Alignments for a candidate for bgl in Stenotrophomonas chelatiphaga DSM 21508

GapMind for catabolism of small carbon sources

Alignments for a candidate for bgl in Stenotrophomonas chelatiphaga DSM 21508

Align β-glucosidase (H1_GH3) (EC 3.2.1.21) (characterized)
to candidate WP_057508205.1 ABB28_RS08430 beta-glucosidase

Query= CAZy::AEW47970.1
         (758 letters)



>NCBI__GCF_001431535.1:WP_057508205.1
          Length = 724

 Score =  615 bits (1585), Expect = e-180
 Identities = 336/733 (45%), Positives = 450/733 (61%), Gaps = 25/733 (3%)

Query: 33  KVDALLSEMTLDEKIGQLNQYTSRWEM----TGPAPQGKGEQELLEMIRKGQVGSMLNVN 88
           ++++L+++MT++EK+GQL  +            P        ++L+ +R G+VGS+ N  
Sbjct: 5   RIESLIAQMTVEEKVGQLGVFADMVRPFAPDVNPEANVSNADQVLQQVRDGKVGSLFNGV 64

Query: 89  GAIATRNAQELAVKNSRLGIPLIFGYDVIHGYKTMFPIPLATAASWDPSAAELSARTAAT 148
           GA   R  Q++A++ SRLGIP+I   DVIHG +T+FPIPL  AAS++P  A  +AR  A 
Sbjct: 65  GADLGRRIQQVAIEESRLGIPVILAADVIHGMRTVFPIPLGEAASFEPELARRTARATAV 124

Query: 149 ETAASGVHWTFAPMVDIARDARWGRIMEGAGEDPYLGAQMAAAQVKGFQGNDLSAENTIA 208
           E  A+G+HWT+AP VDIARD RWGR  EGAGED  LG   AAA+V+GFQG+DL A + + 
Sbjct: 125 EATAAGLHWTYAPAVDIARDQRWGRGAEGAGEDVVLGCAFAAARVRGFQGDDLRAHDALL 184

Query: 209 ACAKHFAAYGFAEAGRDYNTVEITENTLRNVVLPPFKACADAGVATFMNAFNEIGGVTAT 268
           A  KHFAAYG   AG +YN V+I+  TLR+V LPPFKA  DAG  T M++FN+I GV A+
Sbjct: 185 ATPKHFAAYGAVMAGMEYNMVDISPQTLRDVHLPPFKAAFDAGAITVMSSFNDINGVPAS 244

Query: 269 ANKHLVRDILKGEWGFSGYVVSDWNSIGEIYEHGMTPDKKEAAFLAIKAGSDMDMEGNAY 328
           AN  L+ DIL+GEW F G V+SD+ +  E+  HG   D ++A   A  AG D+ M+   Y
Sbjct: 245 ANAELLTDILRGEWNFPGVVISDYTADMELVAHGYAADDRDATAKAFTAGLDLSMQSGFY 304

Query: 329 IAHLKELVEEGRVDESMIDDAVRRILTLKFELGLFDDPFRYSDPGKEKILLSEEHLKA-- 386
             HL  LVE G V  +++D+ VRRIL LK  +GLFDDP+R  DP +E       H+ A  
Sbjct: 305 AEHLPGLVESGEVPMAVLDEGVRRILWLKETIGLFDDPYRSLDPARE---ADNSHIAAHE 361

Query: 387 --ARDVAKKSIVLLKNEKQLLPLKKSGQKIALIGDLADDKDSPLGSWRAQAVAGSAVSLL 444
             +RD A++SIVLLKNE+  LPL++ GQKIALIG    D+++  G W         V L 
Sbjct: 362 ALSRDAARRSIVLLKNEQSALPLRRDGQKIALIGPFVQDRENIEGCWTLFGDKSRYVDLE 421

Query: 445 DGMKNAIQDQRSLTFEQGPVFVTSTPQFTQHLQFNEKDLTGIDQAVELAEKSDVVVLALG 504
            G++ AI D+  L    G              +       GI+ AV  A ++DVVVLALG
Sbjct: 422 TGVRAAIGDEALLEVVPG-------------CELESGIAGGIEAAVAAALRADVVVLALG 468

Query: 505 ENCFQTGEGRSQTEIGLKGVQQQLLEAVYAANKNMVVVLMNGRPLVIDWMAERVPAIVEA 564
           E    +GE +S+ EI L   QQ L EAV  A K MVV+L NGR L +        A+   
Sbjct: 469 EPQRYSGEAQSRVEITLPPAQQALAEAVAMAGKPMVVLLRNGRALALQGAVRNAQAVAIT 528

Query: 565 WHLGSEAGNAIADVLFGDYNPSGKLPVSFPRSVGQCPIYYNHKNTGRP-IDTGTVFWSHY 623
           W+LG++ G+A+ADVLFGDYNPS +LPVSFP+  GQ P +YNH  TGRP + T + F + +
Sbjct: 529 WYLGTQTGHAVADVLFGDYNPSARLPVSFPQVSGQQPYFYNHPRTGRPELPTMSEFKARW 588

Query: 624 TDQSNEPLFPFGYGLSYTTFEYADLKLSSSEIRPGEKLKISVNLKNTGKLSGAEVVQLYI 683
            +  NEPL+ FG+G+SYT+F Y   +LSS+ +   + L I+  L NTG ++G EVVQLYI
Sbjct: 589 REIPNEPLYAFGHGISYTSFAYGVPQLSSTRLGWDDTLTITTTLTNTGSVAGEEVVQLYI 648

Query: 684 RDLYGSVTRPVKELKGFKKISLNPGESRVVEFEISVRDLAFYTADGEWKAEPGHFHLWVG 743
            D   S  RPV+ELK F+K+ L PGES  V F +    LAF   DG  +AE G F LWV 
Sbjct: 649 HDRVASRVRPVRELKDFRKVMLQPGESTEVSFSVQRSQLAFTGRDGVLRAEAGLFDLWVC 708

Query: 744 TNSNEGLKGGFSL 756
            ++  G    F L
Sbjct: 709 ASAISGSPVQFEL 721


Lambda     K      H
   0.317    0.134    0.392 

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: 1276
Number of extensions: 58
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: 758
Length of database: 724
Length adjustment: 40
Effective length of query: 718
Effective length of database: 684
Effective search space:   491112
Effective search space used:   491112
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