biological processes, apoptosis is required to eliminate supernumerary or dangerous (such as pre-cancerous) cells and to promote normal development. Dysregulation of apoptosis can, therefore, contribute to the development of many major diseases including cancer, autoimmunity and neurodegenerative disorders. In most cases, proteins of the caspase family execute the genetic programme that leads to cell death. Bcl-2 proteins are central regulators of caspase activation, and play a key role in cell death by regulating the integrity of the mitochondrial and endoplasmic reticulum (ER) membranes []. At least 20 Bcl-2 proteins have been reported in mammals, and several others have been identified in viruses. Bcl-2 family proteins fall roughly into three subtypes, which either promote cell survival (anti-apoptotic) or trigger cell death (pro-apoptotic). All members contain at least one of four conserved motifs, termed Bcl-2 Homology (BH) domains. Bcl-2 subfamily proteins, which contain at least BH1 and BH2, promote cell survival by inhibiting the adapters needed for the activation of caspases. Pro-apoptotic members potentially exert their effects by displacing the adapters from the pro-survival proteins; these proteins belong either to the Bax subfamily, which contain BH1-BH3, or to the BH3 subfamily, which mostly only feature BH3 []. Thus, the balance between antagonistic family members is believed to play a role in determining cell fate. Members of the wider Bcl-2 family, which also includes Bcl-x, Bcl-w and Mcl-1, are described by their similarity to Bcl-2 protein, a member of the pro-survival Bcl-2 subfamily []. Full-length Bcl-2 proteins feature all four BH domains, seven alpha-helices, and a C-terminal hydrophobic motif that targets the protein to the outer mitochondrial membrane, ER and nuclear envelope. Active cell suicide (apoptosis) is induced by events such as growth factor withdrawal and toxins. It is controlled by regulators, which have either an inhibitory effect on programmed cell death (anti-apoptotic) or block the protective effect of inhibitors (pro-apoptotic) [, ]. Many viruses have found a way of countering defensive apoptosis by encoding their own anti-apoptosis genes preventing their target-cells from dying too soon. All proteins belonging to the Bcl-2 family [] contain either a BH1, BH2, BH3, or BH4 domain. All anti-apoptotic proteins contain BH1 and BH2 domains, some of them contain an additional N-terminal BH4 domain (Bcl-2, Bcl-x(L), Bcl-w), which is never seen in pro-apoptotic proteins, except for Bcl-x(S). On the other hand, all pro-apoptotic proteins contain a BH3 domain (except for Bad) necessary for dimerisation with other proteins of Bcl-2 family and crucial for their killing activity, some of them also contain BH1 and BH2 domains (Bax, Bak). The BH3 domain is also present in some anti-apoptotic protein, such as Bcl-2 or Bcl-x(L). Proteins that are known to contain these domains include vertebrate Bcl-2 (alpha and beta isoforms) and Bcl-x (isoforms (Bcl-x(L) and Bcl-x(S)); mammalian proteins Bax and Bak; mouse protein Bid; Xenopus laevis proteins Xr1 and Xr11; human induced myeloid leukemia cell differentiation protein MCL1 and Caenorhabditis elegans protein ced-9.; GO: 0042981 regulation of apoptosis; PDB: 1AF3_A 2PON_B 1YSN_A 3PL7_B 3R85_A 2O2N_A 2P1L_C 1R2G_A 2O1Y_A 1BXL_A ....
Probab=23.93 E-value=65 Score=18.68 Aligned_cols=20 Identities=25% Similarity=0.358 Sum_probs=15.5
Q ss_pred hHHHHHHHHHhhhcCCCCCC
Q 046632 19 DEEIVAHYLYNKVHGRPVST 38 (225)
Q Consensus 19 DeELv~~YL~~ki~g~~l~~ 38 (225)
-.|||.+|+.-|+.-...++
T Consensus 5 nR~lV~~yi~yKLsQrgy~w 24 (27)
T PF02180_consen 5 NRELVEDYISYKLSQRGYVW 24 (27)
T ss_dssp HHHHHHHHHHHHHHHTTSTS
T ss_pred HHHHHHHHHHHHhhhcCCCC
Confidence 47999999999987655544
No 14
>TIGR02313 HpaI-NOT-DapA 2,4-dihydroxyhept-2-ene-1,7-dioic acid aldolase. This model represents a subset of the DapA (dihydrodipicolinate synthase) family which has apparently evolved a separate function. The product of DapA, dihydrodipicolinate, results from the non-enzymatic cyclization and dehydration of 6-amino-2,4-dihydroxyhept-2-ene-1,7-dioic acid, which is different from the substrate of this reaction only in the presence of the amino group. In the absence of this amino group, and running the reaction in the opposite direction, the reaction corresponds to the HpaI aldolase component of the 4-hydroxyphenylacetic acid catabolism pathway (see TIGR02311). At present, this variant of DapA is found only in Oceanobacillus iheyensis HTE831 and Thermus thermophilus HB27. In both of these cases, one or more other DapA genes can be found and the one identified by this model is part of an operon for 4-hydroxyphenylacetic acid catabolism.
Probab=23.59 E-value=41 Score=29.91 Aligned_cols=21 Identities=24% Similarity=0.466 Sum_probs=15.8
Q ss_pred CCCCCCcceeCCChHHHHHHHH
Q 046632 6 LPALPPGYRFAPTDEEIVAHYL 27 (225)
Q Consensus 6 ~~~LPpGfRF~PTDeELv~~YL 27 (225)
.+-+||-| |.|++++|+.||-
T Consensus 99 v~v~pP~y-~~~~~~~l~~~f~ 119 (294)
T TIGR02313 99 AMVIVPYY-NKPNQEALYDHFA 119 (294)
T ss_pred EEEcCccC-CCCCHHHHHHHHH
Confidence 34566655 8999999998764
No 15
>smart00707 RPEL Repeat in Drosophila CG10860, human KIAA0680 and C. elegans F26H9.2.
Probab=23.30 E-value=57 Score=18.71 Aligned_cols=13 Identities=31% Similarity=0.345 Sum_probs=10.9
Q ss_pred cceeCCChHHHHH
Q 046632 12 GYRFAPTDEEIVA 24 (225)
Q Consensus 12 GfRF~PTDeELv~ 24 (225)
...++||-||||.
T Consensus 6 kl~~RP~~eeLv~ 18 (26)
T smart00707 6 KLSQRPTREELEE 18 (26)
T ss_pred HHHcCCCHHHHHH
Confidence 4568999999996
No 16
>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=22.82 E-value=59 Score=16.60 Aligned_cols=8 Identities=25% Similarity=0.841 Sum_probs=6.3
Q ss_pred cceEEEEE
Q 046632 63 ENALYFFT 70 (225)
Q Consensus 63 ~~~wyFF~ 70 (225)
++.||||.
T Consensus 7 ~~~wYy~~ 14 (19)
T PF01473_consen 7 NGNWYYFD 14 (19)
T ss_dssp TTEEEEET
T ss_pred CCEEEEeC
Confidence 47899994
No 17
>PF13822 ACC_epsilon: Acyl-CoA carboxylase epsilon subunit
Probab=21.13 E-value=50 Score=22.62 Aligned_cols=9 Identities=67% Similarity=0.999 Sum_probs=7.3
Q ss_pred CCChHHHHH
Q 046632 16 APTDEEIVA 24 (225)
Q Consensus 16 ~PTDeELv~ 24 (225)
+||||||-.
T Consensus 10 nPt~eElAA 18 (62)
T PF13822_consen 10 NPTDEELAA 18 (62)
T ss_pred CCCHHHHHH
Confidence 699999854
No 18
>PF08338 DUF1731: Domain of unknown function (DUF1731); InterPro: IPR013549 This domain of unknown function appears towards the C terminus of proteins of the NAD dependent epimerase/dehydratase family (IPR001509 from INTERPRO) in bacteria, eukaryotes and archaea. Many of the proteins in which it is found are involved in cell-division inhibition. ; PDB: 3OH8_A.
Probab=20.88 E-value=69 Score=20.77 Aligned_cols=16 Identities=38% Similarity=0.708 Sum_probs=8.9
Q ss_pred CcceeC-CChHHHHHHH
Q 046632 11 PGYRFA-PTDEEIVAHY 26 (225)
Q Consensus 11 pGfRF~-PTDeELv~~Y 26 (225)
-||+|+ |+=++-+.+-
T Consensus 31 ~GF~F~~p~l~~AL~~l 47 (48)
T PF08338_consen 31 AGFQFRYPTLEEALRDL 47 (48)
T ss_dssp TT---S-SSHHHHHHH-
T ss_pred CCCcccCCCHHHHHhcc
Confidence 499996 8888877654
No 19
>TIGR00674 dapA dihydrodipicolinate synthase. Dihydrodipicolinate synthase is a homotetrameric enzyme of lysine biosynthesis. E. coli has several paralogs closely related to dihydrodipicoline synthase (DapA), as well as the more distant N-acetylneuraminate lyase. In Pyrococcus horikoshii, the bidirectional best hit with E. coli is to an uncharacterized paralog of DapA, not DapA itself, and it is omitted from the seed. The putative members from the Chlamydias (pathogens with a parasitic metabolism) are easily the most divergent members of the multiple alignment.
Probab=20.73 E-value=57 Score=28.68 Aligned_cols=23 Identities=26% Similarity=0.446 Sum_probs=16.7
Q ss_pred CCCCCCCcceeCCChHHHHHHHHH
Q 046632 5 QLPALPPGYRFAPTDEEIVAHYLY 28 (225)
Q Consensus 5 ~~~~LPpGfRF~PTDeELv~~YL~ 28 (225)
+.+-+||-| |.|+++||+.||..
T Consensus 96 ~v~v~pP~y-~~~~~~~i~~~~~~ 118 (285)
T TIGR00674 96 GFLVVTPYY-NKPTQEGLYQHFKA 118 (285)
T ss_pred EEEEcCCcC-CCCCHHHHHHHHHH
Confidence 345566665 78999999987753
No 20
>cd00950 DHDPS Dihydrodipicolinate synthase (DHDPS) is a key enzyme in lysine biosynthesis. It catalyzes the aldol condensation of L-aspartate-beta- semialdehyde and pyruvate to dihydropicolinic acid via a Schiff base formation between pyruvate and a lysine residue. The functional enzyme is a homotetramer consisting of a dimer of dimers. DHDPS is member of dihydrodipicolinate synthase family that comprises several pyruvate-dependent class I aldolases that use the same catalytic step to catalyze different reactions in different pathways.
Probab=20.31 E-value=52 Score=28.74 Aligned_cols=32 Identities=19% Similarity=0.335 Sum_probs=20.4
Q ss_pred CCCCCCCcceeCCChHHHHHHHHHhhhcCCCCCC
Q 046632 5 QLPALPPGYRFAPTDEEIVAHYLYNKVHGRPVST 38 (225)
Q Consensus 5 ~~~~LPpGfRF~PTDeELv~~YL~~ki~g~~l~~ 38 (225)
..+-+||.| |.||++||+.|| +.-+...++|+
T Consensus 98 ~v~~~~P~~-~~~~~~~l~~~~-~~ia~~~~~pi 129 (284)
T cd00950 98 AALVVTPYY-NKPSQEGLYAHF-KAIAEATDLPV 129 (284)
T ss_pred EEEEccccc-CCCCHHHHHHHH-HHHHhcCCCCE
Confidence 345677755 889999999754 44444444554
Done!