Query 035445
Match_columns 38
No_of_seqs 106 out of 157
Neff 3.9
Searched_HMMs 46136
Date Fri Mar 29 03:01:58 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/035445.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/035445hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF10250 O-FucT: GDP-fucose pr 98.7 2.1E-09 4.5E-14 67.4 -0.2 37 1-37 309-345 (351)
2 COG4957 Predicted transcriptio 65.2 3.1 6.7E-05 26.2 0.8 8 4-11 74-81 (148)
3 COG5226 CEG1 mRNA capping enzy 41.6 14 0.0003 26.3 1.0 11 3-13 61-71 (404)
4 PF07821 Alpha-amyl_C2: Alpha- 39.3 27 0.00058 18.6 1.7 16 7-22 13-28 (59)
5 PF01331 mRNA_cap_enzyme: mRNA 37.5 18 0.00038 21.6 0.9 9 5-13 17-25 (192)
6 PF04988 AKAP95: A-kinase anch 34.7 10 0.00022 24.1 -0.5 16 8-23 93-108 (165)
7 PRK10964 ADP-heptose:LPS hepto 31.2 33 0.00071 21.5 1.4 16 10-25 252-267 (322)
8 PF00867 XPG_I: XPG I-region; 30.9 11 0.00024 20.4 -0.7 14 4-17 27-40 (94)
9 cd00559 Cyanase_C Cyanase C-te 30.9 26 0.00056 19.6 0.8 11 1-11 35-45 (69)
10 cd01076 NAD_bind_1_Glu_DH NAD( 30.4 40 0.00087 21.1 1.7 18 5-22 100-117 (227)
11 COG3241 Azurin [Energy product 30.3 12 0.00027 23.5 -0.6 16 18-33 56-71 (151)
12 PF10881 DUF2726: Protein of u 29.3 32 0.0007 19.1 1.0 12 2-13 56-67 (126)
13 PF13506 Glyco_transf_21: Glyc 28.0 42 0.00091 19.9 1.4 15 4-18 32-46 (175)
14 smart00770 Zn_dep_PLPC Zinc de 26.1 15 0.00032 24.1 -0.8 25 12-36 145-170 (241)
15 PF04596 Pox_F15: Poxvirus pro 25.6 14 0.0003 23.0 -1.0 23 9-32 103-125 (136)
16 PF02887 PK_C: Pyruvate kinase 25.5 64 0.0014 17.7 1.8 19 14-32 20-38 (117)
17 PF08206 OB_RNB: Ribonuclease 24.6 56 0.0012 16.4 1.3 24 6-31 12-37 (58)
18 cd05211 NAD_bind_Glu_Leu_Phe_V 23.4 61 0.0013 20.3 1.6 18 6-23 92-109 (217)
19 PF02560 Cyanate_lyase: Cyanat 22.7 43 0.00093 18.8 0.7 11 1-11 39-49 (73)
20 PHA02993 hypothetical protein; 22.3 15 0.00033 23.1 -1.2 23 9-32 114-136 (147)
21 PRK10422 lipopolysaccharide co 21.8 49 0.0011 21.1 0.9 17 10-26 261-277 (352)
22 cd02768 MopB_NADH-Q-OR-NuoG2 M 21.8 62 0.0013 20.7 1.4 17 3-19 318-343 (386)
23 PF03414 Glyco_transf_6: Glyco 20.2 75 0.0016 22.1 1.6 18 4-21 189-206 (337)
24 TIGR02201 heptsyl_trn_III lipo 20.0 55 0.0012 20.7 0.9 16 10-25 259-274 (344)
No 1
>PF10250 O-FucT: GDP-fucose protein O-fucosyltransferase; InterPro: IPR019378 This is a family of conserved proteins representing the enzyme responsible for adding O-fucose to EGF (epidermal growth factor-like) repeats. Six highly conserved cysteines are present as well as a DXD-like motif (ERD), conserved in mammals, Drosophila, and Caenorhabditis elegans. Both features are characteristic of several glycosyltransferase families. The enzyme is a membrane-bound protein released by proteolysis and, as for most glycosyltransferases, is strongly activated by manganese []. ; PDB: 3ZY6_A 3ZY3_A 3ZY5_A 3ZY2_A 3ZY4_A.
Probab=98.71 E-value=2.1e-09 Score=67.44 Aligned_cols=37 Identities=19% Similarity=0.187 Sum_probs=32.3
Q ss_pred CcceeeeeeeccceeeecCCCCHHHHHhhhhhhcccc
Q 035445 1 MAALDYMVSVESDVFIPSHLGNMARAVEGHLMLSVFQ 37 (38)
Q Consensus 1 lAAlDy~V~~~SDvFv~t~~Gnm~~~v~GhR~y~g~~ 37 (38)
+|+||++||++||+||.|...+|...|.++|.+.|+.
T Consensus 309 ~a~vD~~i~~~s~~Figt~~Stfs~~i~~~R~~~g~~ 345 (351)
T PF10250_consen 309 LAMVDQEICSRSDVFIGTCGSTFSSNIARERHYRGKP 345 (351)
T ss_dssp -HHHHHHHHHHSSEEEE-TT-HHHHHHHHHHHHSSSS
T ss_pred hhHHHHHHHhcCCEEEecCcchhHHHhhcccCcCCCC
Confidence 5789999999999999999777999999999999976
No 2
>COG4957 Predicted transcriptional regulator [Transcription]
Probab=65.16 E-value=3.1 Score=26.15 Aligned_cols=8 Identities=38% Similarity=0.887 Sum_probs=7.0
Q ss_pred eeeeeeec
Q 035445 4 LDYMVSVE 11 (38)
Q Consensus 4 lDy~V~~~ 11 (38)
-|||||+|
T Consensus 74 pD~IicLE 81 (148)
T COG4957 74 PDYIICLE 81 (148)
T ss_pred CCeEEEec
Confidence 39999998
No 3
>COG5226 CEG1 mRNA capping enzyme, guanylyltransferase (alpha) subunit [RNA processing and modification]
Probab=41.59 E-value=14 Score=26.34 Aligned_cols=11 Identities=45% Similarity=0.658 Sum_probs=9.7
Q ss_pred ceeeeeeeccc
Q 035445 3 ALDYMVSVESD 13 (38)
Q Consensus 3 AlDy~V~~~SD 13 (38)
+=||+||..||
T Consensus 61 ~~dy~VCEKsD 71 (404)
T COG5226 61 NNDYLVCEKSD 71 (404)
T ss_pred hCCeEEEEccC
Confidence 45999999999
No 4
>PF07821 Alpha-amyl_C2: Alpha-amylase C-terminal beta-sheet domain; InterPro: IPR012850 O-Glycosyl hydrolases 3.2.1. from EC are a widespread group of enzymes that hydrolyse the glycosidic bond between two or more carbohydrates, or between a carbohydrate and a non-carbohydrate moiety. A classification system for glycosyl hydrolases, based on sequence similarity, has led to the definition of 85 different families [, ]. This classification is available on the CAZy (CArbohydrate-Active EnZymes) web site. Alpha-amylase is classified as family 13 of the glycosyl hydrolases and is present in archaea, bacteria, plants and animals. Alpha-amylase is an essential enzyme in alpha-glucan metabolism, acting to catalyse the hydrolysis of alpha-1,4-glucosidic bonds of glycogen, starch and related polysaccharides. Although all alpha-amylases possess the same catalytic function, they can vary with respect to sequence. In general, they are composed of three domains: a TIM barrel containing the active site residues and chloride ion-binding site (domain A), a long loop region inserted between the third beta strand and the alpha-helix of domain A that contains calcium-binding site(s) (domain B), and a C-terminal beta-sheet domain that appears to show some variability in sequence and length between amylases (domain C) []. Amylases have at least one conserved calcium-binding site, as calcium is essential for the stability of the enzyme. The chloride-binding functions to activate the enzyme, which acts by a two-step mechanism involving a catalytic nucleophile base (usually an Asp) and a catalytic proton donor (usually a Glu) that are responsible for the formation of the beta-linked glycosyl-enzyme intermediate. This entry represents the beta-sheet domain that is found in several alpha-amylases, usually at the C terminus. This domain is organised as a five-stranded anti-parallel beta-sheet [, ]. More information about this protein can be found at Protein of the Month: alpha-Amylase [].; GO: 0004556 alpha-amylase activity, 0005509 calcium ion binding, 0005975 carbohydrate metabolic process; PDB: 1AVA_B 1BG9_A 1AMY_A 1RP8_A 2QPU_A 3BSG_A 2QPS_A 3BSH_A 1RP9_A 1HT6_A ....
Probab=39.33 E-value=27 Score=18.61 Aligned_cols=16 Identities=13% Similarity=0.297 Sum_probs=13.7
Q ss_pred eeeeccceeeecCCCC
Q 035445 7 MVSVESDVFIPSHLGN 22 (38)
Q Consensus 7 ~V~~~SDvFv~t~~Gn 22 (38)
|+..++|+|++..+++
T Consensus 13 I~~Ae~d~YaA~Id~k 28 (59)
T PF07821_consen 13 ILAAEADLYAAIIDDK 28 (59)
T ss_dssp EEEEETTEEEEEETTT
T ss_pred EEEecCCcEEEEECCe
Confidence 6788999999998875
No 5
>PF01331 mRNA_cap_enzyme: mRNA capping enzyme, catalytic domain; InterPro: IPR001339 The mRNA capping enzyme in yeasts is composed of two separate chains, alpha a mRNA guanyltransferase and beta an RNA 5'-triphosphate. X-ray crystallography reveals a large conformational change during guanyl transfer by mRNA capping enzymes []. Binding of the enzyme to nucleotides is specific to the GMP moiety of GTP. The viral mRNA capping enzyme is a monomer that transfers a GMP cap onto the end of mRNA that terminates with a 5'-diphosphate tail.; GO: 0004484 mRNA guanylyltransferase activity, 0006370 mRNA capping, 0006397 mRNA processing; PDB: 3RTX_A 3KYH_D 3S24_G 1CKN_B 1CKO_A 1CKM_B 1P16_B.
Probab=37.48 E-value=18 Score=21.55 Aligned_cols=9 Identities=44% Similarity=0.840 Sum_probs=6.9
Q ss_pred eeeeeeccc
Q 035445 5 DYMVSVESD 13 (38)
Q Consensus 5 Dy~V~~~SD 13 (38)
||.||..||
T Consensus 17 ~Y~V~eKaD 25 (192)
T PF01331_consen 17 DYFVCEKAD 25 (192)
T ss_dssp -EEEEEEES
T ss_pred CcEEEECCC
Confidence 788888887
No 6
>PF04988 AKAP95: A-kinase anchoring protein 95 (AKAP95); InterPro: IPR007071 A-kinase (or PKA)-anchoring protein AKAP95 is implicated in mitotic chromosome condensation by acting as a targeting molecule for the condensin complex. The protein contains two zinc fingers which are thought to mediate the binding of AKAP95 to DNA [].; GO: 0003677 DNA binding, 0005634 nucleus
Probab=34.69 E-value=10 Score=24.11 Aligned_cols=16 Identities=31% Similarity=0.515 Sum_probs=13.2
Q ss_pred eeeccceeeecCCCCH
Q 035445 8 VSVESDVFIPSHLGNM 23 (38)
Q Consensus 8 V~~~SDvFv~t~~Gnm 23 (38)
=|...|+|||+..+..
T Consensus 93 hCsACd~~IP~~~~~v 108 (165)
T PF04988_consen 93 HCSACDVFIPMQHSSV 108 (165)
T ss_pred hhhHhhhhccCcHHHH
Confidence 4899999999987643
No 7
>PRK10964 ADP-heptose:LPS heptosyl transferase I; Provisional
Probab=31.24 E-value=33 Score=21.52 Aligned_cols=16 Identities=6% Similarity=0.042 Sum_probs=13.8
Q ss_pred eccceeeecCCCCHHH
Q 035445 10 VESDVFIPSHLGNMAR 25 (38)
Q Consensus 10 ~~SDvFv~t~~Gnm~~ 25 (38)
.++|+||.+.+|.|+=
T Consensus 252 ~~a~l~I~nDSGp~Hl 267 (322)
T PRK10964 252 AGAKAVVSVDTGLSHL 267 (322)
T ss_pred HhCCEEEecCCcHHHH
Confidence 4799999999998864
No 8
>PF00867 XPG_I: XPG I-region; InterPro: IPR006086 This entry represents endonucleases that cleave the 5'-overhanging flap structure that is generated by displacement synthesis when DNA polymerase encounters the 5'-end of a downstream Okazaki fragment. Has 5'-endo-/exonuclease and 5'-pseudo-Y-endonuclease activities. Cleaves the junction between single and double-stranded regions of flap DNA. The endonuclease binds 2 magnesium ions per subunit. which probably participate in the reaction catalyzed by the enzyme. May bind an additional third magnesium ion after substrate binding.; GO: 0004518 nuclease activity, 0006281 DNA repair; PDB: 1UL1_Z 3Q8K_A 3Q8M_A 3Q8L_A 2IZO_A 1A77_A 1A76_A 3QEA_Z 3QE9_Y 3QEB_Z ....
Probab=30.94 E-value=11 Score=20.42 Aligned_cols=14 Identities=21% Similarity=0.501 Sum_probs=11.3
Q ss_pred eeeeeeeccceeee
Q 035445 4 LDYMVSVESDVFIP 17 (38)
Q Consensus 4 lDy~V~~~SDvFv~ 17 (38)
+|++++..||+|+.
T Consensus 27 vd~V~t~DsD~l~f 40 (94)
T PF00867_consen 27 VDAVITEDSDLLLF 40 (94)
T ss_dssp SSEEE-SSSHHHHT
T ss_pred eeEEEecCCCEEee
Confidence 68999999999876
No 9
>cd00559 Cyanase_C Cyanase C-terminal domain. Cyanase (Cyanate lyase) is responsible for the hydrolysis of cyanate. It catalyzes the reaction of cyanate with bicarbonate to produce ammonia and carbon dioxide. This allows organisms that possess the enzyme to overcome the toxicity of environmental cyanate and to use cyanate as a source of nitrogen for growth. This enzyme is a homodecamer, formed by five dimers. Each monomer is composed of two domains, an N-terminal helix-turn-helix and this structurally unique C-terminal domain.
Probab=30.90 E-value=26 Score=19.58 Aligned_cols=11 Identities=36% Similarity=0.830 Sum_probs=9.3
Q ss_pred Ccceeeeeeec
Q 035445 1 MAALDYMVSVE 11 (38)
Q Consensus 1 lAAlDy~V~~~ 11 (38)
|+||||.+.++
T Consensus 35 MSAIdF~~~v~ 45 (69)
T cd00559 35 MSAIDFKLDVD 45 (69)
T ss_pred eeeEEeeeeEE
Confidence 78999998876
No 10
>cd01076 NAD_bind_1_Glu_DH NAD(P) binding domain of glutamate dehydrogenase, subgroup 1. Amino acid dehydrogenase (DH) is a widely distributed family of enzymes that catalyzes the oxidative deamination of an amino acid to its keto acid and ammonia with concomitant reduction of NADP+. Glutamate DH is a multidomain enzyme that catalyzes the reaction from glutamate to 2-oxyoglutarate and ammonia in the presence of NAD or NADP. It is present in all organisms. Enzymes involved in ammonia assimilation are typically NADP+-dependent, while those involved in glutamate catabolism are generally NAD+-dependent. Amino acid DH-like NAD(P)-binding domains are members of the Rossmann fold superfamily and include glutamate, leucine, and phenylalanine DHs, methylene tetrahydrofolate DH, methylene-tetrahydromethanopterin DH, methylene-tetrahydropholate DH/cyclohydrolase, Shikimate DH-like proteins, malate oxidoreductases, and glutamyl tRNA reductase. Amino acid DHs catalyze the deamination of amino acids
Probab=30.40 E-value=40 Score=21.15 Aligned_cols=18 Identities=28% Similarity=0.706 Sum_probs=13.9
Q ss_pred eeeeeeccceeeecCCCC
Q 035445 5 DYMVSVESDVFIPSHLGN 22 (38)
Q Consensus 5 Dy~V~~~SDvFv~t~~Gn 22 (38)
|=+...+.|||+|...+|
T Consensus 100 ~~i~~~~~Dvlip~a~~~ 117 (227)
T cd01076 100 EELLELDCDILIPAALEN 117 (227)
T ss_pred ccceeecccEEEecCccC
Confidence 335677899999998765
No 11
>COG3241 Azurin [Energy production and conversion]
Probab=30.29 E-value=12 Score=23.48 Aligned_cols=16 Identities=31% Similarity=0.524 Sum_probs=14.0
Q ss_pred cCCCCHHHHHhhhhhh
Q 035445 18 SHLGNMARAVEGHLML 33 (38)
Q Consensus 18 t~~Gnm~~~v~GhR~y 33 (38)
++.|+.++.|+||-|-
T Consensus 56 ~HtG~~pk~vMGHNwV 71 (151)
T COG3241 56 KHTGTQPKRVMGHNWV 71 (151)
T ss_pred ecCCCCCccccccceE
Confidence 5789999999999875
No 12
>PF10881 DUF2726: Protein of unknown function (DUF2726); InterPro: IPR024402 This domain found in bacterial proteins has no known function.
Probab=29.31 E-value=32 Score=19.11 Aligned_cols=12 Identities=25% Similarity=0.509 Sum_probs=8.7
Q ss_pred cceeeeeeeccc
Q 035445 2 AALDYMVSVESD 13 (38)
Q Consensus 2 AAlDy~V~~~SD 13 (38)
.-+||+||...+
T Consensus 56 ~~vDFvv~d~~~ 67 (126)
T PF10881_consen 56 KHVDFVVCDKRD 67 (126)
T ss_pred CCccEEEEECCC
Confidence 358999999443
No 13
>PF13506 Glyco_transf_21: Glycosyl transferase family 21
Probab=28.01 E-value=42 Score=19.90 Aligned_cols=15 Identities=40% Similarity=0.811 Sum_probs=12.8
Q ss_pred eeeeeeeccceeeec
Q 035445 4 LDYMVSVESDVFIPS 18 (38)
Q Consensus 4 lDy~V~~~SDvFv~t 18 (38)
=|+++.+.||+.++.
T Consensus 32 ~d~~~~~DsDi~v~p 46 (175)
T PF13506_consen 32 YDYLVISDSDIRVPP 46 (175)
T ss_pred CCEEEEECCCeeECH
Confidence 489999999998864
No 14
>smart00770 Zn_dep_PLPC Zinc dependent phospholipase C (alpha toxin). This domain conveys a zinc dependent phospholipase C activity (EC 3.1.4.3). It is found in a monomeric phospholipase C of Bacillus cereus as well as in the alpha toxin of Clostridium perfringens and Clostridium bifermentans, which is involved in haemolysis and cell rupture. It is also found in a lecithinase of Listeria monocytogenes, which is involved in breaking the 2-membrane vacuoles that surround the bacterium. Structure information: PDB 1ca1.
Probab=26.10 E-value=15 Score=24.09 Aligned_cols=25 Identities=28% Similarity=0.454 Sum_probs=18.6
Q ss_pred cceeeecCCCCHHH-HHhhhhhhccc
Q 035445 12 SDVFIPSHLGNMAR-AVEGHLMLSVF 36 (38)
Q Consensus 12 SDvFv~t~~Gnm~~-~v~GhR~y~g~ 36 (38)
.|+-+|-|.+|.-- .-.|||.|+.+
T Consensus 145 ~D~~~P~Ha~n~~~~~~~~H~~yE~~ 170 (241)
T smart00770 145 GDLSTPYHANNVTAVDSPGHRKFENF 170 (241)
T ss_pred HhcCCccccccccccCCcchhhHHHH
Confidence 58899999988643 22379999865
No 15
>PF04596 Pox_F15: Poxvirus protein F15; InterPro: IPR007675 Protein F15 is found in a number of Poxviruses.
Probab=25.56 E-value=14 Score=22.97 Aligned_cols=23 Identities=22% Similarity=0.411 Sum_probs=17.0
Q ss_pred eeccceeeecCCCCHHHHHhhhhh
Q 035445 9 SVESDVFIPSHLGNMARAVEGHLM 32 (38)
Q Consensus 9 ~~~SDvFv~t~~Gnm~~~v~GhR~ 32 (38)
+++-|+||||..-+++ ++.|-|+
T Consensus 103 ~LninIFiPT~~~~~Y-iIIGLRI 125 (136)
T PF04596_consen 103 SLNINIFIPTLNKSIY-IIIGLRI 125 (136)
T ss_pred ceEEEEEeeccCccEE-EEEEEch
Confidence 4567899999887766 4666665
No 16
>PF02887 PK_C: Pyruvate kinase, alpha/beta domain; InterPro: IPR015795 Pyruvate kinase (2.7.1.40 from EC) (PK) catalyses the final step in glycolysis [], the conversion of phosphoenolpyruvate to pyruvate with concomitant phosphorylation of ADP to ATP: ADP + phosphoenolpyruvate = ATP + pyruvate The enzyme, which is found in all living organisms, requires both magnesium and potassium ions for its activity. In vertebrates, there are four tissue-specific isozymes: L (liver), R (red cells), M1 (muscle, heart and brain), and M2 (early foetal tissue). In plants, PK exists as cytoplasmic and plastid isozymes, while most bacteria and lower eukaryotes have one form, except in certain bacteria, such as Escherichia coli, that have two isozymes. All isozymes appear to be tetramers of identical subunits of ~500 residues. PK helps control the rate of glycolysis, along with phosphofructokinase (IPR000023 from INTERPRO) and hexokinase (IPR001312 from INTERPRO). PK possesses allosteric sites for numerous effectors, yet the isozymes respond differently, in keeping with their different tissue distributions []. The activity of L-type (liver) PK is increased by fructose-1,6-bisphosphate (F1,6BP) and lowered by ATP and alanine (gluconeogenic precursor), therefore when glucose levels are high, glycolysis is promoted, and when levels are low, gluconeogenesis is promoted. L-type PK is also hormonally regulated, being activated by insulin and inhibited by glucagon, which covalently modifies the PK enzyme. M1-type (muscle, brain) PK is inhibited by ATP, but F1,6BP and alanine have no effect, which correlates with the function of muscle and brain, as opposed to the liver. The structure of several pyruvate kinases from various organisms have been determined [, ]. The protein comprises three-four domains: a small N-terminal helical domain (absent in bacterial PK), a beta/alpha-barrel domain, a beta-barrel domain (inserted within the beta/alpha-barrel domain), and a 3-layer alpha/beta/alpha sandwich domain. This entry represents the 3-layer alpha/beta/alpha sandwich domain. This domain has a similar topology to the archaeal hypothetical protein, MTH1675 from Methanobacterium thermoautotrophicum.; PDB: 3QTG_B 1VP8_A 1T57_C 3N25_A 1AQF_C 2G50_B 1F3X_G 1A5U_F 1A49_E 1F3W_C ....
Probab=25.50 E-value=64 Score=17.71 Aligned_cols=19 Identities=16% Similarity=0.175 Sum_probs=14.3
Q ss_pred eeeecCCCCHHHHHhhhhh
Q 035445 14 VFIPSHLGNMARAVEGHLM 32 (38)
Q Consensus 14 vFv~t~~Gnm~~~v~GhR~ 32 (38)
|.++|.+|..++.++=+|-
T Consensus 20 Ivv~T~sG~ta~~isk~RP 38 (117)
T PF02887_consen 20 IVVFTESGRTARLISKYRP 38 (117)
T ss_dssp EEEE-SSSHHHHHHHHT-T
T ss_pred EEEECCCchHHHHHHhhCC
Confidence 6789999999999887774
No 17
>PF08206 OB_RNB: Ribonuclease B OB domain; InterPro: IPR013223 This domain includes the N-terminal OB domain found in ribonuclease B proteins in one or two copies.; PDB: 2ID0_D 2IX1_A 2IX0_A.
Probab=24.59 E-value=56 Score=16.36 Aligned_cols=24 Identities=29% Similarity=0.708 Sum_probs=12.2
Q ss_pred eeeee--ccceeeecCCCCHHHHHhhhh
Q 035445 6 YMVSV--ESDVFIPSHLGNMARAVEGHL 31 (38)
Q Consensus 6 y~V~~--~SDvFv~t~~Gnm~~~v~GhR 31 (38)
|+++. +-|+|||.. +|.+++-|.+
T Consensus 12 Fv~~~~~~~DifIp~~--~l~~A~~gD~ 37 (58)
T PF08206_consen 12 FVIPDDGGEDIFIPPR--NLNGAMDGDK 37 (58)
T ss_dssp EEEECT-TEEEEE-HH--HHTTS-TT-E
T ss_pred EEEECCCCCCEEECHH--HHCCCCCCCE
Confidence 44444 679999974 4444444443
No 18
>cd05211 NAD_bind_Glu_Leu_Phe_Val NAD(P) binding domain of glutamate dehydrogenase, leucine dehydrogenase, phenylalanine dehydrogenase, and valine dehydrogenase. Amino acid dehydrogenase (DH) is a widely distributed family of enzymes that catalyzes the oxidative deamination of an amino acid to its keto acid and ammonia with concomitant reduction of NAD(P)+. This subfamily includes glutamate, leucine, phenylalanine, and valine DHs. Glutamate DH is a multi-domain enzyme that catalyzes the reaction from glutamate to 2-oxyoglutarate and ammonia in the presence of NAD or NADP. It is present in all organisms. Enzymes involved in ammonia assimilation are typically NADP+-dependent, while those involved in glutamate catabolism are generally NAD+-dependent. As in other NAD+-dependent DHs, monomers in this family have 2 domains separated by a deep cleft. Here the c-terminal domain contains a modified NAD-binding Rossmann fold with 7 rather than the usual 6 beta strands and one strand anti-parral
Probab=23.43 E-value=61 Score=20.26 Aligned_cols=18 Identities=33% Similarity=0.794 Sum_probs=14.5
Q ss_pred eeeeeccceeeecCCCCH
Q 035445 6 YMVSVESDVFIPSHLGNM 23 (38)
Q Consensus 6 y~V~~~SDvFv~t~~Gnm 23 (38)
-+...+.||++|.-.+|.
T Consensus 92 ~l~~~~~DVlipaA~~~~ 109 (217)
T cd05211 92 AILGLDVDIFAPCALGNV 109 (217)
T ss_pred cceeccccEEeeccccCc
Confidence 355678999999998874
No 19
>PF02560 Cyanate_lyase: Cyanate lyase C-terminal domain; InterPro: IPR003712 Some bacteria can overcome the toxicity of environmental cyanate by hydrolysis of cyanate. This reaction is catalyzed by cyanate lyase (also known as cyanase) []. Cyanate lyase is found in bacteria and plants and catalyzes the reaction of cyanate with bicarbonate to produce ammonia and carbon dioxide. The cyanate lyase monomer is composed of two domains. The N-terminal domain shows structural similarity to the DNA-binding alpha-helix bundle motif. The C-terminal domain has an 'open fold' with no structural homology to other proteins. The dimer structure reveals the C-terminal domains to be intertwined, and the decamer is formed by a pentamer of these dimers. The active site of the enzyme is located between dimers and is comprised of residues from four adjacent subunits of the homodecamer []. ; GO: 0008824 cyanate hydratase activity, 0009439 cyanate metabolic process; PDB: 2IV1_B 2IUO_A 2IVQ_B 1DW9_A 1DWK_E 2IVG_G 2IU7_J 2IVB_A.
Probab=22.71 E-value=43 Score=18.85 Aligned_cols=11 Identities=45% Similarity=0.851 Sum_probs=8.6
Q ss_pred Ccceeeeeeec
Q 035445 1 MAALDYMVSVE 11 (38)
Q Consensus 1 lAAlDy~V~~~ 11 (38)
|+||||-+.++
T Consensus 39 MSAIdF~~~v~ 49 (73)
T PF02560_consen 39 MSAIDFKMDVE 49 (73)
T ss_dssp EEEEEEEEEEE
T ss_pred EEEeeEEEEEE
Confidence 68999987665
No 20
>PHA02993 hypothetical protein; Provisional
Probab=22.27 E-value=15 Score=23.06 Aligned_cols=23 Identities=22% Similarity=0.407 Sum_probs=16.4
Q ss_pred eeccceeeecCCCCHHHHHhhhhh
Q 035445 9 SVESDVFIPSHLGNMARAVEGHLM 32 (38)
Q Consensus 9 ~~~SDvFv~t~~Gnm~~~v~GhR~ 32 (38)
+++-|+||||..-.++ ++-|-|+
T Consensus 114 ~LniniFiPT~~~~~Y-iIIGLRI 136 (147)
T PHA02993 114 SLNINIFIPTINKSIY-IIIGLRI 136 (147)
T ss_pred ceEEEEEEeccCccEE-EEEEEEe
Confidence 5677999999876655 4556554
No 21
>PRK10422 lipopolysaccharide core biosynthesis protein; Provisional
Probab=21.78 E-value=49 Score=21.14 Aligned_cols=17 Identities=18% Similarity=0.122 Sum_probs=13.9
Q ss_pred eccceeeecCCCCHHHH
Q 035445 10 VESDVFIPSHLGNMARA 26 (38)
Q Consensus 10 ~~SDvFv~t~~Gnm~~~ 26 (38)
..+|+||.+++|.|+=+
T Consensus 261 ~~a~l~v~nDSGp~HlA 277 (352)
T PRK10422 261 DHAQLFIGVDSAPAHIA 277 (352)
T ss_pred HhCCEEEecCCHHHHHH
Confidence 46899999999988643
No 22
>cd02768 MopB_NADH-Q-OR-NuoG2 MopB_NADH-Q-OR-NuoG2: The NuoG/Nad11/75-kDa subunit (second domain) of the NADH-quinone oxidoreductase (NADH-Q-OR)/respiratory complex I/NADH dehydrogenase-1 (NDH-1). The NADH-Q-OR is the first energy-transducting complex in the respiratory chains of many prokaryotes and eukaryotes. Mitochondrial complex I and its bacterial counterpart, NDH-1, function as a redox pump that uses the redox energy to translocate H+ ions across the membrane, resulting in a significant contribution to energy production. The atomic structure of complex I is not known and the mechanisms of electron transfer and proton pumping are not established. The nad11 gene codes for the largest (75-kDa) subunit of the mitochondrial NADH:ubiquinone oxidoreductase, it constitutes the electron input part of the enzyme, or the so-called NADH dehydrogenase fragment. In Escherichia coli, this subunit is encoded by the nuoG gene, and is part of the 14 distinct subunits constituting the 'minimal' fun
Probab=21.77 E-value=62 Score=20.67 Aligned_cols=17 Identities=35% Similarity=0.573 Sum_probs=12.8
Q ss_pred ceeeeeeec---------cceeeecC
Q 035445 3 ALDYMVSVE---------SDVFIPSH 19 (38)
Q Consensus 3 AlDy~V~~~---------SDvFv~t~ 19 (38)
.+|++|+.. +|+++|+.
T Consensus 318 ~~~~~Vv~d~~~teta~~ADvvLP~~ 343 (386)
T cd02768 318 AADAFVVYQGHHGDTGAQADVILPAA 343 (386)
T ss_pred cCCeEEEEeccCchhhhhCCEEeccC
Confidence 467777654 89999986
No 23
>PF03414 Glyco_transf_6: Glycosyltransferase family 6; InterPro: IPR005076 The biosynthesis of disaccharides, oligosaccharides and polysaccharides involves the action of hundreds of different glycosyltransferases. These enzymes catalyse the transfer of sugar moieties from activated donor molecules to specific acceptor molecules, forming glycosidic bonds. A classification of glycosyltransferases using nucleotide diphospho-sugar, nucleotide monophospho-sugar and sugar phosphates (2.4.1.- from EC) and related proteins into distinct sequence based families has been described []. This classification is available on the CAZy (CArbohydrate-Active EnZymes) web site. The same three-dimensional fold is expected to occur within each of the families. Because 3-D structures are better conserved than sequences, several of the families defined on the basis of sequence similarities may have similar 3-D structures and therefore form 'clans'. Glycosyltransferase family 6 GT6 from CAZY comprises enzymes with three known activities; alpha-1,3-galactosyltransferase (2.4.1.151 from EC); alpha-1,3 N-acetylgalactosaminyltransferase (2.4.1.40 from EC); alpha-galactosyltransferase (2.4.1.37 from EC).; GO: 0016758 transferase activity, transferring hexosyl groups, 0005975 carbohydrate metabolic process, 0016020 membrane; PDB: 2Y7A_B 2O1G_A 1R82_A 2RJ1_A 3IOJ_B 2RJ4_A 3I0C_A 3SX8_A 1ZJ1_A 3I0E_A ....
Probab=20.18 E-value=75 Score=22.11 Aligned_cols=18 Identities=28% Similarity=0.791 Sum_probs=12.8
Q ss_pred eeeeeeeccceeeecCCC
Q 035445 4 LDYMVSVESDVFIPSHLG 21 (38)
Q Consensus 4 lDy~V~~~SDvFv~t~~G 21 (38)
.||++|..+|.-+-.+-|
T Consensus 189 vDYLFc~dvd~~F~~~vG 206 (337)
T PF03414_consen 189 VDYLFCMDVDMVFQDHVG 206 (337)
T ss_dssp -SEEEEEESSEEE-S-B-
T ss_pred CCEEEEEecceEEecccC
Confidence 699999999998877766
No 24
>TIGR02201 heptsyl_trn_III lipopolysaccharide heptosyltransferase III, putative. This family consists of examples of the putative ADP-heptose:LPS heptosyltransferase III, an enzyme of LPS inner core region biosynthesis. LPS, composed of lipid A, a core region, and O antigen, is found in the outer membrane of Gram-negative bacteria. This enzyme may be less widely distributed than heptosyltransferases I and II.
Probab=20.02 E-value=55 Score=20.65 Aligned_cols=16 Identities=19% Similarity=0.094 Sum_probs=13.6
Q ss_pred eccceeeecCCCCHHH
Q 035445 10 VESDVFIPSHLGNMAR 25 (38)
Q Consensus 10 ~~SDvFv~t~~Gnm~~ 25 (38)
..||+||.+.+|.|+=
T Consensus 259 ~~a~l~Vs~DSGp~Hl 274 (344)
T TIGR02201 259 DHARLFIGVDSVPMHM 274 (344)
T ss_pred HhCCEEEecCCHHHHH
Confidence 4799999999998864
Done!