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 353094 BT3567 periplasmic beta-glucosidase precursor (NCBI ptt file)

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



>FitnessBrowser__Btheta:353094
          Length = 771

 Score =  964 bits (2491), Expect = 0.0
 Identities = 475/732 (64%), Positives = 584/732 (79%), Gaps = 15/732 (2%)

Query: 1   MTLDEKIGQLNLPSSGDFTTGQAQSSDIGKKIEQGLVGGLFNIKGVNKIKAVQKVAIEKS 60
           MT++EKIGQLNLP +G+ TTGQA+SSDI  KI++G VGGLFN+KGV KI+ VQK A+E+S
Sbjct: 40  MTVEEKIGQLNLPVTGEITTGQAKSSDIAAKIKRGEVGGLFNLKGVEKIRDVQKQAVEQS 99

Query: 61  RLKIPMIFGMDVIHGYETTFPIPLGLASSWDMDLIQRSAQIAAKEASADGINWTFSPMVD 120
           RL IP++FGMDVIHGYET FPIPLGL+ +WDM  I+ SA+IAA EASADGI+WTFSPMVD
Sbjct: 100 RLGIPLLFGMDVIHGYETMFPIPLGLSCTWDMTAIEESARIAAIEASADGISWTFSPMVD 159

Query: 121 VSREPRWGRVSEGSGEDPYLGSEIAKAMVYGYQGKDLSLKNTILACVKHFALYGAPEGGR 180
           +SR+PRWGRVSEGSGEDP+LG+ IA+AMV GYQGKD+   + I+ACVKHFALYGA EGGR
Sbjct: 160 ISRDPRWGRVSEGSGEDPFLGAMIAEAMVLGYQGKDMQRNDEIMACVKHFALYGAGEGGR 219

Query: 181 DYNTVDMSHIRMFNEYFPPYKAAVDAGVGSVMASFNEVDGVPATGNKWLMDDVLRKQWGF 240
           DYNTVDMS  RMFNEY  PY+AAV+AGVGSVMASFNEVDGVPAT NKWLM DVLR QWGF
Sbjct: 220 DYNTVDMSRQRMFNEYMLPYEAAVEAGVGSVMASFNEVDGVPATANKWLMTDVLRGQWGF 279

Query: 241 NGFIVTDYTGINEMIQHGMGDLQQVSALALNAGVDMDMVGEGFLTTLKKSLSEGKVTEQQ 300
           NGF+VTDYTGI+EMI HG+GDLQ VSA A+NAGVDMDMV EGF++TLKKS+ EGKV+ + 
Sbjct: 280 NGFVVTDYTGISEMIDHGIGDLQTVSARAINAGVDMDMVSEGFVSTLKKSIQEGKVSMET 339

Query: 301 ITLAARRILEAKYDLGLFDDPYRYTDEKRAKAEVFSKPHREEARNIAAQSMVLLKNDKQT 360
           +  A RRILEAKY LGLFD+PY+Y D KR   ++F+K HR+ AR IAA+S VLLKND  T
Sbjct: 340 LNTACRRILEAKYKLGLFDNPYKYCDLKRPARDIFTKAHRDAARRIAAESFVLLKNDNVT 399

Query: 361 ----------LPLKAGGTVAVIGPLANNNENMTGTWSVASRMKDAVSIMTGLKETVKG-V 409
                     LP    G +AVIGPLA++  NM GTWSVA+ +    S++ GLKE   G  
Sbjct: 400 LRPGTPAEPLLPFNPKGNIAVIGPLADSRTNMPGTWSVAAVLDRCPSLVEGLKEMTAGKA 459

Query: 410 NFIYAKGSNVFYDAKMEEKATMFGKTANRDSRSKEELLKEAVATANKADVVVLAIGETAE 469
           N +YAKGSN+  DA  EE+ATMFG++ NRD+R+ E+LL EA+  AN++D+++ A+GE++E
Sbjct: 460 NILYAKGSNLISDASYEERATMFGRSLNRDNRTDEQLLNEALTVANQSDIIIAALGESSE 519

Query: 470 LSGESSSRANIEIPQAQKDLLTELKKTGKPIVMVLFTGRPLVLNDENKQADAIVNAWFAG 529
           +SGESSSR ++ IP  Q++LL EL KTGKP+V+VLFTGRPL L  E +   AI+N WF G
Sbjct: 520 MSGESSSRTDLNIPDVQQNLLKELLKTGKPVVLVLFTGRPLTLTWEQEHVPAILNVWFGG 579

Query: 530 SEAGYAIADVLYGKVNPSGKLPMTFPRSVGQVPIYYNAKNTGRPLSDERSDKCEFEKFRS 589
           SEA YAI D L+G VNP GKL M+FP++VGQ+P+YY  KNTGRPL+  +     FEKFRS
Sbjct: 580 SEAAYAIGDALFGYVNPGGKLTMSFPKNVGQIPLYYAHKNTGRPLAQGK----WFEKFRS 635

Query: 590 NYIDECNTPLFPFGYGLSYTTFNYSDIQLNKTQLSGNDQLTASVTLTNNGKYDGNEVVQL 649
           NY+D  N PL+PFGYGLSYTTF+Y DI L+++ +    +LTA+V +TN G + G+EVVQL
Sbjct: 636 NYLDVDNEPLYPFGYGLSYTTFSYGDIDLSRSTIDMTGELTAAVMVTNTGTWPGSEVVQL 695

Query: 650 YIRDMVGSVTRPVKELKGFQKVFLKAGESKIVTFNITPEDLKFYNSALKYDWEPGEFDIM 709
           YIRD+VGS TRPVKELKGFQK+FL+ G+S+IV F I PE L++YN  L+   EPGEF++M
Sbjct: 696 YIRDLVGSTTRPVKELKGFQKIFLEPGQSEIVRFKIAPEMLRYYNYDLQLVAEPGEFEVM 755

Query: 710 IGTNSHDVKHAK 721
           IGTNS DVK A+
Sbjct: 756 IGTNSRDVKSAR 767


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: 1522
Number of extensions: 69
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: 771
Length adjustment: 40
Effective length of query: 686
Effective length of database: 731
Effective search space:   501466
Effective search space used:   501466
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