Alignments for a candidate for bgl in Pseudomonas stutzeri RCH2

GapMind for catabolism of small carbon sources

Alignments for a candidate for bgl in Pseudomonas stutzeri RCH2

Align β-glucosidase (BglX) (EC 3.2.1.21) (characterized)
to candidate GFF1538 Psest_1575 Beta-glucosidase-related glycosidases

Query= CAZy::AAA60495.1
         (789 letters)



>FitnessBrowser__psRCH2:GFF1538
          Length = 763

 Score =  891 bits (2302), Expect = 0.0
 Identities = 447/755 (59%), Positives = 575/755 (76%), Gaps = 5/755 (0%)

Query: 39  LQPALADDLFGNHPLTP-EARDAFVTELLKKMTVDEKIGQLRLISVGPDNPKEAIREMIK 97
           L  A++   F   P  P + R A +  LL++MT+ EKIGQLRLIS+G D P+E I E I 
Sbjct: 10  LAGAMSPFAFAAPPALPLDDRQALIETLLERMTLAEKIGQLRLISIGGDMPRERIAEEIA 69

Query: 98  DGQVGAIFNTVTRQDIRAMQDQVMELSRLKIPLFFAYDVLHGQRTVFPISLGLASSFNLD 157
            G++GA FN+VTR D R MQD  +  SRL IP+FFAYDV+HG RT+FPISL LASS++L+
Sbjct: 70  AGRIGATFNSVTRADNRPMQDAALR-SRLGIPIFFAYDVIHGHRTIFPISLALASSWDLE 128

Query: 158 AVKTVGRVSAYEAADDGLNMTWAPMVDVSRDPRWGRASEGFGEDTYLTSTMGKTMVEAMQ 217
           A+   GRVSA EA+ DGL++T+APMVD++RDPRWGR SEGFGED YL S +  T+V A Q
Sbjct: 129 AIALSGRVSAIEASADGLDLTFAPMVDITRDPRWGRTSEGFGEDPYLVSQIAGTLVRAYQ 188

Query: 218 GKSPADRYSVMTSVKHFAAYGAVEGGKEYNTVDMSPQRLFNDYMPPYKAGLDAGSGAVMV 277
           G+  +   SVM SVKHFA YGAVEGG++YN VDMSPQR+  DY+PPY+A +DAG+G VMV
Sbjct: 189 GERLSAADSVMASVKHFALYGAVEGGRDYNVVDMSPQRMHQDYLPPYRAAVDAGAGGVMV 248

Query: 278 ALNSLNGTPATSDSWLLKDVLRDQWGFKGITVSDHGAIKELIKHGTAADPEDAVRVALKS 337
           ALN++NG PA+++ WLL+D+LRD WGF+G+ +SDHGAI EL++HG A D  +A R+A+++
Sbjct: 249 ALNTVNGMPASANRWLLRDLLRDDWGFRGLNISDHGAIDELLRHGVARDGREAARLAIEA 308

Query: 338 GINMSMSDEYYSKYLPGLIKSGKVTMAELDDAARHVLNVKYDMGLFNDPYSHLGPKESDP 397
           GI++SM D  Y + LPGL++ G+V +  +D A   VL  KYD+GLF+DPY  +G    DP
Sbjct: 309 GIDLSMHDSLYLQELPGLVERGEVPIELIDQAVGRVLGAKYDLGLFHDPYRRIGQAADDP 368

Query: 398 VDTNAESRLHRKEAREVARESLVLLKNRLETLPLKKSATIAVVGPLADSKRDVMGSWSAA 457
           V+ NAESRLHR+ AR VAR+SLVLL+N  +TLPL+K ATIA+VGPLADS  D++GSWSAA
Sbjct: 369 VEVNAESRLHRQAARRVARDSLVLLENPEQTLPLRKDATIALVGPLADSHVDMLGSWSAA 428

Query: 458 GVADQSVTVLTGIKNAVGENGKVLYAKGANVTSDKGII---DFLNQYEEAVKVDPRSPQE 514
           GVA Q+VT+  G++ AVG+ G++++A+GA+VT D G+I   +FLN     V +DPR+PQ 
Sbjct: 429 GVAAQTVTLRQGLEAAVGKGGQIIHARGASVTDDAGMIKYLNFLNWDRPEVSLDPRTPQA 488

Query: 515 MIDEAVQTAKQSDVVVAVVGEAQGMAHEASSRTDITIPQSQRDLIAALKATGKPLVLVLM 574
           MIDEAV+ A+++DV+VA VGEA+GM+HE+SSRT + +P SQ+ L+ AL ATGKPLV+VLM
Sbjct: 489 MIDEAVRAAREADVIVAAVGEARGMSHESSSRTSLALPASQQALLEALVATGKPLVVVLM 548

Query: 575 NGRPLALVKEDQQADAILETWFAGTEGGNAIADVLFGDYNPSGKLPMSFPRSVGQIPVYY 634
           NGRPL L    + ADA+LETWFAGTEGG+AIADVLFG +NPSGKLP+SFPRSVGQIP YY
Sbjct: 549 NGRPLQLGWVKEHADAVLETWFAGTEGGHAIADVLFGAHNPSGKLPISFPRSVGQIPTYY 608

Query: 635 SHLNTGRPYNADKPNKYTSRYFDEANGALYPFGYGLSYTTFTVSDVKLSAPTMKRDGKVT 694
           +H   GRPY   +P  YTS+YF+E NGALYPFGYGLSYT F +S  +LS  T+ R  K+ 
Sbjct: 609 NHPRLGRPYVEGRPGNYTSQYFEEPNGALYPFGYGLSYTDFELSKPQLSRRTLNRGQKLE 668

Query: 695 ASVQVTNTGKREGATVVQMYLQDVTASMSRPVKQLKGFEKITLKPGETQTVSFPIDIEAL 754
            SV V NTG R GATVVQ+YLQD+  S  RPVK+LKGF K+ L+PGETQ V F +  E L
Sbjct: 669 VSVTVKNTGARAGATVVQLYLQDLVGSSVRPVKELKGFTKLMLEPGETQLVRFVLGEEDL 728

Query: 755 KFWNQQMKYDAEPGKFNVFIGTDSARVKKGEFELL 789
           KF++ ++ + AEPG+F V +G DS  V    FELL
Sbjct: 729 KFYDARLDHVAEPGEFEVQLGLDSQSVLSERFELL 763


Lambda     K      H
   0.316    0.132    0.380 

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: 1500
Number of extensions: 56
Number of successful extensions: 3
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: 789
Length of database: 763
Length adjustment: 41
Effective length of query: 748
Effective length of database: 722
Effective search space:   540056
Effective search space used:   540056
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 17 2021. The underlying query database was built on Sep 17 2021.

Downloads

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

Related tools

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