Alignments for a candidate for bgl in Echinicola vietnamensis KMM 6221, DSM 17526

GapMind for catabolism of small carbon sources

Alignments for a candidate for bgl in Echinicola vietnamensis KMM 6221, DSM 17526

Align β-glucosidase (SCO0458) (EC 3.2.1.21) (characterized)
to candidate Echvi_2412 Echvi_2412 Beta-glucosidase-related glycosidases

Query= CAZy::CAB56688.1
         (762 letters)



>FitnessBrowser__Cola:Echvi_2412
          Length = 799

 Score =  559 bits (1440), Expect = e-163
 Identities = 325/766 (42%), Positives = 444/766 (57%), Gaps = 23/766 (3%)

Query: 4   PLYRDPAAPVPDRVRDLLGRMTLAEKVGQVNQRMYGWDAYERAGDGHRLTDAFRAEVAAF 63
           PLY+    PV  RV DLLGRMTL EKVGQ++  + GW  YE+  D  +++ AF  E    
Sbjct: 35  PLYKQATVPVDQRVEDLLGRMTLEEKVGQLST-LLGWKMYEKRDDHVKVSKAFE-EAVQQ 92

Query: 64  DGMGALYGLQRADAWSGVGFADGLDARDGARTAAAVQRYVMDHTRLGIPVLLVEEMPHGH 123
             +G L+   RAD W+      GL+ +  A    A+Q+YV+++TRLGIP++L EE PHGH
Sbjct: 93  QHIGMLWATLRADPWTQKTLVTGLNPKQAAEATNAMQKYVLENTRLGIPMMLAEECPHGH 152

Query: 124 QALDGTVLPVNLAVGATWDPDLYADAVAGAAAELRARGAHIALVSALDLVRDPRWGRSEE 183
            A+  TV P ++   +TW+P L  +  A  A E R +G HI     LDL R+PRW R EE
Sbjct: 153 MAIGTTVFPTSIGQASTWNPALIQEMAAAIALEARLQGGHIGYGPVLDLAREPRWSRVEE 212

Query: 184 CFSEDPYLAARMTEALVEGARRAGVAV------VLKHFAGQGATVGGRNSAATELGPREL 237
            + EDPY+ ++M  A+V G +   +A        LKHF   G   GG N  +  +G REL
Sbjct: 213 TYGEDPYINSQMGRAMVSGFQGESIASGKNVISTLKHFTAYGVPEGGHNGTSVSVGQREL 272

Query: 238 HEVHLAAARAGVAAGAAGVMAAYNEFDGLPCVANRYLLTDLLRTEWGFEGVVMADGTAVD 297
           HE +L   +A VA GA  VM AYN  DG+PC +N +LL D+LR +WGF G V++D  ++ 
Sbjct: 273 HESYLPPFKAAVAEGALSVMTAYNSIDGVPCTSNGHLLNDVLRDDWGFNGFVVSDLGSIS 332

Query: 298 RLV---RLTGDPVSAGALALDAGCDLSLWDASFTR-LGEAVERGLVSESALDAAVARVLT 353
            L     +T     A  LA++AG D  L    F + L  AV+ G VS+  LD AV RVL 
Sbjct: 333 GLRGSHHVTETAEGAAQLAINAGVDSDLGGYGFGKNLLAAVQAGGVSQEVLDEAVRRVLK 392

Query: 354 LKFRLGLFEQP-LPPARSET-VELPDPAELGERIARASVTLLAHEGGVLPLSRAVRRIAV 411
           +KF +GLFE P + P+++E+ V       L  ++AR SV LL +E  +LPL + V  IAV
Sbjct: 393 VKFDMGLFENPYVDPSKAESLVRSAKHIALARKVARESVVLLKNENDLLPLRKKVNSIAV 452

Query: 412 LGPNADSVAQQIGDYTAPQRPGGGITVLEGIRAAVAAGTEVVHDRGCALVGDDVSGVPAA 471
           +GPNAD+   Q+GDYTAPQ     +TVLEGI+  V     V + +GCA+     S +  A
Sbjct: 453 IGPNADNTYNQLGDYTAPQPNENVVTVLEGIKNKVGKDVRVNYVKGCAIRDTTQSEIGKA 512

Query: 472 VALAAGSDVAVLVLGGSSARSPDTVFDANGAAVTGTGTP----SGMTCGEGVDLADLALP 527
            +LAA SDVAV+VLGGSSAR  DT ++   AA           S M  GEG D   L L 
Sbjct: 513 ASLAARSDVAVVVLGGSSARDFDTEYEETAAAKVSEAEEGQVISDMESGEGFDRMTLDLL 572

Query: 528 PGQRALLTAVSATGTPVVVVLVQGRPHALTELDAPAAAVLSAWYPGPRGGRAVAEVLFGD 587
             Q  L+ AV ATGTPVVVVL++GRP  L  +D    A++ AWYPG  GG A+A+VLFGD
Sbjct: 573 GDQLKLVQAVQATGTPVVVVLIKGRPLNLNWIDEHVPAIVDAWYPGQEGGNAIADVLFGD 632

Query: 588 AEPRGRLPVSVPRSAAQLPVYYNGKDHRYRGYADQSAGPLHAFGHGLSYTSVVYGAPRLS 647
             P GRL +SVPRS  QLPV+YN ++ +   Y + SA PL+AFGHGLSY    Y    ++
Sbjct: 633 YNPSGRLTISVPRSVGQLPVFYNYRNPKRHDYVEGSAEPLYAFGHGLSYADFEYDNLEVT 692

Query: 648 QARVGTRAPRLTCRVTVRNTGSRPAEETVQLYVRRLSGGSSWPRVRELRGFVRLTIAPGE 707
            + +   +P +     V N  +   EE VQLYVR  +G +  P + EL+ F ++ +  GE
Sbjct: 693 ASGM-AGSPTVRVHFQVSNISNVDGEEVVQLYVRDEAGSTVRP-LLELKRFEKVMVPAGE 750

Query: 708 EAEAVFEVDRDTLASVGRDLRLAVEPGLVELETGPASDRTTGVRLE 753
            ++  F +  + L  +G+D+   VEPG  ++  G +S     +RLE
Sbjct: 751 SSKITFMLTAEDLQVLGQDMNWLVEPGSFQVLVGRSS---RDIRLE 793


Lambda     K      H
   0.318    0.135    0.398 

Gapped
Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 1
Number of Hits to DB: 1220
Number of extensions: 50
Number of successful extensions: 9
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 1
Number of HSP's successfully gapped: 1
Length of query: 762
Length of database: 799
Length adjustment: 41
Effective length of query: 721
Effective length of database: 758
Effective search space:   546518
Effective search space used:   546518
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 55 (25.8 bits)

This GapMind analysis is from Apr 09 2024. The underlying query database was built on Sep 17 2021.

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Protein sequences (fasta format)
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About GapMind

Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.

A candidate for a step is "high confidence" if either:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

where "other" refers to the best ublast hit to a sequence that is not annotated as performing this step (and is not "ignored").

Otherwise, a candidate is "medium confidence" if either:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

Other blast hits with at least 50% coverage are "low confidence."

Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).

For more information, see:

the paper from 2019 on GapMind for amino acid biosynthesis
the paper from 2022 on GapMind for carbon sources
the source code
instructions for running GapMind on your computer

If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know

by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory

GapMind for catabolism of small carbon sources