Alignments for a candidate for bgl in Echinicola vietnamensis KMM 6221, DSM 17526

GapMind for catabolism of small carbon sources

Alignments for a candidate for bgl in Echinicola vietnamensis KMM 6221, DSM 17526

Align β-glucosidase (Bgl;Fbgl;FmBGL) (EC 3.2.1.21) (characterized)
to candidate Echvi_2491 Echvi_2491 Beta-glucosidase-related glycosidases

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



>FitnessBrowser__Cola:Echvi_2491
          Length = 766

 Score = 1006 bits (2602), Expect = 0.0
 Identities = 489/727 (67%), Positives = 602/727 (82%), Gaps = 5/727 (0%)

Query: 1   MTLDEKIGQLNLPSSGDFTTGQAQSSDIGKKIEQGLVGGLFNIKGVNKIKAVQKVAIEKS 60
           MTL+EKIGQLNLP++GDFTTGQA SS+I +KI+ G VGGLFNIK V KI+ VQ+VA+E+S
Sbjct: 44  MTLEEKIGQLNLPAAGDFTTGQASSSNIAEKIKAGKVGGLFNIKTVQKIRDVQRVAVEES 103

Query: 61  RLKIPMIFGMDVIHGYETTFPIPLGLASSWDMDLIQRSAQIAAKEASADGINWTFSPMVD 120
           RL IP++FGMDVIHGYET FPIPLGL+S+WDM+LI++SAQ+AAKEASADGINWTFSPM D
Sbjct: 104 RLGIPLLFGMDVIHGYETIFPIPLGLSSTWDMELIKKSAQLAAKEASADGINWTFSPMTD 163

Query: 121 VSREPRWGRVSEGSGEDPYLGSEIAKAMVYGYQGKDLSLKNTILACVKHFALYGAPEGGR 180
           +SR+PRWGRVSEGSGEDPYLG++IAKAMV GYQG DLSL +T++ACVKHFALYGAPE GR
Sbjct: 164 ISRDPRWGRVSEGSGEDPYLGAQIAKAMVEGYQGDDLSLSHTLMACVKHFALYGAPEAGR 223

Query: 181 DYNTVDMSHIRMFNEYFPPYKAAVDAGVGSVMASFNEVDGVPATGNKWLMDDVLRKQWGF 240
           DYNTVDMS  RM+NEYFPPYKAAVDAGVG+VM +FNEV+G+PA+ NKWLM +VLR QWGF
Sbjct: 224 DYNTVDMSRQRMYNEYFPPYKAAVDAGVGTVMTAFNEVEGIPASANKWLMTEVLRNQWGF 283

Query: 241 NGFIVTDYTGINEMIQHGMGDLQQVSALALNAGVDMDMVGEGFLTTLKKSLSEGKVTEQQ 300
           +GF+VTDYT INEM  HG+GDL+ VSA AL AGVDMDMVGEGFL+TLK SL EG +TE Q
Sbjct: 284 DGFVVTDYTAINEMTAHGIGDLKTVSAKALKAGVDMDMVGEGFLSTLKASLEEGTITETQ 343

Query: 301 ITLAARRILEAKYDLGLFDDPYRYTDEKRAKAEVFSKPHREEARNIAAQSMVLLKNDKQT 360
           I  A RRIL AK+ LGLF+DPYRY D +RA+ E+F+  +R+ +R IAAQS VL+KN+ Q 
Sbjct: 344 IDEACRRILVAKFKLGLFEDPYRYCDAERAETEIFNAENRQLSREIAAQSFVLMKNEGQV 403

Query: 361 LPLKAGGTVAVIGPLANNNENMTGTWSVASRMKDAVSIMTGLKETV-KGVNFIYAKGSNV 419
           LPLK  GT+A+IGP+A+N ENMTGTWSVA R K+++S+  G++  V   V  I A+G+N+
Sbjct: 404 LPLKKTGTIALIGPMADNAENMTGTWSVAGRFKESISLKQGIQHAVGDQVKIIEARGANI 463

Query: 420 FYDAKMEEKATMFGKTANRDSRSKEELLKEAVATANKADVVVLAIGETAELSGESSSRAN 479
             D+ +E + ++FGK   RD R +EEL++EA+  A  ADV+V A+GE+AE+SGESSSR+ 
Sbjct: 464 VADSLLESRVSVFGKPTYRDQRPEEELIEEALEAAKAADVIVAAMGESAEMSGESSSRST 523

Query: 480 IEIPQAQKDLLTELKKTGKPIVMVLFTGRPLVLNDENKQADAIVNAWFAGSEAGYAIADV 539
           IE+P+ Q+ LL  L KTGKP+VMVLF+GRPL +  E +   +I+N WF GSEAG AIADV
Sbjct: 524 IELPENQRRLLKALAKTGKPVVMVLFSGRPLAIQWEAEHIPSILNVWFGGSEAGDAIADV 583

Query: 540 LYGKVNPSGKLPMTFPRSVGQVPIYYNAKNTGRPLSDERSDKCEFEKFRSNYIDECNTPL 599
           L+G+VNPSGKL MTFP++ GQ+P+YYN KNTGRPL + +     F+KFRSN++D  N PL
Sbjct: 584 LFGEVNPSGKLTMTFPQNTGQIPLYYNHKNTGRPLPEGQ----WFQKFRSNFLDVPNAPL 639

Query: 600 FPFGYGLSYTTFNYSDIQLNKTQLSGNDQLTASVTLTNNGKYDGNEVVQLYIRDMVGSVT 659
           FPFGYGLSYT F+Y DI L+  +LSG+  L A++TLTN G++DG EVVQLY+RDMVGS+T
Sbjct: 640 FPFGYGLSYTEFDYGDITLSTEKLSGHQTLYATITLTNAGRFDGKEVVQLYVRDMVGSMT 699

Query: 660 RPVKELKGFQKVFLKAGESKIVTFNITPEDLKFYNSALKYDWEPGEFDIMIGTNSHDVKH 719
           RPVKELKGFQKVFLKAGE+K VTF +T EDLKFYN  L + +EPGEF+IMIGTNSHDV  
Sbjct: 700 RPVKELKGFQKVFLKAGETKEVTFELTQEDLKFYNHDLDFVFEPGEFEIMIGTNSHDVSS 759

Query: 720 AKINWNK 726
            K+NW +
Sbjct: 760 MKVNWEE 766


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: 1582
Number of extensions: 68
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: 726
Length of database: 766
Length adjustment: 40
Effective length of query: 686
Effective length of database: 726
Effective search space:   498036
Effective search space used:   498036
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