Alignments for a candidate for bgl in Pedobacter sp. GW460-11-11-14-LB5

GapMind for catabolism of small carbon sources

Alignments for a candidate for bgl in Pedobacter sp. GW460-11-11-14-LB5

Align β-glucosidase (Bgl;Fbgl;FmBGL) (EC 3.2.1.21) (characterized)
to candidate CA265_RS15320 CA265_RS15320 beta-glucosidase

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



>FitnessBrowser__Pedo557:CA265_RS15320
          Length = 765

 Score =  959 bits (2478), Expect = 0.0
 Identities = 476/720 (66%), Positives = 573/720 (79%), Gaps = 7/720 (0%)

Query: 1   MTLDEKIGQLNLPSSGDFTTGQAQSSDIGKKIEQGLVGGLFNIKGVNKIKAVQKVAIEKS 60
           MT+DEKIGQLNLPSSGD TTGQA SSDI KKI +G VGGLFNIKGV+KIKAVQK+A+E S
Sbjct: 44  MTVDEKIGQLNLPSSGDITTGQANSSDISKKIREGQVGGLFNIKGVDKIKAVQKIAVENS 103

Query: 61  RLKIPMIFGMDVIHGYETTFPIPLGLASSWDMDLIQRSAQIAAKEASADGINWTFSPMVD 120
           R+KIP++FGMDVIHGY T FPIPLG++  WDM+ +Q+SA++AA EASA GINWTFSPMVD
Sbjct: 104 RMKIPLLFGMDVIHGYNTVFPIPLGMSCVWDMNTVQKSARVAAIEASASGINWTFSPMVD 163

Query: 121 VSREPRWGRVSEGSGEDPYLGSEIAKAMVYGYQGKDLSLKNTILACVKHFALYGAPEGGR 180
           +SR+PRWGR+SEGSGED YLGS+IA AMV GYQGK L   N ILACVKH+ALYGA E GR
Sbjct: 164 ISRDPRWGRISEGSGEDAYLGSQIAAAMVKGYQGK-LQATNEILACVKHYALYGAAEAGR 222

Query: 181 DYNTVDMSHIRMFNEYFPPYKAAVDAGVGSVMASFNEVDGVPATGNKWLMDDVLRKQWGF 240
           DYNT DMS +RM+NEYFPPYKAAVDAG  S+MASFNEVDG+PATG+KWLM DVLR QWGF
Sbjct: 223 DYNTTDMSKVRMYNEYFPPYKAAVDAGAASIMASFNEVDGIPATGSKWLMTDVLRNQWGF 282

Query: 241 NGFIVTDYTGINEMIQHGMGDLQQVSALALNAGVDMDMVGEGFLTTLKKSLSEGKVTEQQ 300
            GF+VTDYTGI EMI HGMGDLQ VSALALNAG+DMDMVGEGFL TLKKSL+E KV   Q
Sbjct: 283 KGFVVTDYTGIPEMIAHGMGDLQTVSALALNAGIDMDMVGEGFLGTLKKSLAEKKVGITQ 342

Query: 301 ITLAARRILEAKYDLGLFDDPYRYTDEKRAKAEVFSKPHREEARNIAAQSMVLLKNDKQT 360
           I  A R +L+AKY LGLF DPY++ + +RA+ EVFS  +R+ AR IAA+S VLLKN    
Sbjct: 343 IDRACRLVLQAKYKLGLFADPYKFCNTERAEKEVFSPANRQVAREIAAESFVLLKNKNNV 402

Query: 361 LPLKAGGTVAVIGPLANNNENMTGTWSVASRMKDAVSIMTGLKETV-KGVNFIYAKGSNV 419
           LPLK  GT+ +IGPLA+N  NM GTWSVA+    +V+++ GLK  +      + A+G+N 
Sbjct: 403 LPLKKSGTIGLIGPLADNTANMYGTWSVAALFDQSVTVLQGLKNVIGDKAKILTARGANF 462

Query: 420 FYDAKMEEK-ATMFGKTANRDSRSKEELLKEAVATANKADVVVLAIGETAELSGESSSRA 478
             D+ ME +   +   T  RD R++ E++KEA+  A K+DV+V  IGE +E +GESSS  
Sbjct: 463 LADSTMEHRYVNIHNPTYKRDPRTEAEMIKEALEVAKKSDVIVATIGEGSEFTGESSSVT 522

Query: 479 NIEIPQAQKDLLTELKKTGKPIVMVLFTGRPLVLNDENKQADAIVNAWFAGSEAGYAIAD 538
           +I+IP+ QK+LL  L KTGKP+V+VLFTGRPL LN E +   AI+N WF GSEAG AIAD
Sbjct: 523 DIQIPETQKNLLKALAKTGKPVVLVLFTGRPLALNWEQENIPAILNVWFPGSEAGNAIAD 582

Query: 539 VLYGKVNPSGKLPMTFPRSVGQVPIYYNAKNTGRPLSDERSDKCEFEKFRSNYIDECNTP 598
           VL+G VNPSGKL  TFP++VGQVP+YY  KNTGRPL++ +     FEKFRSNY+D  N P
Sbjct: 583 VLFGDVNPSGKLSTTFPQNVGQVPLYYAHKNTGRPLAEGK----WFEKFRSNYLDVSNDP 638

Query: 599 LFPFGYGLSYTTFNYSDIQLNKTQLSGNDQLTASVTLTNNGKYDGNEVVQLYIRDMVGSV 658
           L+PFG+GLSYT+F YSD++L+   LS    +TASVTL+N GKY+G EVVQLYI+D+VGS+
Sbjct: 639 LYPFGFGLSYTSFTYSDVKLSANTLSKGKSITASVTLSNTGKYEGKEVVQLYIQDLVGSI 698

Query: 659 TRPVKELKGFQKVFLKAGESKIVTFNITPEDLKFYNSALKYDWEPGEFDIMIGTNSHDVK 718
           TRPVKELKGFQK+ LKAGESK +TFNI+  DLKFYN+ LK+  EPG+F + IGTNS DVK
Sbjct: 699 TRPVKELKGFQKINLKAGESKTITFNISENDLKFYNADLKFVAEPGDFKVFIGTNSRDVK 758


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: 1576
Number of extensions: 64
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: 765
Length adjustment: 40
Effective length of query: 686
Effective length of database: 725
Effective search space:   497350
Effective search space used:   497350
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