Query 028024
Match_columns 215
No_of_seqs 89 out of 91
Neff 4.0
Searched_HMMs 46136
Date Fri Mar 29 05:05:07 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/028024.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/028024hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF11152 DUF2930: Protein of u 100.0 2.1E-50 4.6E-55 345.7 14.4 149 62-214 1-156 (195)
2 PF10605 3HBOH: 3HB-oligomer h 63.7 6.7 0.00015 40.2 3.2 38 52-89 607-644 (690)
3 KOG0429 Ubiquitin-conjugating 30.6 23 0.00049 32.4 0.8 23 44-66 63-87 (258)
4 PF13334 DUF4094: Domain of un 29.3 44 0.00095 26.0 2.1 26 93-118 4-29 (95)
5 KOG4580 Component of vacuolar 29.0 50 0.0011 27.0 2.5 25 57-81 82-106 (112)
6 PF00144 Beta-lactamase: Beta- 27.0 1.2E+02 0.0027 26.0 4.7 18 155-172 12-29 (329)
7 TIGR02761 TraE_TIGR type IV co 26.3 2E+02 0.0043 24.3 5.8 55 104-158 30-86 (181)
8 COG5264 VTC1 Vacuolar transpor 25.8 56 0.0012 27.2 2.2 25 57-81 97-121 (126)
9 PF05309 TraE: TraE protein; 24.2 2.2E+02 0.0048 23.9 5.7 53 106-158 32-86 (187)
10 PRK13284 flagellar assembly pr 23.6 47 0.001 27.6 1.5 17 45-61 16-32 (145)
11 PRK13285 flagellar assembly pr 22.9 49 0.0011 27.5 1.5 17 45-61 16-32 (148)
12 PF01299 Lamp: Lysosome-associ 22.5 75 0.0016 28.7 2.7 18 59-76 270-287 (306)
13 PF02623 FliW: FliW protein; 21.0 45 0.00098 26.7 0.8 18 133-150 51-68 (121)
No 1
>PF11152 DUF2930: Protein of unknown function (DUF2930); InterPro: IPR021325 This family of proteins has no known function.
Probab=100.00 E-value=2.1e-50 Score=345.74 Aligned_cols=149 Identities=36% Similarity=0.470 Sum_probs=142.4
Q ss_pred hhHHHHHHHHHHHHhhhhccCCCCCchHHHHHHHHHHHHHhhhhhhhhhhhhcccCCCCCCCCCCCCeeceEeccCccHH
Q 028024 62 LPRWIGYGFGSLIVLNHFAFSNSVTSAQLRSEVLGLSLAAFSVTLPYLGKFLKGASPVSQKSLPESGEQIFVMSQNISDA 141 (215)
Q Consensus 62 LPl~vG~l~~~llL~Nr~~s~a~~t~sQ~RadvLg~~Lsa~lv~LiL~Gllw~~~qP~~~~~v~l~Geq~F~l~~~Lsd~ 141 (215)
||+++|+++++++++||++++ ++||||+||||||++||+++ ||+|++|+++||++++.|++.|+|+|+|+++|||+
T Consensus 1 LPl~vG~l~~~lll~N~~~~~-~~t~sq~RaevLg~~ls~~l---iL~g~lw~~l~p~~~~~v~L~G~~~f~l~~~L~~~ 76 (195)
T PF11152_consen 1 LPLIVGLLGGSLLLLNRLSGA-DATPSQSRAEVLGLILSAVL---ILTGLLWQRLKPRSPEAVDLPGEQGFELSPDLSDA 76 (195)
T ss_pred CceEehHHHHHHHHhhhcccC-CCCHHHHHHHHHHHHHHHHH---HHHHHHHhhccCCCCCccCCCCccceEECCCCCHH
Confidence 799999999999999997776 79999999999999999666 89999999999999999999999999999999999
Q ss_pred HHHHHHHHHHHHhhhccccEEEEEECCEEE-EEeeecCCCCCChhHHHHHHHHhccccccccC------CccccccCCCC
Q 028024 142 LKENLAWATYVLLRNTNSISVLISIRGELC-VRGYWQTPDGASKTQLLEWFERQIENIGLSDL------KDSLYFPQSAG 214 (215)
Q Consensus 142 ~k~ELAWaS~~LLtnT~a~svlV~~~g~~l-~RG~l~~p~d~~~g~I~~~~~~~~~~~yLanL------~~~~Yfp~~~~ 214 (215)
+|+|||||||+|||||+|+||+|||||++| +||++++++++++|+||+++|++++.+||+|+ .|+-|+|+|+.
T Consensus 77 ~k~ELAWas~~LLt~T~a~svlV~~~g~~llrrG~~~~~~~~~~g~i~~~~~~~~~~~yL~nl~lyPGr~Ef~~lP~ntq 156 (195)
T PF11152_consen 77 AKEELAWASYALLTNTNARSVLVYYDGRVLLRRGILGSPSKFKPGPICQRAMESGKLIYLVNLKLYPGRVEFDYLPENTQ 156 (195)
T ss_pred HHHHHHHHHHHHHhhCCceEEEEEECCEEEEEeeccCCCCCcchHHHHHHHHhcCCceeccccccCCCchhhhhcCCCCc
Confidence 999999999999999999999999999996 58999999999999999999999999999999 58889999873
No 2
>PF10605 3HBOH: 3HB-oligomer hydrolase (3HBOH) ; InterPro: IPR016582 This entry represents a group of predicted D-(-)-3-hydroxybutyrate oligomer hydrolases (also known as 3HB-oligomer hydrolase), which function in the degradation of poly-3-hydroxybutyrate (PHB). These enzymes catalyse the hydrolysis of D(-)-3-hydroxybutyrate oligomers (3HB-oligomers) into 3HB-monomers [, ].; GO: 0047989 hydroxybutyrate-dimer hydrolase activity, 0019605 butyrate metabolic process, 0005615 extracellular space
Probab=63.71 E-value=6.7 Score=40.19 Aligned_cols=38 Identities=18% Similarity=0.359 Sum_probs=34.5
Q ss_pred cCCCCCCCCChhHHHHHHHHHHHHhhhhccCCCCCchH
Q 028024 52 FGIPGFDESYLPRWIGYGFGSLIVLNHFAFSNSVTSAQ 89 (215)
Q Consensus 52 lgipg~dd~~LPl~vG~l~~~llL~Nr~~s~a~~t~sQ 89 (215)
++.||||++++|+-.=..-.+=++-+|+.++.+++|||
T Consensus 607 ~~~pG~~~r~VPlh~Y~~qALd~M~a~L~~G~~LPpSQ 644 (690)
T PF10605_consen 607 LDFPGFDTRFVPLHPYFFQALDLMWAHLKSGAALPPSQ 644 (690)
T ss_pred ccCCCCCcccccccHHHHHHHHHHHHHhhcCCCCCccc
Confidence 46999999999999988888889999999997789998
No 3
>KOG0429 consensus Ubiquitin-conjugating enzyme-related protein Ft1, involved in programmed cell death [Posttranslational modification, protein turnover, chaperones]
Probab=30.60 E-value=23 Score=32.41 Aligned_cols=23 Identities=52% Similarity=0.785 Sum_probs=19.6
Q ss_pred cceeeeeecCCCC-C-CCCChhHHH
Q 028024 44 NLSVLRFTFGIPG-F-DESYLPRWI 66 (215)
Q Consensus 44 ~~sv~Rftlgipg-~-dd~~LPl~v 66 (215)
..+|||||.=||. | ||..||++|
T Consensus 63 aggVFRFtIliPdnfPdd~dlPrvv 87 (258)
T KOG0429|consen 63 AGGVFRFTILIPDNFPDDSDLPRVV 87 (258)
T ss_pred cCceEEEEEEcCccCCCcCCCCeEE
Confidence 4589999999997 3 799999986
No 4
>PF13334 DUF4094: Domain of unknown function (DUF4094)
Probab=29.31 E-value=44 Score=26.03 Aligned_cols=26 Identities=19% Similarity=0.273 Sum_probs=21.2
Q ss_pred HHHHHHHHHhhhhhhhhhhhhcccCC
Q 028024 93 EVLGLSLAAFSVTLPYLGKFLKGASP 118 (215)
Q Consensus 93 dvLg~~Lsa~lv~LiL~Gllw~~~qP 118 (215)
=++-++++.||+++.++|++|.--.|
T Consensus 4 w~l~Lc~~SF~~G~lft~R~W~~pe~ 29 (95)
T PF13334_consen 4 WVLLLCIASFCAGMLFTNRMWTVPES 29 (95)
T ss_pred HHHHHHHHHHHHHHHHhcccccCCcc
Confidence 37888999999999999999954333
No 5
>KOG4580 consensus Component of vacuolar transporter chaperone (Vtc) involved in vacuole fusion [Intracellular trafficking, secretion, and vesicular transport; Posttranslational modification, protein turnover, chaperones]
Probab=29.03 E-value=50 Score=26.98 Aligned_cols=25 Identities=12% Similarity=0.210 Sum_probs=23.3
Q ss_pred CCCCChhHHHHHHHHHHHHhhhhcc
Q 028024 57 FDESYLPRWIGYGFGSLIVLNHFAF 81 (215)
Q Consensus 57 ~dd~~LPl~vG~l~~~llL~Nr~~s 81 (215)
+||+.=|.+++....+.+++|-.+.
T Consensus 82 yDd~~GP~~v~~vl~valivN~~~~ 106 (112)
T KOG4580|consen 82 YDDRLGPTLVCVVLLVALIVNFILA 106 (112)
T ss_pred CCCcccchHHHHHHHHHHHHHHHHh
Confidence 8999999999999999999998764
No 6
>PF00144 Beta-lactamase: Beta-lactamase; InterPro: IPR001466 This entry represents the serine beta-lactamase-like superfamily. It is a group of diverse group of sequences that includes D-alanyl-D-alanine carboxypeptidase B, aminopeptidase (DmpB), alkaline D-peptidase, animal D-Ala-D-Ala carboxypeptidase homologues and the class A and C beta-lactamases and eukaryotic beta-lactamase homologues which are variously described as: transesterases, non-ribosomal peptide synthetases and hypothetical proteins. Many are serine peptidases belonging to MEROPS peptidase families S11 (D-Ala-D-Ala carboxypeptidase A family) and S12 (D-Ala-D-Ala carboxypeptidase B family, clan SE). The beta-lactamases are classified as both S11 and S12 non-peptidase homologues; these either have been found experimentally to be without peptidase activity, or lack amino acid residues that are believed to be essential for the catalytic activity. Beta-lactamase catalyses the opening and hydrolysis of the beta-lactam ring of beta-lactam antibiotics such as penicillins and cephalosporins []. There are four groups, classed A, B, C and D according to sequence, substrate specificity, and kinetic behaviour: class A (penicillinase-type) is the most common []. The genes for class A beta-lactamases are widely distributed in bacteria, frequently located on transmissible plasmids in Gram-negative organisms, although an equivalent chromosomal gene has been found in a few species []. Class A, C and D beta-lactamases are serine-utilising hydrolases - class B enzymes utilise a catalytic zinc centre instead. The 3 classes of serine beta-lactamase are evolutionarily related and belong to a superfamily that also includes DD-peptidases and other penicillin-binding proteins []. All these proteins contain an S-x-x-K motif, the Ser being the active site residue. Although clearly related, however, the sequences of the 3 classes of serine beta-lactamases vary considerably outside the active site. ; PDB: 1CI8_A 1CI9_B 1PW8_A 1PW1_A 1CEF_A 3PTE_A 1MPL_A 1PWG_A 1CEG_A 1IKG_A ....
Probab=27.02 E-value=1.2e+02 Score=25.97 Aligned_cols=18 Identities=11% Similarity=0.167 Sum_probs=14.1
Q ss_pred hhccccEEEEEECCEEEE
Q 028024 155 RNTNSISVLISIRGELCV 172 (215)
Q Consensus 155 tnT~a~svlV~~~g~~l~ 172 (215)
...+..+++|+++|+++.
T Consensus 12 ~~~~g~a~~v~~~g~~~~ 29 (329)
T PF00144_consen 12 YGIPGAAVAVIHNGKIVY 29 (329)
T ss_dssp TTESEEEEEEEETTEEEE
T ss_pred CCCcEEEEEEEECCEEEE
Confidence 345677889999999864
No 7
>TIGR02761 TraE_TIGR type IV conjugative transfer system protein TraE. TraE is a component of type IV secretion systems involved in conjugative transfer of plasmid DNA. The function of the TraE protein is unknown.
Probab=26.34 E-value=2e+02 Score=24.29 Aligned_cols=55 Identities=15% Similarity=0.112 Sum_probs=33.0
Q ss_pred hhhhhhhhhhcccCCCCCCCCCCCCeeceEec-cCccHHHHHHHH-HHHHHHhhhcc
Q 028024 104 VTLPYLGKFLKGASPVSQKSLPESGEQIFVMS-QNISDALKENLA-WATYVLLRNTN 158 (215)
Q Consensus 104 v~LiL~Gllw~~~qP~~~~~v~l~Geq~F~l~-~~Lsd~~k~ELA-WaS~~LLtnT~ 158 (215)
++.++.+..|...+-....-+|+..++.|.++ ...+++=.++++ +..+++|+-|+
T Consensus 30 ~~~ll~~~~~~~~~~~~~iivPp~i~~~~~vs~~~as~~YLe~ma~~~~~L~lNvTP 86 (181)
T TIGR02761 30 VNVLLSIVLIVALKKTRTVVVPPTISQAFTVSAASADATYLELMGLYFIQLRLNVTP 86 (181)
T ss_pred HHHHHHHHHHHHcCCceEEEECCCCCccEEEeCCcCCHHHHHHHHHHHHHHhccCCh
Confidence 44455556666544344556777778888884 456666666665 44445555444
No 8
>COG5264 VTC1 Vacuolar transporter chaperone [Posttranslational modification, protein turnover, chaperones]
Probab=25.76 E-value=56 Score=27.21 Aligned_cols=25 Identities=16% Similarity=0.289 Sum_probs=23.4
Q ss_pred CCCCChhHHHHHHHHHHHHhhhhcc
Q 028024 57 FDESYLPRWIGYGFGSLIVLNHFAF 81 (215)
Q Consensus 57 ~dd~~LPl~vG~l~~~llL~Nr~~s 81 (215)
+||+.=|..++..+.+.+++|-++.
T Consensus 97 yDD~~GP~lv~vvL~valivNf~~~ 121 (126)
T COG5264 97 YDDRLGPTLVCVVLLVALIVNFFLA 121 (126)
T ss_pred CccccCCchhHHHHHHHHHHHHhhc
Confidence 8999999999999999999998764
No 9
>PF05309 TraE: TraE protein; InterPro: IPR007973 This family consists of several bacterial sex pilus assembly and synthesis proteins (TraE). Conjugal transfer of plasmids from donor to recipient cells is a complex process in which a cell-to-cell contact plays a key role. Many genes encoded by self-transmissible plasmids are required for various processes of conjugation, including pilus formation, stabilisation of mating pairs, conjugative DNA metabolism, surface exclusion and regulation of transfer gene expression []. The exact function of the TraE protein is unknown.; GO: 0000746 conjugation
Probab=24.17 E-value=2.2e+02 Score=23.86 Aligned_cols=53 Identities=13% Similarity=0.085 Sum_probs=35.1
Q ss_pred hhhhhhhhcccCCCCCCCCCCCCeeceEe-ccCccHHHHHHHHHH-HHHHhhhcc
Q 028024 106 LPYLGKFLKGASPVSQKSLPESGEQIFVM-SQNISDALKENLAWA-TYVLLRNTN 158 (215)
Q Consensus 106 LiL~Gllw~~~qP~~~~~v~l~Geq~F~l-~~~Lsd~~k~ELAWa-S~~LLtnT~ 158 (215)
+++.+.+|.-.+-.+..-+|+.-++.|.+ ....+++-.+++++- .+++++.|+
T Consensus 32 v~l~~~~~~~~~~~~~vivPp~~~~~~~vs~~~as~~Yl~~m~~~~~~L~lNvtP 86 (187)
T PF05309_consen 32 VVLGYLLYAASTNQRTVIVPPTLNKPFWVSGNSASAEYLEQMGRYVAQLLLNVTP 86 (187)
T ss_pred HHHHHHHHHHhcCCeEEEECCcccccEEEECCcCCHHHHHHHHHHHHHHhcCCCh
Confidence 45556677777655566678888888888 456778888888743 444444444
No 10
>PRK13284 flagellar assembly protein FliW; Provisional
Probab=23.57 E-value=47 Score=27.64 Aligned_cols=17 Identities=35% Similarity=0.825 Sum_probs=14.1
Q ss_pred ceeeeeecCCCCCCCCC
Q 028024 45 LSVLRFTFGIPGFDESY 61 (215)
Q Consensus 45 ~sv~Rftlgipg~dd~~ 61 (215)
-.+++|.-|||||.|-+
T Consensus 16 ~~ii~Fp~Gi~GFe~~k 32 (145)
T PRK13284 16 EKVITFPAGLPGFEDCK 32 (145)
T ss_pred cceEECCCCCCCCCccc
Confidence 35799999999999854
No 11
>PRK13285 flagellar assembly protein FliW; Provisional
Probab=22.92 E-value=49 Score=27.48 Aligned_cols=17 Identities=35% Similarity=0.776 Sum_probs=14.4
Q ss_pred ceeeeeecCCCCCCCCC
Q 028024 45 LSVLRFTFGIPGFDESY 61 (215)
Q Consensus 45 ~sv~Rftlgipg~dd~~ 61 (215)
-.+++|.-|||||.+-+
T Consensus 16 ~~ii~Fp~Gi~GFe~~~ 32 (148)
T PRK13285 16 EDIITFPEGIPGFEDLK 32 (148)
T ss_pred hceEECCCCCCCCCccc
Confidence 35899999999999854
No 12
>PF01299 Lamp: Lysosome-associated membrane glycoprotein (Lamp); InterPro: IPR002000 Lysosome-associated membrane glycoproteins (lamp) [] are integral membrane proteins, specific to lysosomes, and whose exact biological function is not yet clear. Structurally, the lamp proteins consist of two internally homologous lysosome-luminal domains separated by a proline-rich hinge region; at the C-terminal extremity there is a transmembrane region (TM) followed by a very short cytoplasmic tail (C). In each of the duplicated domains, there are two conserved disulphide bonds. This structure is schematically represented in the figure below. +-----+ +-----+ +-----+ +-----+ | | | | | | | | xCxxxxxCxxxxxxxxxxxxCxxxxxCxxxxxxxxxCxxxxxCxxxxxxxxxxxxCxxxxxCxxxxxxxx +--------------------------++Hinge++--------------------------++TM++C+ In mammals, there are two closely related types of lamp: lamp-1 and lamp-2, which form major components of the lysosome membrane. In chicken lamp-1 is known as LEP100. Also included in this entry is the macrophage protein CD68 (or macrosialin) [] is a heavily glycosylated integral membrane protein whose structure consists of a mucin-like domain followed by a proline-rich hinge; a single lamp-like domain; a transmembrane region and a short cytoplasmic tail. Similar to CD68, mammalian lamp-3, which is expressed in lymphoid organs, dendritic cells and in lung, contains all the C-terminal regions but lacks the N-terminal lamp-like region []. In a lamp-family protein from nematodes [] only the part C-terminal to the hinge is conserved. ; GO: 0016020 membrane
Probab=22.50 E-value=75 Score=28.73 Aligned_cols=18 Identities=17% Similarity=0.495 Sum_probs=13.9
Q ss_pred CCChhHHHHHHHHHHHHh
Q 028024 59 ESYLPRWIGYGFGSLIVL 76 (215)
Q Consensus 59 d~~LPl~vG~l~~~llL~ 76 (215)
+..+|++||+.++.|+++
T Consensus 270 ~~~vPIaVG~~La~lvli 287 (306)
T PF01299_consen 270 SDLVPIAVGAALAGLVLI 287 (306)
T ss_pred cchHHHHHHHHHHHHHHH
Confidence 467999999887776664
No 13
>PF02623 FliW: FliW protein; InterPro: IPR003775 The protein BSU35380 from Bacillus subtilis (renamed FliW) was characterised as being a flagellar assembly factor and is involved in Bacterial flagellum biogenesis. Experimental characterisation was also carried out in Treponema pallidum (TP0658). In Campylobacter jejuni, Cj1075 has been shown to be involved in motility and flagellin biosynthesis. The two paralogs in Helicobacter pylori 26695 (HP1154 and HP1377) were found to be able to bind to flagellin. For additional reading see [, , ].; GO: 0009296 flagellum assembly, 0019861 flagellum; PDB: 2AJ7_A.
Probab=21.04 E-value=45 Score=26.66 Aligned_cols=18 Identities=11% Similarity=0.067 Sum_probs=7.2
Q ss_pred EeccCccHHHHHHHHHHH
Q 028024 133 VMSQNISDALKENLAWAT 150 (215)
Q Consensus 133 ~l~~~Lsd~~k~ELAWaS 150 (215)
.+...++++.+++|...+
T Consensus 51 dY~~~l~~~~~~~L~~~~ 68 (121)
T PF02623_consen 51 DYEPELPDEDLAALGIES 68 (121)
T ss_dssp T------HHHHHHTT--S
T ss_pred CCCCCCCHHHHHhcCCCC
Confidence 566778888887776554
Done!