Query 035401
Match_columns 50
No_of_seqs 112 out of 155
Neff 3.7
Searched_HMMs 46136
Date Fri Mar 29 02:44:54 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/035401.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/035401hhsearch_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 98.6 5.2E-09 1.1E-13 70.1 -0.2 41 1-41 309-349 (351)
2 COG4957 Predicted transcriptio 58.0 4.9 0.00011 26.9 0.8 8 4-11 74-81 (148)
3 COG5226 CEG1 mRNA capping enzy 29.2 28 0.00062 26.4 1.0 18 3-20 61-83 (404)
4 PF07821 Alpha-amyl_C2: Alpha- 28.6 44 0.00095 18.9 1.5 17 7-23 13-29 (59)
5 PF01331 mRNA_cap_enzyme: mRNA 27.9 31 0.00067 21.8 0.9 9 5-13 17-25 (192)
6 COG3241 Azurin [Energy product 26.5 17 0.00037 24.3 -0.5 17 18-34 56-72 (151)
7 PF00867 XPG_I: XPG I-region; 25.7 16 0.00036 21.0 -0.6 14 4-17 27-40 (94)
8 PRK10964 ADP-heptose:LPS hepto 25.7 45 0.00097 22.3 1.4 23 10-32 252-275 (322)
9 cd01076 NAD_bind_1_Glu_DH NAD( 24.1 58 0.0012 21.8 1.7 19 5-23 100-118 (227)
10 PF13506 Glyco_transf_21: Glyc 21.9 62 0.0013 20.4 1.4 15 4-18 32-46 (175)
11 cd00559 Cyanase_C Cyanase C-te 21.7 46 0.00099 19.8 0.8 11 1-11 35-45 (69)
12 PF04988 AKAP95: A-kinase anch 21.7 24 0.00053 23.9 -0.5 16 8-23 93-108 (165)
13 PF01520 Amidase_3: N-acetylmu 20.7 39 0.00086 20.5 0.3 37 4-47 68-109 (175)
14 KOG2520 5'-3' exonuclease [Rep 20.4 85 0.0019 25.8 2.2 44 4-49 502-560 (815)
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=98.63 E-value=5.2e-09 Score=70.06 Aligned_cols=41 Identities=20% Similarity=0.254 Sum_probs=33.1
Q ss_pred CcceeeeeeeccceeeecCCCCHHHHHhhhhhhccCcchhh
Q 035401 1 MAALDYMVSVESDVFIPSHLGNMARAVEGHLMLRIEQDYRN 41 (50)
Q Consensus 1 lAAlDy~V~~~SDvFv~t~~GNm~~~v~GhR~y~g~~~~k~ 41 (50)
+|+||++||++||+||.|....|...|+++|.+.|+|.+|.
T Consensus 309 ~a~vD~~i~~~s~~Figt~~Stfs~~i~~~R~~~g~~~~~~ 349 (351)
T PF10250_consen 309 LAMVDQEICSRSDVFIGTCGSTFSSNIARERHYRGKPKRKS 349 (351)
T ss_dssp -HHHHHHHHHHSSEEEE-TT-HHHHHHHHHHHHSSSS---E
T ss_pred hhHHHHHHHhcCCEEEecCcchhHHHhhcccCcCCCCCCCC
Confidence 57899999999999999996679999999999999998763
No 2
>COG4957 Predicted transcriptional regulator [Transcription]
Probab=58.01 E-value=4.9 Score=26.90 Aligned_cols=8 Identities=38% Similarity=0.887 Sum_probs=7.0
Q ss_pred eeeeeeec
Q 035401 4 LDYMVSVE 11 (50)
Q Consensus 4 lDy~V~~~ 11 (50)
-|||||+|
T Consensus 74 pD~IicLE 81 (148)
T COG4957 74 PDYIICLE 81 (148)
T ss_pred CCeEEEec
Confidence 49999998
No 3
>COG5226 CEG1 mRNA capping enzyme, guanylyltransferase (alpha) subunit [RNA processing and modification]
Probab=29.16 E-value=28 Score=26.40 Aligned_cols=18 Identities=28% Similarity=0.501 Sum_probs=13.4
Q ss_pred ceeeeeeeccc-----eeeecCC
Q 035401 3 ALDYMVSVESD-----VFIPSHL 20 (50)
Q Consensus 3 AlDy~V~~~SD-----vFv~t~~ 20 (50)
+=||+||..|| .||.-++
T Consensus 61 ~~dy~VCEKsDGvR~Ll~vte~p 83 (404)
T COG5226 61 NNDYLVCEKSDGVRALLLVTEEP 83 (404)
T ss_pred hCCeEEEEccCCeEEEEEEEecc
Confidence 45999999999 4565554
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=28.58 E-value=44 Score=18.90 Aligned_cols=17 Identities=12% Similarity=0.311 Sum_probs=14.3
Q ss_pred eeeeccceeeecCCCCH
Q 035401 7 MVSVESDVFIPSHLGNM 23 (50)
Q Consensus 7 ~V~~~SDvFv~t~~GNm 23 (50)
|+..++|+|++..+++.
T Consensus 13 I~~Ae~d~YaA~Id~kv 29 (59)
T PF07821_consen 13 ILAAEADLYAAIIDDKV 29 (59)
T ss_dssp EEEEETTEEEEEETTTE
T ss_pred EEEecCCcEEEEECCeE
Confidence 67889999999998854
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=27.88 E-value=31 Score=21.84 Aligned_cols=9 Identities=44% Similarity=0.840 Sum_probs=6.5
Q ss_pred eeeeeeccc
Q 035401 5 DYMVSVESD 13 (50)
Q Consensus 5 Dy~V~~~SD 13 (50)
||.||..||
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
>COG3241 Azurin [Energy production and conversion]
Probab=26.49 E-value=17 Score=24.28 Aligned_cols=17 Identities=29% Similarity=0.450 Sum_probs=15.1
Q ss_pred cCCCCHHHHHhhhhhhc
Q 035401 18 SHLGNMARAVEGHLMLR 34 (50)
Q Consensus 18 t~~GNm~~~v~GhR~y~ 34 (50)
++.|+.++.||||-|-.
T Consensus 56 ~HtG~~pk~vMGHNwVl 72 (151)
T COG3241 56 KHTGTQPKRVMGHNWVL 72 (151)
T ss_pred ecCCCCCccccccceEE
Confidence 57899999999999876
No 7
>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=25.75 E-value=16 Score=20.99 Aligned_cols=14 Identities=21% Similarity=0.501 Sum_probs=11.6
Q ss_pred eeeeeeeccceeee
Q 035401 4 LDYMVSVESDVFIP 17 (50)
Q Consensus 4 lDy~V~~~SDvFv~ 17 (50)
+|++++..||+|+.
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 68999999999986
No 8
>PRK10964 ADP-heptose:LPS heptosyl transferase I; Provisional
Probab=25.69 E-value=45 Score=22.32 Aligned_cols=23 Identities=4% Similarity=-0.055 Sum_probs=16.7
Q ss_pred eccceeeecCCCCHHHHH-hhhhh
Q 035401 10 VESDVFIPSHLGNMARAV-EGHLM 32 (50)
Q Consensus 10 ~~SDvFv~t~~GNm~~~v-~GhR~ 32 (50)
.++|+||.+.+|.|+=+. .|-++
T Consensus 252 ~~a~l~I~nDSGp~HlA~A~g~p~ 275 (322)
T PRK10964 252 AGAKAVVSVDTGLSHLTAALDRPN 275 (322)
T ss_pred HhCCEEEecCCcHHHHHHHhCCCE
Confidence 479999999999887442 44443
No 9
>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=24.07 E-value=58 Score=21.80 Aligned_cols=19 Identities=26% Similarity=0.651 Sum_probs=14.4
Q ss_pred eeeeeeccceeeecCCCCH
Q 035401 5 DYMVSVESDVFIPSHLGNM 23 (50)
Q Consensus 5 Dy~V~~~SDvFv~t~~GNm 23 (50)
|=+...+.|||+|...+|.
T Consensus 100 ~~i~~~~~Dvlip~a~~~~ 118 (227)
T cd01076 100 EELLELDCDILIPAALENQ 118 (227)
T ss_pred ccceeecccEEEecCccCc
Confidence 3356778999999987643
No 10
>PF13506 Glyco_transf_21: Glycosyl transferase family 21
Probab=21.89 E-value=62 Score=20.42 Aligned_cols=15 Identities=40% Similarity=0.811 Sum_probs=12.9
Q ss_pred eeeeeeeccceeeec
Q 035401 4 LDYMVSVESDVFIPS 18 (50)
Q Consensus 4 lDy~V~~~SDvFv~t 18 (50)
=||++.+.|||.++.
T Consensus 32 ~d~~~~~DsDi~v~p 46 (175)
T PF13506_consen 32 YDYLVISDSDIRVPP 46 (175)
T ss_pred CCEEEEECCCeeECH
Confidence 489999999999864
No 11
>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=21.75 E-value=46 Score=19.75 Aligned_cols=11 Identities=36% Similarity=0.830 Sum_probs=9.3
Q ss_pred Ccceeeeeeec
Q 035401 1 MAALDYMVSVE 11 (50)
Q Consensus 1 lAAlDy~V~~~ 11 (50)
|+||||-+.++
T Consensus 35 MSAIdF~~~v~ 45 (69)
T cd00559 35 MSAIDFKLDVD 45 (69)
T ss_pred eeeEEeeeeEE
Confidence 68999988876
No 12
>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=21.69 E-value=24 Score=23.86 Aligned_cols=16 Identities=31% Similarity=0.515 Sum_probs=13.2
Q ss_pred eeeccceeeecCCCCH
Q 035401 8 VSVESDVFIPSHLGNM 23 (50)
Q Consensus 8 V~~~SDvFv~t~~GNm 23 (50)
=|...|+|||+..+..
T Consensus 93 hCsACd~~IP~~~~~v 108 (165)
T PF04988_consen 93 HCSACDVFIPMQHSSV 108 (165)
T ss_pred hhhHhhhhccCcHHHH
Confidence 4889999999987743
No 13
>PF01520 Amidase_3: N-acetylmuramoyl-L-alanine amidase; InterPro: IPR002508 The cell wall envelope of Gram-positive bacteria is a macromolecular, exoskeletal organelle that is assembled and turned over at designated sites. The cell wall also functions as a surface organelle that allows Gram-positive pathogens to interact with their environment, in particular the tissues of the infected host. All of these functions require that surface proteins and enzymes be properly targeted to the cell wall envelope. Two basic mechanisms, cell wall sorting and targeting, have been identified. Cell well sorting is the covalent attachment of surface proteins to the peptidoglycan via a C-terminal sorting signal that contains a consensus LPXTG sequence. More than 100 proteins that possess cell wall-sorting signals, including the M proteins of Streptococcus pyogenes, protein A of Staphylococcus aureus, and several internalins of Listeria monocytogenes, have been identified. Cell wall targeting involves the noncovalent attachment of proteins to the cell surface via specialised binding domains. Several of these wall-binding domains appear to interact with secondary wall polymers that are associated with the peptidoglycan, for example teichoic acids and polysaccharides. Proteins that are targeted to the cell surface include muralytic enzymes such as autolysins, lysostaphin, and phage lytic enzymes. Other examples for targeted proteins are the surface S-layer proteins of bacilli and clostridia, as well as virulence factors required for the pathogenesis of L. monocytogenes (internalin B) and Streptococcus pneumoniae (PspA) infections []. Autolysin 3.5.1.28 from EC hydrolyses the link between N-acetylmuramoyl residues and L-amino acid residues in certain bacterial cell wall glycopeptides.; GO: 0008745 N-acetylmuramoyl-L-alanine amidase activity, 0009253 peptidoglycan catabolic process; PDB: 3QAY_A 3CZX_A 1JWQ_A 1XOV_A 3NE8_A.
Probab=20.66 E-value=39 Score=20.46 Aligned_cols=37 Identities=11% Similarity=0.071 Sum_probs=19.6
Q ss_pred eeeeeeeccceeeecCCCCHHHHHhhhhhhc-----cCcchhhhhhhhc
Q 035401 4 LDYMVSVESDVFIPSHLGNMARAVEGHLMLR-----IEQDYRNKYKIVV 47 (50)
Q Consensus 4 lDy~V~~~SDvFv~t~~GNm~~~v~GhR~y~-----g~~~~k~l~~lf~ 47 (50)
-|++||+|.|.+-... ..|-..|. +.+.-++||+.+.
T Consensus 68 ad~~isiH~na~~~~~-------~~G~ev~~~~~~~~~~~s~~lA~~i~ 109 (175)
T PF01520_consen 68 ADLFISIHFNASNGGA-------ARGTEVYYSYNSSNSAKSKKLAKSIQ 109 (175)
T ss_dssp SSEEEEEEEE-SSSTT---------SEEEEEHHHCCCCHHHHHHHHHHH
T ss_pred cCEEEEEeecCccCCc-------CCceEEEEecccccchhhHHHHHHHH
Confidence 3666777766542221 25666665 5666666666553
No 14
>KOG2520 consensus 5'-3' exonuclease [Replication, recombination and repair]
Probab=20.43 E-value=85 Score=25.84 Aligned_cols=44 Identities=18% Similarity=0.208 Sum_probs=28.2
Q ss_pred eeeeeeeccceeeecCCC-CHHHHHhhhhhhc--------------cCcchhhhhhhhccC
Q 035401 4 LDYMVSVESDVFIPSHLG-NMARAVEGHLMLR--------------IEQDYRNKYKIVVGD 49 (50)
Q Consensus 4 lDy~V~~~SDvFv~t~~G-Nm~~~v~GhR~y~--------------g~~~~k~l~~lf~~~ 49 (50)
.|.+|...||||. ++| +-++..--.+.|. .++|.=.||.|+-+|
T Consensus 502 vdGiITDDSDV~L--FGg~~VYrn~F~knk~ve~y~~~di~kel~l~R~~lI~lA~LlGsD 560 (815)
T KOG2520|consen 502 VDGIITDDSDVFL--FGGTRVYRNFFNKNKYVEKYQLDDIEKELGLDRPNLISLAQLLGSD 560 (815)
T ss_pred cceeeccccccee--eccchhhHHHhhcCccceeeehHHHHHHHccCchhhHHHHHhcccc
Confidence 6899999999998 555 2355443344442 256666677766554
Done!