Alignments for a candidate for bgl in Derxia gummosa DSM 723

GapMind for catabolism of small carbon sources

Alignments for a candidate for bgl in Derxia gummosa DSM 723

Align β-glucosidase (SalA) (EC 3.2.1.21) (characterized)
to candidate WP_051378274.1 H566_RS23475 glycosyl hydrolase

Query= CAZy::AAF21798.1
         (732 letters)



>NCBI__GCF_000482785.1:WP_051378274.1
          Length = 789

 Score =  843 bits (2179), Expect = 0.0
 Identities = 436/720 (60%), Positives = 528/720 (73%), Gaps = 27/720 (3%)

Query: 21  AGGAMAQAKGAWQNTSLSPDERARLLDAELTLDERISLLHGPMPLPFPGSPPIPEGPSLV 80
           AG A A+    W +  L PDERARLL+AELTLDERI+L+HGPM LPF G P +P+G    
Sbjct: 53  AGDAAARP---WLDAHLPPDERARLLEAELTLDERIALVHGPMALPFAGKP-VPKGALGS 108

Query: 81  PVIFPGVPRLGIPALKETDASLGVTNPMNVRPGDTATALPSGLALASTFNPKLSYDGGAA 140
               PGVPRLGIPAL+ETDASLGV NP +VRPGD ATALPS LALA++F+P+L++D GA 
Sbjct: 109 AGYVPGVPRLGIPALQETDASLGVANPADVRPGDGATALPSSLALAASFDPQLAFDSGAM 168

Query: 141 IAKEAASKGFNVLLAGGANLARDPRNGRNFEYLGEDPLLAGILAGESIRGIQSQNIISTV 200
           I +EA +KGFNVLLAGGANLARDPRNGRNFEYLGEDPLLAG LAGESIRGIQSQ +IST+
Sbjct: 169 IGREARAKGFNVLLAGGANLARDPRNGRNFEYLGEDPLLAGTLAGESIRGIQSQRVISTL 228

Query: 201 KHFSLNGQETNRHWGNSVIDEAAHRESDLLAFQIAIERGQPGSVMCAYNLVNGAYSCGND 260
           KHFSLN QETNR   ++ IDEAAHRESDLLAFQ+A+ERG+PGSVMC YNLVNG ++CGN 
Sbjct: 229 KHFSLNAQETNRQAVDACIDEAAHRESDLLAFQLAVERGRPGSVMCGYNLVNGEHACGNA 288

Query: 261 HLLNKVLKGDWGYKGWVMSDWGAVPATDFALKGLDQQSGQQLDEKIWFGDLLKEAAAAGT 320
           HLLN+VLKGDWGY GWVMSDWGAV A   AL GLDQ+SG+QLD +++FG  LK A  AG 
Sbjct: 289 HLLNRVLKGDWGYPGWVMSDWGAVHAVRDALAGLDQESGEQLDAQVFFGAPLKAAVEAGE 348

Query: 321 IPAERLSDMSRRILRSMFAAGFFDGKP----------------------GKPVVDLDAHA 358
           +P ERLSDM RR+LRSMFA G FD  P                       +  +D  AHA
Sbjct: 349 VPRERLSDMVRRVLRSMFAVGLFDAAPMATNAGGAASSAPATVGAAPACDREPIDRAAHA 408

Query: 359 AIAKQVADEGIVLLANDKGLLPLAAGSQKIAVIGGFADQGVLSGAGSSQVTSVGGNPVVI 418
           A+A++VA EG+VLLAN  GLLPL AG+++IAVIG  AD GV SG GSSQV   GG   V+
Sbjct: 409 AVARKVAAEGMVLLANRDGLLPLGAGTKRIAVIGAHADVGVPSGGGSSQVMPWGGPAAVV 468

Query: 419 PVG-GEGMLAAFLRQAYHNSSPLKALKERLPNATIRFNDGRYSAAAAALARQSDIVILFA 477
           PVG G   + A+ +  +H S+PL AL+ERLP A I F++GRY + AAALAR++D+ ++F 
Sbjct: 469 PVGQGGSWMQAWSKVVWHPSAPLAALRERLPGARIEFDNGRYPSRAAALAREADVAVVFV 528

Query: 478 NQWMSEGMDAYDLKLPQGQDALIEAVAEANPNAVIVLQTGGPVLMPWKDKVGAIVSAWYS 537
            QWM E +DA DL LP+GQDAL+  VA ANPN V+VLQTGGPVLMPW   V A+++AWY+
Sbjct: 529 EQWMIEALDAPDLSLPEGQDALVAEVARANPNTVVVLQTGGPVLMPWLGGVKAVLAAWYA 588

Query: 538 GQKGGEAIADILVGKTNPSGRLPSTFPASADQYPHPEVPGWNLPEKQQFDVVYEEGSDVG 597
           G +GG AIAD+L G  NPSGRLP +FPAS DQ P   +P       ++F V Y EGSDVG
Sbjct: 589 GGEGGAAIADVLTGAVNPSGRLPVSFPASLDQTPRGPLPLREGAPGERFAVEYREGSDVG 648

Query: 598 YRRFAAKGMKPLFPFGHGLSYTTFAYDKLKVKGGETLEVSFQVTNTGKLQGKDAPQIYLA 657
           YR  AA+G KPLF FGHGLSYT F +++L  +GG T+ V   V NTG   G +  Q+Y  
Sbjct: 649 YRWHAARGNKPLFAFGHGLSYTRFVHERLAARGGATVAVELDVVNTGARAGAEVVQLYAE 708

Query: 658 GANGQKLQRLIGFEKIDLKPGERRTVTIKADPRLLARFDEQGHQWRIDGGDYDVVVGRSA 717
            A+G+  +RLIGF +++L  GERR V+I+ADPRLLA FD   + W + GG+  V+V R A
Sbjct: 709 PASGRPGRRLIGFTRVELTSGERRRVSIEADPRLLADFDAAANGWHLRGGERRVLVARDA 768


Lambda     K      H
   0.316    0.135    0.401 

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: 1699
Number of extensions: 79
Number of successful extensions: 5
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 1
Length of query: 732
Length of database: 789
Length adjustment: 40
Effective length of query: 692
Effective length of database: 749
Effective search space:   518308
Effective search space used:   518308
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 (21.6 bits)
S2: 55 (25.8 bits)

This GapMind analysis is from Sep 24 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