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 Beta-glucosidase BoGH3A; Glycosyl hydrolase family protein 3A; BoGH3A; EC 3.2.1.21 (characterized)
to candidate 352841 BT3314 thermostable beta-glucosidase B (NCBI ptt file)

Query= SwissProt::A7LXS8
         (747 letters)



>FitnessBrowser__Btheta:352841
          Length = 764

 Score =  830 bits (2144), Expect = 0.0
 Identities = 416/761 (54%), Positives = 538/761 (70%), Gaps = 40/761 (5%)

Query: 16  LSVQTGMVAIAQDKEQTPVYLDDTQPIEVRVQDALNRMTVEEKTRLSYAQGKFSSPGCPR 75
           L +    V    +  QTPVYLD ++PIE RV+DAL+RMT+EEK ++++AQ KFSSPG PR
Sbjct: 10  LGLSIAAVLPTMNMAQTPVYLDTSKPIEERVKDALSRMTLEEKVKMTHAQSKFSSPGVPR 69

Query: 76  LGIPELWMSDGPHGVRAEINWNDWGYAGWTNDSCTAFPALTCLAASWNPLLAAKYGYAIG 135
           LGIPE+W +DGPHG+R E+ W++W  AGWTNDSC A+PALTCL+A+WNP ++  YG +IG
Sbjct: 70  LGIPEVWATDGPHGIRPEVLWDEWDQAGWTNDSCIAYPALTCLSATWNPEMSYLYGKSIG 129

Query: 136 EEARYREKDVLLGPGVNIYRTPLNGRNFEYMGEDPYLASELCVPYIQGVQKNGVAACVKH 195
           EEARYR+KD+LLGPGVNIYRTPLNGRNFEYMGEDPYL+S + VPYI+GVQ+NGVAACVKH
Sbjct: 130 EEARYRKKDILLGPGVNIYRTPLNGRNFEYMGEDPYLSSMMVVPYIKGVQENGVAACVKH 189

Query: 196 YALNNQELWRGHIDVQLSDRALYEIYLPAFKAAVERGKAWSIMGAYN------------K 243
           YALNNQE  R   +V LSDRALYEIYLPAFKAAV+ G AW+IMGAYN             
Sbjct: 190 YALNNQEFNRHTTNVHLSDRALYEIYLPAFKAAVQEGGAWAIMGAYNLYSFSEDTDSGKL 249

Query: 244 VRGTHATHHKLLNNDILKGEWNFDGCVITDWGAAHDTYEAAMYGLDIEMGSYTNGLTSES 303
            +  HA H+K L  DIL+ EW FDG V++DWG  HDT++A   GLD+E GS+TNGL++ +
Sbjct: 250 YKTQHACHNKRLLQDILRKEWGFDGVVVSDWGGVHDTFQAISNGLDMEFGSWTNGLSAGT 309

Query: 304 EFGYDDYYLGKSYLKMVREGKIPMEVVNDKAARVLRLIFRTAMNRRKPFGALTSEEHYRT 363
              YD+YYL   YLK++++G +  + +++K + +LRLIFRT+MN  KPFG+L S EH + 
Sbjct: 310 RNAYDNYYLAHPYLKLIQDGTVGTKELDEKVSNILRLIFRTSMNPHKPFGSLASPEHGQA 369

Query: 364 AYEIATEGIVLLKNGTGKKQPALLPVPQGKYKRILVVGDNATRNLMLGGGSSELKVQKVI 423
             +I  EGIVLL+N     +  +LP+   K ++I V+G+NA + + +GGGSS LKV+  I
Sbjct: 370 GRKIGEEGIVLLQN-----KDNVLPIDLKKARKIAVIGENAIKMMTVGGGSSSLKVKYEI 424

Query: 424 SSLDGIKAKFGD--GVVYAQGYTSGRP------MYGRADVIPQVTVDSLRNDAVEKAMNS 475
           S LDG+K + G    V+Y +GY  G P      +    D+    + D L  +AVE + ++
Sbjct: 425 SPLDGLKNRVGSQAEVLYVRGYV-GDPTGEYNGVQTGQDLKDDRSEDELLAEAVEVSKDA 483

Query: 476 DLVIFVGGLNKNHFQDCEGGDRLSYELPFAQNELIEALLKVNKNLVAVIVSGNAVEMPWV 535
           D VIF GGLNK++ QDCE  DR S  LP+AQ+ +I  L KVNKNL+ V +SGNAV MPWV
Sbjct: 484 DYVIFFGGLNKSNHQDCEDSDRASLGLPYAQDRVIGELAKVNKNLIVVNISGNAVAMPWV 543

Query: 536 KEIPSIVQSWYLGSVGGEALADVLSGEVTPSGKLPFSYPVKLEDCPAHFFGEISYP---- 591
            E+P+IVQ W+LGS  G ALA VL G+  PSGKLPF++P +LED  AH  GE  YP    
Sbjct: 544 NEVPAIVQGWFLGSEAGTALASVLLGDANPSGKLPFTFPARLEDVGAHKLGE--YPGNKE 601

Query: 592 --------GDSIRQEYKEDILVGYRWYDTKKVQPLFPFGYGMSYTTFEYSKPVISAQTMN 643
                   GD+I + Y+EDI VGYRW D +K++PLFPFG+G+SYTTF Y KP    + M 
Sbjct: 602 ELAHSKNNGDTINEIYREDIFVGYRWADKEKIKPLFPFGHGLSYTTFAYGKPSADKKVMT 661

Query: 644 TDGSIDVSVKVKNTGKVAGKEIIQLYIGDEECSVLRPVKELKDFRKVQLLPNEEKEVKFT 703
            D +I  ++ VKNTG   G+E+IQLY+ D++ S+ RPVKELK F+KV+L P EEK V  T
Sbjct: 662 ADDTISFTINVKNTGTREGQEVIQLYVSDKKSSLPRPVKELKGFKKVKLAPGEEKAVTLT 721

Query: 704 IKPEALQFFDDKQRTWVAEPGKFKAYIAASSSDIRGTVTFE 744
           I  +AL FFDD +  W+ EPGKF+A I  SS DI+G V FE
Sbjct: 722 IDKKALSFFDDVKHEWMTEPGKFEAVIGTSSRDIKGIVPFE 762


Lambda     K      H
   0.318    0.136    0.411 

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: 1667
Number of extensions: 68
Number of successful extensions: 5
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: 747
Length of database: 764
Length adjustment: 40
Effective length of query: 707
Effective length of database: 724
Effective search space:   511868
Effective search space used:   511868
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 Sep 17 2021. 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