Alignments for a candidate for bgl in Bacteroides thetaiotaomicron VPI-5482

GapMind for catabolism of small carbon sources

Alignments for a candidate for bgl in Bacteroides thetaiotaomicron VPI-5482

Align β-glucosidase (Bgl;Fbgl;FmBGL) (EC 3.2.1.21) (characterized)
to candidate 351400 BT1872 periplasmic beta-glucosidase precursor (NCBI ptt file)

Query= CAZy::AAB66561.1
         (726 letters)



>FitnessBrowser__Btheta:351400
          Length = 759

 Score =  855 bits (2208), Expect = 0.0
 Identities = 421/719 (58%), Positives = 533/719 (74%), Gaps = 8/719 (1%)

Query: 1   MTLDEKIGQLNLPSSGDFTTGQAQSSDIGKKIEQGLVGGLFNIKGVNKIKAVQKVAIEKS 60
           MT+ EK+GQLNLPS GD  TG   + ++   I +  +GG FN+KG+ KI  +Q++A+E++
Sbjct: 41  MTIREKLGQLNLPSGGDLVTGSVMNCELSDMIRKEEIGGFFNVKGIKKIYDLQRLAVEET 100

Query: 61  RLKIPMIFGMDVIHGYETTFPIPLGLASSWDMDLIQRSAQIAAKEASADGINWTFSPMVD 120
           RLKIP+I G DVIHGYET FPIPL L+ SWD   IQR A+I+A EASADGI WTFSPMVD
Sbjct: 101 RLKIPLIVGADVIHGYETIFPIPLALSCSWDTLAIQRMARISAIEASADGICWTFSPMVD 160

Query: 121 VSREPRWGRVSEGSGEDPYLGSEIAKAMVYGYQGKDLSLKNTILACVKHFALYGAPEGGR 180
           + R+ RWGR++EGSGEDPYL S +AKA V+GYQG  +  K+ IL+CVKHFALYGA E G+
Sbjct: 161 ICRDARWGRIAEGSGEDPYLASLLAKAYVHGYQGDSMQGKDEILSCVKHFALYGASEAGK 220

Query: 181 DYNTVDMSHIRMFNEYFPPYKAAVDAGVGSVMASFNEVDGVPATGNKWLMDDVLRKQWGF 240
           DYNTVDMSH+RM+NEYF PY+AAV+AGVGSVM+SFN VDG+PAT NKWL+ DVLR +WGF
Sbjct: 221 DYNTVDMSHLRMYNEYFAPYRAAVEAGVGSVMSSFNIVDGIPATANKWLLTDVLRDEWGF 280

Query: 241 NGFIVTDYTGINEMIQHGMGDLQQVSALALNAGVDMDMVGEGFLTTLKKSLSEGKVTEQQ 300
            G +VTDY  I EM  HG+  L++ S  AL AG DMDMV  GFL TL++SL EGKVTE Q
Sbjct: 281 QGLLVTDYNSIAEMSIHGVAPLKEASVRALQAGTDMDMVSCGFLNTLEESLKEGKVTEAQ 340

Query: 301 ITLAARRILEAKYDLGLFDDPYRYTDEKRAKAEVFSKPHREEARNIAAQSMVLLKNDKQT 360
           I  A RR+LEAKY LGLF DPY+Y D  RA+ E+++  HR  AR +AA++ VLLKN+   
Sbjct: 341 IDAACRRVLEAKYKLGLFADPYKYCDTLRAEKELYTPEHRAVAREVAAETFVLLKNENHL 400

Query: 361 LPLKAGGTVAVIGPLANNNENMTGTWSVASRMKDAVSIMTGLKETV-KGVNFIYAKGSNV 419
           LPL+  G +A+IGP+A+   NM G WS+        +++ G++  V      +YAKGSNV
Sbjct: 401 LPLEEKGKIALIGPMADARNNMCGMWSMTCTPSRHGTLLEGIRSAVGDKAEILYAKGSNV 460

Query: 420 FYDAKMEEKATMFGKTANRDSRSKEELLKEAVATANKADVVVLAIGETAELSGESSSRAN 479
           +YDA+ME+ A         +  + ++LL EA+ TA +ADV+V A+GE AE+SGES SR N
Sbjct: 461 YYDAEMEKGAVGIRPL---ERGNDQQLLAEALRTAARADVIVAAVGECAEMSGESPSRTN 517

Query: 480 IEIPQAQKDLLTELKKTGKPIVMVLFTGRPLVLNDENKQADAIVNAWFAGSEAGYAIADV 539
           +EIP AQ+DLL  L KTGKP+V++LFTGRPL+LN E++   +I+N WF GSE G A+ADV
Sbjct: 518 LEIPDAQQDLLKALVKTGKPVVLLLFTGRPLILNWESEHIPSILNVWFGGSETGDAVADV 577

Query: 540 LYGKVNPSGKLPMTFPRSVGQVPIYYNAKNTGRPLSDERSDKCEFEKFRSNYIDECNTPL 599
           L+GK  P GKL  TFPRSVGQ+P++YN  NTGRP  D R     F ++ SNY+DE N PL
Sbjct: 578 LFGKAVPCGKLTTTFPRSVGQLPLFYNHLNTGRPDPDNR----VFNRYASNYLDESNEPL 633

Query: 600 FPFGYGLSYTTFNYSDIQLNKTQLSGNDQLTASVTLTNNGKYDGNEVVQLYIRDMVGSVT 659
           +PFGYGLSYT F Y D+QL+   L  N  LTASVT+TN G +DG E VQ+Y+RD+   V 
Sbjct: 634 YPFGYGLSYTDFVYGDLQLSSETLPKNGNLTASVTVTNKGNHDGYETVQIYLRDIYAEVA 693

Query: 660 RPVKELKGFQKVFLKAGESKIVTFNITPEDLKFYNSALKYDWEPGEFDIMIGTNSHDVK 718
           RPVKELKGF ++FLK GES+ V F +T +DLKFYNS L+Y +EPGEFD+MIGTNS DV+
Sbjct: 694 RPVKELKGFDRIFLKKGESREVKFVLTEDDLKFYNSGLQYIYEPGEFDVMIGTNSRDVQ 752


Lambda     K      H
   0.315    0.133    0.383 

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: 1458
Number of extensions: 53
Number of successful extensions: 4
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: 726
Length of database: 759
Length adjustment: 40
Effective length of query: 686
Effective length of database: 719
Effective search space:   493234
Effective search space used:   493234
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 (21.5 bits)
S2: 55 (25.8 bits)

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

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Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

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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