Query 027682
Match_columns 220
No_of_seqs 127 out of 250
Neff 4.5
Searched_HMMs 46136
Date Fri Mar 29 13:36:34 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/027682.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/027682hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG2233 Alpha-N-acetylglucosam 100.0 1.7E-44 3.6E-49 342.8 7.4 109 102-219 5-113 (666)
2 PF12971 NAGLU_N: Alpha-N-acet 100.0 3.3E-28 7.2E-33 184.2 8.6 86 53-152 1-86 (86)
3 PF02838 Glyco_hydro_20b: Glyc 57.0 48 0.001 25.3 6.4 36 83-125 73-108 (124)
4 PF03648 Glyco_hydro_67N: Glyc 46.7 35 0.00075 26.8 4.2 35 84-121 88-122 (122)
5 PF12048 DUF3530: Protein of u 32.3 1.4E+02 0.003 27.4 6.3 30 184-213 178-208 (310)
6 PLN02183 ferulate 5-hydroxylas 27.6 38 0.00082 32.3 1.9 12 1-12 1-12 (516)
7 PF02622 DUF179: Uncharacteriz 20.1 44 0.00095 27.5 0.6 50 162-219 108-161 (161)
8 PF00352 TBP: Transcription fa 18.9 1.9E+02 0.0042 21.3 3.8 23 102-124 58-81 (86)
9 PF14711 Nitr_red_bet_C: Respi 18.7 1.3E+02 0.0028 23.1 2.8 32 25-65 24-55 (83)
10 TIGR03822 AblA_like_2 lysine-2 18.5 83 0.0018 28.9 2.1 29 182-211 120-149 (321)
No 1
>KOG2233 consensus Alpha-N-acetylglucosaminidase [Intracellular trafficking, secretion, and vesicular transport]
Probab=100.00 E-value=1.7e-44 Score=342.76 Aligned_cols=109 Identities=58% Similarity=1.141 Sum_probs=99.9
Q ss_pred CeEEEEecCHHHHHHHHHHHHHHhcCceeeecCCCCcccccCCCCCCCCCCCCCceeEecccceeeecccccCCcccccc
Q 027682 102 PEIVISGVTGVEVLAGLHWYLRYWCGSHISWDKTGGVQVASMPKLGSFPRVQDAGVFVKRPIPLNYYQNAVTSSYTFAWW 181 (220)
Q Consensus 102 ~kI~I~G~s~vala~Gln~YLK~~c~~~iSW~~~~G~ql~~lp~P~~LP~v~~~~v~~~s~~~~RYy~N~cTfsYS~awW 181 (220)
++|.|+|+|||++|+||||||||.|++|++|++. ++. +|.+||+++.+ +.+.+| ||||||+||+||||+||
T Consensus 5 ~~il~~g~tGv~~~~~lh~ylk~~~~~~v~w~k~---~~s---lp~~lprv~~e-~~~~~p--~~YyqNvcT~SYSfaWW 75 (666)
T KOG2233|consen 5 GRILIKGTTGVEIASGLHWYLKYKCNAHVSWDKQ---VAS---LPQHLPRVDSE-IFIARP--WNYYQNVCTFSYSFAWW 75 (666)
T ss_pred ceEEEecCchhhhhhcccHHHHHhhcCceeehhe---eee---CCCcCCCCCcc-eeeccc--hHhhcceeeeeeeeeee
Confidence 6899999999999999999999999999999963 543 56699999874 555555 99999999999999999
Q ss_pred ChhhHhhhHhHHHhcCCCccccccchHHHHHHHHHHhc
Q 027682 182 DWKRWEKEIDWMALQGINLPLAFTGQETIWQKVFQVAF 219 (220)
Q Consensus 182 dW~rWErEIDWMAL~GINlpLA~~GqEaIW~~V~~~~~ 219 (220)
+|+|||||||||||||||++||++|||+|||+||+.+|
T Consensus 76 ~w~qWeR~iDWmALnGinl~la~~gQEaIWqkVf~~lg 113 (666)
T KOG2233|consen 76 GWEQWEREIDWMALNGINLVLAPLGQEAIWQKVFMGLG 113 (666)
T ss_pred chHHHHhHhhHHHHcCcceeeccchhHHHHHHHHHHcC
Confidence 99999999999999999999999999999999999876
No 2
>PF12971 NAGLU_N: Alpha-N-acetylglucosaminidase (NAGLU) N-terminal domain; InterPro: IPR024240 Alpha-N-acetylglucosaminidase, is a lysosomal enzyme required for the stepwise degradation of heparan sulphate []. Mutations on the alpha-N-acetylglucosaminidase (NAGLU) gene can lead to Mucopolysaccharidosis type IIIB (MPS IIIB; or Sanfilippo syndrome type B) characterised by neurological dysfunction but relatively mild somatic manifestations []. The structure shows that the enzyme is composed of three domains. This entry represents the N-terminal domain of Alpha-N-acetylglucosaminidase which has an alpha-beta fold [].; PDB: 4A4A_A 2VC9_A 2VCC_A 2VCB_A 2VCA_A.
Probab=99.95 E-value=3.3e-28 Score=184.18 Aligned_cols=86 Identities=43% Similarity=0.821 Sum_probs=59.3
Q ss_pred HHHHHHHHHHhhcCCCCCceEEEEeecCCCCCceeEEEecCCCCCCCCCCeEEEEecCHHHHHHHHHHHHHHhcCceeee
Q 027682 53 QLAAAYAVLQRLLPSHYSAFQFRIISKKQCGGEYCFILRNHPSSYIRGTPEIVISGVTGVEVLAGLHWYLRYWCGSHISW 132 (220)
Q Consensus 53 q~~aa~~ll~Rllp~~~~~F~~~i~~~~~~~g~d~F~i~~~~~~~~~g~~kI~I~G~s~vala~Gln~YLK~~c~~~iSW 132 (220)
|++|+++||+|+||+|+.+|+|++++.. ++.|+|+|++. .+ +||+|+|||+||+|+||||||||||++||||
T Consensus 1 q~~a~~~li~Rll~~~~~~f~~~~~~~~--~~~d~F~l~~~----~~--gki~I~G~s~vala~Gl~~YLk~~c~~~isW 72 (86)
T PF12971_consen 1 QISAARGLIERLLPEHASQFTFELIPSS--NGKDVFELSSA----DN--GKIVIRGNSGVALASGLNWYLKYYCHVHISW 72 (86)
T ss_dssp --HHHHHHHHHHC-GGGGGEEEEE---B--TTBEEEEEEE-----SS--S-EEEEESSHHHHHHHHHHHHHHHS--B--T
T ss_pred CcHHHHHHHHhhcccccceEEEEEecCC--CCCCEEEEEeC----CC--CeEEEEeCCHHHHHHHHHHHHHHHhCceEee
Confidence 6789999999999999999999998753 48999999861 23 6999999999999999999999999999999
Q ss_pred cCCCCcccccCCCCCCCCCC
Q 027682 133 DKTGGVQVASMPKLGSFPRV 152 (220)
Q Consensus 133 ~~~~G~ql~~lp~P~~LP~v 152 (220)
+ |+|++ +|++||.|
T Consensus 73 ~---g~~~~---lP~~LP~v 86 (86)
T PF12971_consen 73 N---GDQLE---LPASLPAV 86 (86)
T ss_dssp T-----B-------SS----
T ss_pred c---CCccc---CCCCCCCC
Confidence 8 45775 68899975
No 3
>PF02838 Glyco_hydro_20b: Glycosyl hydrolase family 20, domain 2; InterPro: IPR015882 Glycoside hydrolase family 20 GH20 from CAZY comprises enzymes with several known activities; beta-hexosaminidase (3.2.1.52 from EC); lacto-N-biosidase (3.2.1.140 from EC). Carbonyl oxygen of the C-2 acetamido group of the substrate acts as the catalytic nucleophile/base in this family of enzymes. In the brain and other tissues, beta-hexosaminidase A degrades GM2 gangliosides; specifically, the enzyme hydrolyses terminal non-reducing N-acetyl-D-hexosamine residues in N-acetyl-beta-D-hexosaminides. There are 3 forms of beta-hexosaminidase: hexosaminidase A is a trimer, with one alpha, one beta-A and one beta-B chain; hexosaminidase B is a tetramer of two beta-A and two beta-B chains; and hexosaminidase S is a homodimer of alpha chains. The two beta chains are derived from the cleavage of a precursor. Mutations in the beta-chain lead to Sandhoff disease, a lysosomal storage disorder characterised by accumulation of GM2 ganglioside []. This entry represents the alpha and beta subunit of beta-N-acetylhexosaminidase. It contains a similar fold but lacks the catalytic centre.; GO: 0004563 beta-N-acetylhexosaminidase activity, 0005975 carbohydrate metabolic process; PDB: 3SUT_A 3SUS_A 3GH7_A 3SUR_A 3SUW_A 3SUV_A 3SUU_A 3GH5_A 3GH4_A 2J4G_B ....
Probab=57.04 E-value=48 Score=25.30 Aligned_cols=36 Identities=22% Similarity=0.230 Sum_probs=27.4
Q ss_pred CCceeEEEecCCCCCCCCCCeEEEEecCHHHHHHHHHHHHHHh
Q 027682 83 GGEYCFILRNHPSSYIRGTPEIVISGVTGVEVLAGLHWYLRYW 125 (220)
Q Consensus 83 ~g~d~F~i~~~~~~~~~g~~kI~I~G~s~vala~Gln~YLK~~ 125 (220)
.+.+.|+|+-.+ ++|+|+|++...+.+|+.--+.-.
T Consensus 73 ~~~E~Y~L~i~~-------~~I~I~a~~~~G~~yg~qTL~Qll 108 (124)
T PF02838_consen 73 LGEEGYRLSISP-------KGITIEASDPAGLFYGLQTLRQLL 108 (124)
T ss_dssp STTT-EEEEEES-------SEEEEEESSHHHHHHHHHHHHHHS
T ss_pred CCCcceEEEEEC-------CEEEEEEcCchHHHHHHHHHHHHh
Confidence 567889998532 489999999999999998766543
No 4
>PF03648 Glyco_hydro_67N: Glycosyl hydrolase family 67 N-terminus; InterPro: IPR005154 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. This represents a family of alpha-glucuronidases (GH67 from CAZY). Deletion mutants have indicated that the central region is responsible for the catalytic activity. Within this central domain, the invariant Glu and Asp (residues 391 and 364 respectively from Bacillus stearothermophilus (Geobacillus stearothermophilus)) are thought to from the the catalytic centre [].; GO: 0046559 alpha-glucuronidase activity, 0045493 xylan catabolic process; PDB: 1GQL_A 1GQI_B 1GQJ_B 1GQK_A 1H41_A 1MQR_A 1K9F_A 1K9E_A 1L8N_A 1K9D_A ....
Probab=46.69 E-value=35 Score=26.83 Aligned_cols=35 Identities=31% Similarity=0.351 Sum_probs=25.7
Q ss_pred CceeEEEecCCCCCCCCCCeEEEEecCHHHHHHHHHHH
Q 027682 84 GEYCFILRNHPSSYIRGTPEIVISGVTGVEVLAGLHWY 121 (220)
Q Consensus 84 g~d~F~i~~~~~~~~~g~~kI~I~G~s~vala~Gln~Y 121 (220)
+.|-|.|..... +++ +.|.|.|++...+.+|.+++
T Consensus 88 ~~EGy~I~~v~~--~~~-~~lvI~g~~~~G~LYGvF~l 122 (122)
T PF03648_consen 88 GEEGYIIRTVEI--GGK-NVLVIAGKTERGVLYGVFHL 122 (122)
T ss_dssp STT-EEEEEEES--SSS-EEEEEEESSHHHHHHHHHHH
T ss_pred CCccEEEEEEec--CCC-CEEEEEeCCCcEEEEEEeeC
Confidence 668898875321 122 57999999999999999875
No 5
>PF12048 DUF3530: Protein of unknown function (DUF3530); InterPro: IPR022529 This family of proteins is functionally uncharacterised. This protein is found in bacteria. Proteins in this family are typically between 272 to 336 amino acids in length. These proteins are distantly related to alpa/beta hydrolases so they may act as enzymes.
Probab=32.31 E-value=1.4e+02 Score=27.35 Aligned_cols=30 Identities=27% Similarity=0.338 Sum_probs=19.2
Q ss_pred hhHhhhHhHHHhcCCC-ccccccchHHHHHH
Q 027682 184 KRWEKEIDWMALQGIN-LPLAFTGQETIWQK 213 (220)
Q Consensus 184 ~rWErEIDWMAL~GIN-lpLA~~GqEaIW~~ 213 (220)
+|-+--|+-..-+|.+ ..|.-.|.=|-|--
T Consensus 178 ari~Aa~~~~~~~~~~~ivlIg~G~gA~~~~ 208 (310)
T PF12048_consen 178 ARIEAAIAFAQQQGGKNIVLIGHGTGAGWAA 208 (310)
T ss_pred HHHHHHHHHHHhcCCceEEEEEeChhHHHHH
Confidence 3555556666677765 66666777776653
No 6
>PLN02183 ferulate 5-hydroxylase
Probab=27.64 E-value=38 Score=32.28 Aligned_cols=12 Identities=42% Similarity=0.523 Sum_probs=9.9
Q ss_pred CCCCchhHHHHH
Q 027682 1 MDSPFRSVSLIL 12 (220)
Q Consensus 1 ~~~~~~~~~~~~ 12 (220)
|||||+++..+-
T Consensus 1 ~~~~~~~~~~~~ 12 (516)
T PLN02183 1 MDSPLQSLLTSP 12 (516)
T ss_pred CCcHHHhhhccc
Confidence 899999987654
No 7
>PF02622 DUF179: Uncharacterized ACR, COG1678; InterPro: IPR003774 This entry describes proteins of unknown function.; PDB: 2DO8_A 2EW0_A 2GS5_A 2HRX_A 2AJ2_A 2HAF_A 2GZO_A.
Probab=20.15 E-value=44 Score=27.52 Aligned_cols=50 Identities=20% Similarity=0.490 Sum_probs=36.0
Q ss_pred ccceeeecccccCCccccccChhhHhhhHh---HHHhcCCCccccc-cchHHHHHHHHHHhc
Q 027682 162 PIPLNYYQNAVTSSYTFAWWDWKRWEKEID---WMALQGINLPLAF-TGQETIWQKVFQVAF 219 (220)
Q Consensus 162 ~~~~RYy~N~cTfsYS~awWdW~rWErEID---WMAL~GINlpLA~-~GqEaIW~~V~~~~~ 219 (220)
+.++|+|..||- |...+=|+||+ |.-..--+ .+.+ +.-|.+|+++++.+|
T Consensus 108 ~~~~~~f~Gysg-------W~~gQLe~Ei~~g~W~~~~a~~-~~vf~~~~~~~W~~~l~~~G 161 (161)
T PF02622_consen 108 PEDFRFFLGYSG-------WGPGQLEDEIARGSWLVAPASP-DIVFETPPEELWREALRRLG 161 (161)
T ss_dssp CSSEEEEEEEEE-------ECTTHHHHHHHTTTEEEEE--H-HHHCTSTSSHHHHHHHHCTT
T ss_pred CceEEEEEEECC-------CCHHHHHHHHHcCCEEEeeCCH-HHhhCCCHHHHHHHHHHHCc
Confidence 567999999887 78899999995 54443322 2223 567889999999876
No 8
>PF00352 TBP: Transcription factor TFIID (or TATA-binding protein, TBP); InterPro: IPR000814 The TATA-box binding protein (TBP) is required for the initiation of transcription by RNA polymerases I, II and III, from promoters with or without a TATA box [, ]. TBP associates with a host of factors, including the general transcription factors TFIIA, -B, -D, -E, and -H, to form huge multi-subunit pre-initiation complexes on the core promoter. Through its association with different transcription factors, TBP can initiate transcription from different RNA polymerases. There are several related TBPs, including TBP-like (TBPL) proteins []. The C-terminal core of TBP (~180 residues) is highly conserved and contains two 77-amino acid repeats that produce a saddle-shaped structure that straddles the DNA; this region binds to the TATA box and interacts with transcription factors and regulatory proteins []. By contrast, the N-terminal region varies in both length and sequence.; GO: 0003677 DNA binding, 0006355 regulation of transcription, DNA-dependent, 0006367 transcription initiation from RNA polymerase II promoter; PDB: 1D3U_A 1PCZ_B 1AIS_A 1NGM_A 1TBP_A 1TBA_B 1YTB_A 1RM1_A 1YTF_A 1NH2_A ....
Probab=18.87 E-value=1.9e+02 Score=21.28 Aligned_cols=23 Identities=26% Similarity=0.307 Sum_probs=18.2
Q ss_pred CeEEEEec-CHHHHHHHHHHHHHH
Q 027682 102 PEIVISGV-TGVEVLAGLHWYLRY 124 (220)
Q Consensus 102 ~kI~I~G~-s~vala~Gln~YLK~ 124 (220)
|||+|+|. |.-.+..++...++-
T Consensus 58 Gki~itGaks~~~~~~a~~~i~~~ 81 (86)
T PF00352_consen 58 GKIVITGAKSEEEAKKAIEKILPI 81 (86)
T ss_dssp SEEEEEEESSHHHHHHHHHHHHHH
T ss_pred CEEEEEecCCHHHHHHHHHHHHHH
Confidence 69999997 777777788777653
No 9
>PF14711 Nitr_red_bet_C: Respiratory nitrate reductase beta C-terminal; PDB: 3IR7_B 1Y5N_B 1R27_D 3EGW_B 1Y5I_B 1Q16_B 1Y4Z_B 1Y5L_B 3IR6_B 3IR5_B ....
Probab=18.70 E-value=1.3e+02 Score=23.08 Aligned_cols=32 Identities=25% Similarity=0.396 Sum_probs=23.1
Q ss_pred hhhhcchhHHHHHHhhccccccCCCchhHHHHHHHHHHhhc
Q 027682 25 VAQSSTIGVQYISRLLDIQDRERAPPSVQLAAAYAVLQRLL 65 (220)
Q Consensus 25 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~q~~aa~~ll~Rll 65 (220)
..-+..+|++||.+++.-+ .++.++.+++|++
T Consensus 24 ~id~lRIPi~YLAnLftAG---------d~~~V~~~L~rL~ 55 (83)
T PF14711_consen 24 AIDSLRIPIEYLANLFTAG---------DEEPVRRALKRLL 55 (83)
T ss_dssp -GGGBSS-HHHHHHHHSTT----------HHHHHHHHHHHH
T ss_pred hHHHhcccHHHHHHHHccC---------ChHHHHHHHHHHH
Confidence 3346778999999999874 4668888888886
No 10
>TIGR03822 AblA_like_2 lysine-2,3-aminomutase-related protein. Members of this protein form a distinctive clade, homologous to lysine-2,3-aminomutase (of Bacillus, Clostridium, and methanogenic archaea) and likely similar in function. Members of this family are found in Rhodopseudomonas, Caulobacter crescentus, Bradyrhizobium, etc.
Probab=18.47 E-value=83 Score=28.87 Aligned_cols=29 Identities=14% Similarity=0.173 Sum_probs=22.7
Q ss_pred ChhhHhhhHhHHHhc-CCCccccccchHHHH
Q 027682 182 DWKRWEKEIDWMALQ-GINLPLAFTGQETIW 211 (220)
Q Consensus 182 dW~rWErEIDWMAL~-GINlpLA~~GqEaIW 211 (220)
++++|++-||+++-| ||+-.+ ++|=|-.-
T Consensus 120 ~~~e~~~~i~~i~~~~~I~~Vi-lSGGDPl~ 149 (321)
T TIGR03822 120 SPAELDAAFAYIADHPEIWEVI-LTGGDPLV 149 (321)
T ss_pred CHHHHHHHHHHHHhCCCccEEE-EeCCCccc
Confidence 679999999999966 898755 67766543
Done!