Query 038778
Match_columns 127
No_of_seqs 115 out of 821
Neff 7.3
Searched_HMMs 46136
Date Fri Mar 29 03:11:24 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/038778.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/038778hhsearch_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 2.3E-46 5.1E-51 261.1 5.7 121 3-127 1-124 (129)
2 PHA00692 hypothetical protein 62.4 3.1 6.7E-05 25.3 0.4 10 2-11 36-45 (74)
3 PF07960 CBP4: CBP4; InterPro 54.0 7.1 0.00015 27.3 1.1 11 10-20 30-40 (128)
4 PF13822 ACC_epsilon: Acyl-CoA 47.7 9.9 0.00022 23.0 0.9 9 10-18 10-18 (62)
5 smart00707 RPEL Repeat in Dros 44.2 17 0.00036 18.4 1.3 13 6-18 6-18 (26)
6 PLN02417 dihydrodipicolinate s 43.9 13 0.00029 28.8 1.3 18 3-21 103-120 (280)
7 cd00954 NAL N-Acetylneuraminic 43.9 13 0.00027 28.9 1.2 18 3-21 103-120 (288)
8 cd00952 CHBPH_aldolase Trans-o 42.5 14 0.00031 29.1 1.3 18 2-20 109-126 (309)
9 TIGR02313 HpaI-NOT-DapA 2,4-di 42.3 15 0.00032 28.7 1.4 18 3-21 102-119 (294)
10 PF01473 CW_binding_1: Putativ 41.1 22 0.00047 16.0 1.3 8 58-65 7-14 (19)
11 smart00265 BH4 BH4 Bcl-2 homol 40.6 23 0.0005 18.0 1.5 17 11-27 3-19 (27)
12 KOG3238 Chloride ion current i 40.1 29 0.00062 26.2 2.5 59 5-64 111-170 (216)
13 cd00950 DHDPS Dihydrodipicolin 38.0 19 0.00042 27.6 1.4 18 2-20 101-118 (284)
14 TIGR00674 dapA dihydrodipicoli 37.1 23 0.0005 27.3 1.7 19 3-22 100-118 (285)
15 PRK03170 dihydrodipicolinate s 36.8 21 0.00047 27.5 1.5 17 3-20 103-119 (292)
16 PF07131 DUF1382: Protein of u 34.2 30 0.00064 21.0 1.5 14 5-18 22-39 (61)
17 PRK04147 N-acetylneuraminate l 32.6 26 0.00055 27.2 1.3 17 4-21 107-123 (293)
18 TIGR03249 KdgD 5-dehydro-4-deo 28.8 35 0.00075 26.6 1.5 18 3-21 106-123 (296)
19 PF02755 RPEL: RPEL repeat; I 28.6 35 0.00076 17.1 1.0 10 9-18 9-18 (26)
20 cd00408 DHDPS-like Dihydrodipi 28.1 36 0.00078 26.0 1.5 18 3-21 99-116 (281)
21 PRK03620 5-dehydro-4-deoxygluc 26.9 36 0.00079 26.6 1.3 18 3-21 108-125 (303)
22 PF09174 Maf1: Maf1 regulator; 25.1 24 0.00052 25.8 -0.0 14 34-48 137-150 (179)
23 PTZ00079 NADP-specific glutama 25.0 61 0.0013 27.4 2.4 43 5-48 98-148 (454)
24 PF02180 BH4: Bcl-2 homology r 24.5 68 0.0015 16.3 1.6 15 12-26 4-18 (27)
25 PF02375 JmjN: jmjN domain; I 23.4 40 0.00088 18.0 0.7 11 8-18 2-12 (34)
26 PHA02696 hypothetical protein; 22.4 88 0.0019 19.6 2.1 25 16-41 23-48 (79)
27 PF00701 DHDPS: Dihydrodipicol 22.4 31 0.00067 26.6 0.1 18 3-21 103-120 (289)
28 cd00490 Met_repressor_MetJ Met 21.6 1E+02 0.0022 20.3 2.4 39 10-52 50-88 (103)
29 TIGR03874 4cys_cytochr c-type 20.9 81 0.0017 22.4 2.0 24 5-29 93-120 (143)
30 PF10107 Endonuc_Holl: Endonuc 20.7 37 0.00079 24.6 0.2 22 2-32 84-105 (156)
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=2.3e-46 Score=261.11 Aligned_cols=121 Identities=36% Similarity=0.666 Sum_probs=91.5
Q ss_pred CCCCceEcCCHHHHHHHHHHHhcCCCCC--ccceeecCCcCCCCCccccccCccCCCCceEEEEeccccccCCCCccccc
Q 038778 3 SLMGFRFQPSNEQIFCLLEKKRLNPHFS--HHTIKDIDDICSLEPWDLAGASKTESEDRVCYFFCKPYYKYKKSTRAHRR 80 (127)
Q Consensus 3 lppG~rF~PtDeELi~~yL~~k~~g~~~--~~~I~~~~dvy~~~P~~L~~~~~~~~~~~~wyFF~~~~~~~~~g~r~~r~ 80 (127)
|||||||+|||+|||.+||++|+.|+++ .++|+++ |||+.|||+|+... ..++++||||+++++++.++.|.+|+
T Consensus 1 LP~G~rF~PtD~ELi~~yL~~k~~g~~~~~~~~i~~~-Diy~~~P~~L~~~~--~~~~~~~yFF~~~~~~~~~~~r~~R~ 77 (129)
T PF02365_consen 1 LPPGFRFRPTDEELINHYLRPKILGEPLPCEDVIHDV-DIYSAHPWELPAKF--KGGDEEWYFFSPRKKKYPNGGRPNRV 77 (129)
T ss_dssp --TTEEE---HHHHHHCTHHHHHTT-HHCS-CHSEE---GGGS-GGGCHHHS--SS-SSEEEEEEE----------S-EE
T ss_pred CCCceEecCChHHHHHHHHHHHhcCCCCCcccceeec-ccCccChHHhhhhc--cCCCceEEEEEecccccCCccccccc
Confidence 8999999999999999999999999998 4899999 99999999999532 23577999999999999999999999
Q ss_pred CCCceeEeeCCCeeeee-CCeeEEEEEEEEeeeeCCCCCCCCcCceeC
Q 038778 81 TNAGYWKVTGRGSKIKT-RNGLSGTKKILTFKYHGPASKKAKIGWVMH 127 (127)
Q Consensus 81 ~~~G~Wk~~g~~~~i~~-~g~~iG~k~~l~f~y~g~~~~~~kt~W~Mh 127 (127)
+++|+||++|+.++|.+ ++.+||+|++|+| |.++.+++.+|+|+||
T Consensus 78 ~~~G~Wk~~g~~~~i~~~~g~~iG~k~~l~f-~~~~~~~~~kt~W~M~ 124 (129)
T PF02365_consen 78 TGGGYWKSTGKEKPIKDPGGKVIGFKKTLVF-YSGKSPNGKKTGWVMH 124 (129)
T ss_dssp ETTEEEEEECEEEEEEE-TTCEEEEEEEEEE-EESSTTS-EEEEEEEE
T ss_pred ccceEEeecccccccccccceeeeeEEEEEE-EeccCCCCCcCCeEEE
Confidence 99999999999999998 9999999999999 9988888999999998
No 2
>PHA00692 hypothetical protein
Probab=62.43 E-value=3.1 Score=25.34 Aligned_cols=10 Identities=50% Similarity=0.657 Sum_probs=7.9
Q ss_pred CCCCCceEcC
Q 038778 2 ESLMGFRFQP 11 (127)
Q Consensus 2 ~lppG~rF~P 11 (127)
+.||||||--
T Consensus 36 eyppgfrfgg 45 (74)
T PHA00692 36 EYPPGFRFGG 45 (74)
T ss_pred ecCCCccccc
Confidence 5799999953
No 3
>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=54.03 E-value=7.1 Score=27.32 Aligned_cols=11 Identities=27% Similarity=0.609 Sum_probs=9.8
Q ss_pred cCCHHHHHHHH
Q 038778 10 QPSNEQIFCLL 20 (127)
Q Consensus 10 ~PtDeELi~~y 20 (127)
.||||||+..|
T Consensus 30 tPTeEeL~~r~ 40 (128)
T PF07960_consen 30 TPTEEELFKRY 40 (128)
T ss_pred CCCHHHHHHhc
Confidence 69999999876
No 4
>PF13822 ACC_epsilon: Acyl-CoA carboxylase epsilon subunit
Probab=47.74 E-value=9.9 Score=22.99 Aligned_cols=9 Identities=22% Similarity=0.678 Sum_probs=7.8
Q ss_pred cCCHHHHHH
Q 038778 10 QPSNEQIFC 18 (127)
Q Consensus 10 ~PtDeELi~ 18 (127)
+||||||-.
T Consensus 10 nPt~eElAA 18 (62)
T PF13822_consen 10 NPTDEELAA 18 (62)
T ss_pred CCCHHHHHH
Confidence 799999865
No 5
>smart00707 RPEL Repeat in Drosophila CG10860, human KIAA0680 and C. elegans F26H9.2.
Probab=44.18 E-value=17 Score=18.39 Aligned_cols=13 Identities=15% Similarity=0.263 Sum_probs=10.7
Q ss_pred CceEcCCHHHHHH
Q 038778 6 GFRFQPSNEQIFC 18 (127)
Q Consensus 6 G~rF~PtDeELi~ 18 (127)
....+|+.+|||.
T Consensus 6 kl~~RP~~eeLv~ 18 (26)
T smart00707 6 KLSQRPTREELEE 18 (26)
T ss_pred HHHcCCCHHHHHH
Confidence 3567899999997
No 6
>PLN02417 dihydrodipicolinate synthase
Probab=43.90 E-value=13 Score=28.77 Aligned_cols=18 Identities=17% Similarity=0.052 Sum_probs=14.6
Q ss_pred CCCCceEcCCHHHHHHHHH
Q 038778 3 SLMGFRFQPSNEQIFCLLE 21 (127)
Q Consensus 3 lppG~rF~PtDeELi~~yL 21 (127)
.|| +.|.||++||+.||-
T Consensus 103 ~~P-~y~~~~~~~i~~~f~ 120 (280)
T PLN02417 103 INP-YYGKTSQEGLIKHFE 120 (280)
T ss_pred cCC-ccCCCCHHHHHHHHH
Confidence 466 558999999999874
No 7
>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=43.88 E-value=13 Score=28.91 Aligned_cols=18 Identities=17% Similarity=-0.134 Sum_probs=13.9
Q ss_pred CCCCceEcCCHHHHHHHHH
Q 038778 3 SLMGFRFQPSNEQIFCLLE 21 (127)
Q Consensus 3 lppG~rF~PtDeELi~~yL 21 (127)
+||- .|.||++||+.||.
T Consensus 103 ~~P~-y~~~~~~~i~~~~~ 120 (288)
T cd00954 103 ITPF-YYKFSFEEIKDYYR 120 (288)
T ss_pred eCCC-CCCCCHHHHHHHHH
Confidence 4554 47899999999874
No 8
>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=42.51 E-value=14 Score=29.09 Aligned_cols=18 Identities=0% Similarity=-0.138 Sum_probs=14.8
Q ss_pred CCCCCceEcCCHHHHHHHH
Q 038778 2 ESLMGFRFQPSNEQIFCLL 20 (127)
Q Consensus 2 ~lppG~rF~PtDeELi~~y 20 (127)
-+|| |.|.||++||+.||
T Consensus 109 v~~P-~y~~~~~~~l~~yf 126 (309)
T cd00952 109 LGRP-MWLPLDVDTAVQFY 126 (309)
T ss_pred ECCC-cCCCCCHHHHHHHH
Confidence 3567 56899999999987
No 9
>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=42.33 E-value=15 Score=28.70 Aligned_cols=18 Identities=11% Similarity=0.270 Sum_probs=14.3
Q ss_pred CCCCceEcCCHHHHHHHHH
Q 038778 3 SLMGFRFQPSNEQIFCLLE 21 (127)
Q Consensus 3 lppG~rF~PtDeELi~~yL 21 (127)
.||-| |.|++++|+.||-
T Consensus 102 ~pP~y-~~~~~~~l~~~f~ 119 (294)
T TIGR02313 102 IVPYY-NKPNQEALYDHFA 119 (294)
T ss_pred cCccC-CCCCHHHHHHHHH
Confidence 45554 8999999999873
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=41.13 E-value=22 Score=16.04 Aligned_cols=8 Identities=25% Similarity=0.612 Sum_probs=6.5
Q ss_pred CceEEEEe
Q 038778 58 DRVCYFFC 65 (127)
Q Consensus 58 ~~~wyFF~ 65 (127)
++.||||.
T Consensus 7 ~~~wYy~~ 14 (19)
T PF01473_consen 7 NGNWYYFD 14 (19)
T ss_dssp TTEEEEET
T ss_pred CCEEEEeC
Confidence 57899994
No 11
>smart00265 BH4 BH4 Bcl-2 homology region 4.
Probab=40.60 E-value=23 Score=18.04 Aligned_cols=17 Identities=12% Similarity=0.130 Sum_probs=13.6
Q ss_pred CCHHHHHHHHHHHhcCC
Q 038778 11 PSNEQIFCLLEKKRLNP 27 (127)
Q Consensus 11 PtDeELi~~yL~~k~~g 27 (127)
.+-.|||.+|+.-|+.-
T Consensus 3 ~~nRelV~~yv~yKLsQ 19 (27)
T smart00265 3 LDNRELVVDYVTYKLSQ 19 (27)
T ss_pred cchHHHHHHHHHHHHhh
Confidence 35689999999998853
No 12
>KOG3238 consensus Chloride ion current inducer protein [Inorganic ion transport and metabolism]
Probab=40.09 E-value=29 Score=26.24 Aligned_cols=59 Identities=17% Similarity=0.209 Sum_probs=33.1
Q ss_pred CCceEcCCHHHHHHHHHHHhcCCCCC-ccceeecCCcCCCCCccccccCccCCCCceEEEE
Q 038778 5 MGFRFQPSNEQIFCLLEKKRLNPHFS-HHTIKDIDDICSLEPWDLAGASKTESEDRVCYFF 64 (127)
Q Consensus 5 pG~rF~PtDeELi~~yL~~k~~g~~~-~~~I~~~~dvy~~~P~~L~~~~~~~~~~~~wyFF 64 (127)
-+|||+|+|..-+...--.....+.+ +....+. +-|.-+=|+........++...||=+
T Consensus 111 ~e~rfvpsDk~~l~a~f~qfcecqel~p~P~ED~-~~~dgee~~mea~d~~~gDs~~~~t~ 170 (216)
T KOG3238|consen 111 TEFRFVPSDKSALEAMFTQFCECQELNPDPDEDE-DDYDGEEYDMEAHDAGQGDSPNSYTY 170 (216)
T ss_pred ccceecCCchhHHHHHHHHHHhhhhcCCCccccc-cccccchhhhhhhhccCCCCcccccc
Confidence 58999999987666433333334444 4444455 66666666665443333444445444
No 13
>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=38.03 E-value=19 Score=27.61 Aligned_cols=18 Identities=17% Similarity=0.270 Sum_probs=14.0
Q ss_pred CCCCCceEcCCHHHHHHHH
Q 038778 2 ESLMGFRFQPSNEQIFCLL 20 (127)
Q Consensus 2 ~lppG~rF~PtDeELi~~y 20 (127)
-.||.| |.|+++||+.||
T Consensus 101 ~~~P~~-~~~~~~~l~~~~ 118 (284)
T cd00950 101 VVTPYY-NKPSQEGLYAHF 118 (284)
T ss_pred Eccccc-CCCCHHHHHHHH
Confidence 356754 889999999966
No 14
>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=37.08 E-value=23 Score=27.34 Aligned_cols=19 Identities=11% Similarity=0.240 Sum_probs=14.6
Q ss_pred CCCCceEcCCHHHHHHHHHH
Q 038778 3 SLMGFRFQPSNEQIFCLLEK 22 (127)
Q Consensus 3 lppG~rF~PtDeELi~~yL~ 22 (127)
+||-| |.||++||+.||..
T Consensus 100 ~pP~y-~~~~~~~i~~~~~~ 118 (285)
T TIGR00674 100 VTPYY-NKPTQEGLYQHFKA 118 (285)
T ss_pred cCCcC-CCCCHHHHHHHHHH
Confidence 45555 78999999998753
No 15
>PRK03170 dihydrodipicolinate synthase; Provisional
Probab=36.78 E-value=21 Score=27.54 Aligned_cols=17 Identities=12% Similarity=0.253 Sum_probs=13.9
Q ss_pred CCCCceEcCCHHHHHHHH
Q 038778 3 SLMGFRFQPSNEQIFCLL 20 (127)
Q Consensus 3 lppG~rF~PtDeELi~~y 20 (127)
+||-| |.|+++||+.||
T Consensus 103 ~pP~~-~~~~~~~i~~~~ 119 (292)
T PRK03170 103 VTPYY-NKPTQEGLYQHF 119 (292)
T ss_pred CCCcC-CCCCHHHHHHHH
Confidence 56655 899999999976
No 16
>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=34.20 E-value=30 Score=21.02 Aligned_cols=14 Identities=36% Similarity=0.888 Sum_probs=10.6
Q ss_pred CCceEcC----CHHHHHH
Q 038778 5 MGFRFQP----SNEQIFC 18 (127)
Q Consensus 5 pG~rF~P----tDeELi~ 18 (127)
.|+||.| ||+|+..
T Consensus 22 ~GIRFVpiPv~~dee~~~ 39 (61)
T PF07131_consen 22 IGIRFVPIPVVTDEEFHT 39 (61)
T ss_pred cCceeeccccccHHHHHH
Confidence 5999999 6777654
No 17
>PRK04147 N-acetylneuraminate lyase; Provisional
Probab=32.58 E-value=26 Score=27.25 Aligned_cols=17 Identities=18% Similarity=-0.092 Sum_probs=13.3
Q ss_pred CCCceEcCCHHHHHHHHH
Q 038778 4 LMGFRFQPSNEQIFCLLE 21 (127)
Q Consensus 4 ppG~rF~PtDeELi~~yL 21 (127)
||- -|.||+++|+.||-
T Consensus 107 ~P~-y~~~~~~~l~~~f~ 123 (293)
T PRK04147 107 TPF-YYPFSFEEICDYYR 123 (293)
T ss_pred CCc-CCCCCHHHHHHHHH
Confidence 444 48999999999773
No 18
>TIGR03249 KdgD 5-dehydro-4-deoxyglucarate dehydratase. 5-dehydro-4-deoxyglucarate dehydratase not only catalyzes the dehydration of the substrate (diol to ketone + water), but causes the decarboxylation of the intermediate product to yield 2-oxoglutarate semialdehyde (2,5-dioxopentanoate). The gene for the enzyme is usually observed in the vicinity of transporters and dehydratases handling D-galactarate and D-gluconate as well as aldehyde dehydrogenases which convert the product to alpha-ketoglutarate.
Probab=28.75 E-value=35 Score=26.58 Aligned_cols=18 Identities=11% Similarity=0.216 Sum_probs=13.9
Q ss_pred CCCCceEcCCHHHHHHHHH
Q 038778 3 SLMGFRFQPSNEQIFCLLE 21 (127)
Q Consensus 3 lppG~rF~PtDeELi~~yL 21 (127)
+|| |-|.|++++|+.||-
T Consensus 106 ~pP-~y~~~s~~~i~~~f~ 123 (296)
T TIGR03249 106 LPP-YLINGEQEGLYAHVE 123 (296)
T ss_pred CCC-CCCCCCHHHHHHHHH
Confidence 566 457899999999773
No 19
>PF02755 RPEL: RPEL repeat; InterPro: IPR004018 The RPEL repeat is named after four conserved amino acids it contains. The function of the RPEL repeat is unknown however it might be a DNA binding repeat based on the observation that Q9VZY2 from SWISSPROT contains a SAP domain that is also implicated in DNA binding.; PDB: 2YJE_M 2V52_M 2YJF_M 2V51_E.
Probab=28.58 E-value=35 Score=17.10 Aligned_cols=10 Identities=20% Similarity=0.451 Sum_probs=5.9
Q ss_pred EcCCHHHHHH
Q 038778 9 FQPSNEQIFC 18 (127)
Q Consensus 9 F~PtDeELi~ 18 (127)
.+|+-+|||.
T Consensus 9 ~RP~~~eLv~ 18 (26)
T PF02755_consen 9 QRPTREELVE 18 (26)
T ss_dssp T---HHHHHH
T ss_pred cCCCHHHHHH
Confidence 4799999987
No 20
>cd00408 DHDPS-like Dihydrodipicolinate synthase family. A member of the class I aldolases, which use an active-site lysine which stablilzes a reaction intermediate via Schiff base formation, and have TIM beta/alpha barrel fold. The dihydrodipicolinate synthase family comprises several pyruvate-dependent class I aldolases that use the same catalytic step to catalyze different reactions in different pathways and includes such proteins as N-acetylneuraminate lyase, MosA protein, 5-keto-4-deoxy-glucarate dehydratase, trans-o-hydroxybenzylidenepyruvate hydratase-aldolase, trans-2'-carboxybenzalpyruvate hydratase-aldolase, and 2-keto-3-deoxy- gluconate aldolase. The family is also referred to as the N-acetylneuraminate lyase (NAL) family.
Probab=28.13 E-value=36 Score=25.97 Aligned_cols=18 Identities=22% Similarity=0.239 Sum_probs=13.4
Q ss_pred CCCCceEcCCHHHHHHHHH
Q 038778 3 SLMGFRFQPSNEQIFCLLE 21 (127)
Q Consensus 3 lppG~rF~PtDeELi~~yL 21 (127)
+||-| |.|+++|++.||-
T Consensus 99 ~pP~y-~~~~~~~~~~~~~ 116 (281)
T cd00408 99 VPPYY-NKPSQEGIVAHFK 116 (281)
T ss_pred CCCcC-CCCCHHHHHHHHH
Confidence 45544 6799999999763
No 21
>PRK03620 5-dehydro-4-deoxyglucarate dehydratase; Provisional
Probab=26.90 E-value=36 Score=26.61 Aligned_cols=18 Identities=11% Similarity=0.078 Sum_probs=14.3
Q ss_pred CCCCceEcCCHHHHHHHHH
Q 038778 3 SLMGFRFQPSNEQIFCLLE 21 (127)
Q Consensus 3 lppG~rF~PtDeELi~~yL 21 (127)
+|| +.|.||+++|+.||-
T Consensus 108 ~pP-~y~~~~~~~i~~~f~ 125 (303)
T PRK03620 108 LPP-YLTEAPQEGLAAHVE 125 (303)
T ss_pred CCC-CCCCCCHHHHHHHHH
Confidence 455 667899999999874
No 22
>PF09174 Maf1: Maf1 regulator; InterPro: IPR015257 Maf1 is a negative regulator of RNA polymerase III [, ]. It targets the initiation factor TFIIIB []. ; PDB: 3NR5_A.
Probab=25.14 E-value=24 Score=25.80 Aligned_cols=14 Identities=43% Similarity=0.473 Sum_probs=7.3
Q ss_pred eeecCCcCCCCCccc
Q 038778 34 IKDIDDICSLEPWDL 48 (127)
Q Consensus 34 I~~~~dvy~~~P~~L 48 (127)
+.+| |||++.|..-
T Consensus 137 l~~C-~iYsy~pd~~ 150 (179)
T PF09174_consen 137 LKDC-DIYSYNPDSD 150 (179)
T ss_dssp GGG--EEEEE---GG
T ss_pred ccCc-eEEEEccCCC
Confidence 4567 9999999543
No 23
>PTZ00079 NADP-specific glutamate dehydrogenase; Provisional
Probab=24.99 E-value=61 Score=27.37 Aligned_cols=43 Identities=21% Similarity=0.145 Sum_probs=28.2
Q ss_pred CCceEcCCHHHHHHHHH------HHhcCCCCC--ccceeecCCcCCCCCccc
Q 038778 5 MGFRFQPSNEQIFCLLE------KKRLNPHFS--HHTIKDIDDICSLEPWDL 48 (127)
Q Consensus 5 pG~rF~PtDeELi~~yL------~~k~~g~~~--~~~I~~~~dvy~~~P~~L 48 (127)
=|.||+|+..+=+..+| +.-+.|.|+ .--..++ |.-...+.+|
T Consensus 98 GGlRfhp~v~~~~vk~La~~mt~KnAl~gLP~GGgKGGi~~-dPk~~s~~El 148 (454)
T PTZ00079 98 GGLRFHPSVNLSILKFLGFEQIFKNSLTTLPMGGGKGGSDF-DPKGKSDNEV 148 (454)
T ss_pred CCEEeeCCCCHHHHHHHHHHHHHHHHhcCCCCCCcceeeec-CCCCCCHHHH
Confidence 48999999887777777 455677787 3333355 5555555444
No 24
>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=24.50 E-value=68 Score=16.31 Aligned_cols=15 Identities=13% Similarity=0.118 Sum_probs=11.8
Q ss_pred CHHHHHHHHHHHhcC
Q 038778 12 SNEQIFCLLEKKRLN 26 (127)
Q Consensus 12 tDeELi~~yL~~k~~ 26 (127)
.-.|||.+|+.-|+.
T Consensus 4 ~nR~lV~~yi~yKLs 18 (27)
T PF02180_consen 4 DNRELVEDYISYKLS 18 (27)
T ss_dssp HHHHHHHHHHHHHHH
T ss_pred cHHHHHHHHHHHHhh
Confidence 357999999988773
No 25
>PF02375 JmjN: jmjN domain; InterPro: IPR003349 Jumonji protein is required for neural tube formation in mice [].There is evidence of domain swapping within the jumonji family of transcription factors []. This domain is often associated with JmjC (see IPR003347 from INTERPRO).; PDB: 2XML_A 2W2I_C 3DXT_A 3DXU_A 2OX0_B 2OQ6_B 2WWJ_A 2Q8D_A 3PDQ_A 2YBK_A ....
Probab=23.43 E-value=40 Score=17.95 Aligned_cols=11 Identities=27% Similarity=0.304 Sum_probs=5.2
Q ss_pred eEcCCHHHHHH
Q 038778 8 RFQPSNEQIFC 18 (127)
Q Consensus 8 rF~PtDeELi~ 18 (127)
-|.||.||--+
T Consensus 2 vf~Pt~eEF~d 12 (34)
T PF02375_consen 2 VFYPTMEEFKD 12 (34)
T ss_dssp EE---HHHHS-
T ss_pred cccCCHHHHhC
Confidence 38899998754
No 26
>PHA02696 hypothetical protein; Provisional
Probab=22.38 E-value=88 Score=19.60 Aligned_cols=25 Identities=16% Similarity=0.177 Sum_probs=19.8
Q ss_pred HHHHHHHHhcCCCCC-ccceeecCCcC
Q 038778 16 IFCLLEKKRLNPHFS-HHTIKDIDDIC 41 (127)
Q Consensus 16 Li~~yL~~k~~g~~~-~~~I~~~~dvy 41 (127)
|+. .|++++-+++- ..+|..+||=|
T Consensus 23 Lc~-~lRrrv~r~~gYVsViQtCdDDY 48 (79)
T PHA02696 23 LCI-WLRRRVGREPGYVSVIQTCDDDY 48 (79)
T ss_pred HHH-HHHHHhcCCCceEEeeeeccccc
Confidence 444 79999999998 89999996544
No 27
>PF00701 DHDPS: Dihydrodipicolinate synthetase family; InterPro: IPR002220 Dihydropicolinate synthase (DHDPS) is the key enzyme in lysine biosynthesis via the diaminopimelate pathway of prokaryotes, some phycomycetes and higher plants. The enzyme catalyses the condensation of L-aspartate-beta- semialdehyde and pyruvate to dihydropicolinic acid via a ping-pong mechanism in which pyruvate binds to the enzyme by forming a Schiff-base with a lysine residue []. Three other proteins are structurally related to DHDPS and probably also act via a similar catalytic mechanism. These are Escherichia coli N-acetylneuraminate lyase (4.1.3.3 from EC) (gene nanA), which catalyzes the condensation of N-acetyl-D-mannosamine and pyruvate to form N-acetylneuraminate; Rhizobium meliloti (Sinorhizobium meliloti) protein mosA [], which is involved in the biosynthesis of the rhizopine 3-o-methyl-scyllo-inosamine; and E. coli hypothetical protein yjhH. The sequences of DHDPS from different sources are well-conserved. The structure takes the form of a homotetramer, in which 2 monomers are related by an approximate 2-fold symmetry []. Each monomer comprises 2 domains: an 8-fold alpha-/beta-barrel, and a C-terminal alpha-helical domain. The fold resembles that of N-acetylneuraminate lyase. The active site lysine is located in the barrel domain, and has access via 2 channels on the C-terminal side of the barrel.; GO: 0016829 lyase activity, 0008152 metabolic process; PDB: 3B4U_B 3S8H_A 3QZE_B 1XXX_F 3L21_F 3IRD_A 3A5F_B 3G0S_B 3DAQ_C 3UQN_A ....
Probab=22.35 E-value=31 Score=26.58 Aligned_cols=18 Identities=22% Similarity=0.447 Sum_probs=14.1
Q ss_pred CCCCceEcCCHHHHHHHHH
Q 038778 3 SLMGFRFQPSNEQIFCLLE 21 (127)
Q Consensus 3 lppG~rF~PtDeELi~~yL 21 (127)
+|| +.|.||++||+.||.
T Consensus 103 ~~P-~~~~~s~~~l~~y~~ 120 (289)
T PF00701_consen 103 IPP-YYFKPSQEELIDYFR 120 (289)
T ss_dssp EES-TSSSCCHHHHHHHHH
T ss_pred ecc-ccccchhhHHHHHHH
Confidence 345 668899999999874
No 28
>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=21.60 E-value=1e+02 Score=20.34 Aligned_cols=39 Identities=13% Similarity=0.182 Sum_probs=27.5
Q ss_pred cCCHHHHHHHHHHHhcCCCCCccceeecCCcCCCCCccccccC
Q 038778 10 QPSNEQIFCLLEKKRLNPHFSHHTIKDIDDICSLEPWDLAGAS 52 (127)
Q Consensus 10 ~PtDeELi~~yL~~k~~g~~~~~~I~~~~dvy~~~P~~L~~~~ 52 (127)
+-|..||++.-...-..|+|++. +. |+-...|.++|...
T Consensus 50 HATNSELLCEAFLHAfTGQPLP~---D~-Dl~K~~~d~iP~~a 88 (103)
T cd00490 50 HATNSELLCEAFLHAFTGQPLPD---DA-DLRKERSDEIPEAA 88 (103)
T ss_pred hcccHHHHHHHHHHHhcCCCCCC---hh-hhhhcCcccccHHH
Confidence 34667888766666778999832 33 77778888888653
No 29
>TIGR03874 4cys_cytochr c-type cytochrome, methanol metabolism-related. This family represents a c-type cytochrome related to (but excluding) cytochrome c-555 of Methylococcus capsulatus. Members contain four invariant Cys residues, including two from a heme-binding motif shared with c-555, and two others.
Probab=20.89 E-value=81 Score=22.41 Aligned_cols=24 Identities=13% Similarity=0.199 Sum_probs=18.6
Q ss_pred CCceEcCCHH----HHHHHHHHHhcCCCC
Q 038778 5 MGFRFQPSNE----QIFCLLEKKRLNPHF 29 (127)
Q Consensus 5 pG~rF~PtDe----ELi~~yL~~k~~g~~ 29 (127)
|+|.-..+|+ +|+. ||+....|..
T Consensus 93 PaF~~~LsD~~eIa~L~~-YLR~~~~g~~ 120 (143)
T TIGR03874 93 PAFGDNPNVMCYLDDLYV-YLRARGTDAL 120 (143)
T ss_pred CCccccCCcHHHHHHHHH-HHHhccCCCc
Confidence 7898899987 4455 8999888753
No 30
>PF10107 Endonuc_Holl: Endonuclease related to archaeal Holliday junction resolvase; InterPro: IPR019287 This domain is found in various predicted bacterial endonucleases which are distantly related to archaeal Holliday junction resolvases.
Probab=20.74 E-value=37 Score=24.57 Aligned_cols=22 Identities=18% Similarity=0.255 Sum_probs=15.9
Q ss_pred CCCCCceEcCCHHHHHHHHHHHhcCCCCCcc
Q 038778 2 ESLMGFRFQPSNEQIFCLLEKKRLNPHFSHH 32 (127)
Q Consensus 2 ~lppG~rF~PtDeELi~~yL~~k~~g~~~~~ 32 (127)
.+-|+|.++|+|. +..|.|..-
T Consensus 84 P~lp~F~ynP~D~---------RFlG~PVD~ 105 (156)
T PF10107_consen 84 PFLPEFPYNPKDA---------RFLGSPVDF 105 (156)
T ss_pred hccCCCCCChhhh---------eecCCCceE
Confidence 3569999999995 456777633
Done!