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 (H1_GH3) (EC 3.2.1.21) (characterized)
to candidate CA265_RS07180 CA265_RS07180 glycosyl hydrolase

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



>FitnessBrowser__Pedo557:CA265_RS07180
          Length = 739

 Score =  758 bits (1958), Expect = 0.0
 Identities = 403/762 (52%), Positives = 525/762 (68%), Gaps = 27/762 (3%)

Query: 1   MRKKVIVMLLLPVMICITSRSMLAGEKPDIRTKVDALLSEMTLDEKIGQLNQYTSRWEMT 60
           MRK + + L+L V     S S +A +K  I  ++D++L  MTLDEKIGQLNQYT   + T
Sbjct: 1   MRKYLPLALILGV-----SLSAVAQDKK-IEKRIDSVLKLMTLDEKIGQLNQYTGDRDAT 54

Query: 61  GPAPQGKGEQELLEMIRKGQVGSMLNVNGAIATRNAQELAVKNSRLGIPLIFGYDVIHGY 120
           GP      +   L+ IR G++GSMLNV GA  TR  QE+A++ SR+ IPLIFG DVIHGY
Sbjct: 55  GPITNNPNK---LKDIRDGKLGSMLNVRGAKETREVQEVAMQ-SRMKIPLIFGLDVIHGY 110

Query: 121 KTMFPIPLATAASWDPSAAELSARTAATETAASGVHWTFAPMVDIARDARWGRIMEGAGE 180
           +  FPIPLA AASWD +  E +AR AA ETAASGVHWTFAPMVDIARD RWGR+MEGAGE
Sbjct: 111 RVTFPIPLAEAASWDLAEMENAARVAARETAASGVHWTFAPMVDIARDPRWGRVMEGAGE 170

Query: 181 DPYLGAQMAAAQVKGFQGNDLSAENTIAACAKHFAAYGFAEAGRDYNTVEITENTLRNVV 240
           D YLG+++A A+VKGFQG  L   + I ACAKHFAAYG A AGRDYN V+++E+TL    
Sbjct: 171 DTYLGSKIAFARVKGFQGKGLGNLDAIMACAKHFAAYGAAIAGRDYNAVDMSEHTLWETY 230

Query: 241 LPPFKACADAGVATFMNAFNEIGGVTATANKHLVRDILKGEWGFSGYVVSDWNSIGEIYE 300
           LPPFKA  DAG ATFMN+FN + G+ AT N +L RDILKG+W + G+VVSDW SIGE+  
Sbjct: 231 LPPFKAAVDAGAATFMNSFNTLNGIPATGNAYLQRDILKGQWKYQGFVVSDWGSIGEMIA 290

Query: 301 HGMTPDKKEAAFLAIKAGSDMDMEGNAYIAHLKELVEEGRVDESMIDDAVRRILTLKFEL 360
           HG   DK++AA LA+KAGSDMDME  +Y+  L +L+ + +V  ++IDDAVRRIL  KFEL
Sbjct: 291 HGYAKDKEQAAELALKAGSDMDMESRSYLPSLAKLLADKKVPVALIDDAVRRILRKKFEL 350

Query: 361 GLFDDPFRYSDPGK-EKILLSEEHLKAARDVAKKSIVLLKNEKQLLPLKKSGQKIALIGD 419
           GLFDDP+R+S+  + EK L S E+ KA+  +A+KSIVLLKNE Q+LPL K  +KIA+IG 
Sbjct: 351 GLFDDPYRFSNESRQEKELNSAENRKASLKMAEKSIVLLKNENQVLPLSKHLKKIAVIGP 410

Query: 420 LADDKDSPLGSWRAQAVAGSAVSLLDGMKNAIQDQRSLTFEQGPVFVTSTPQFTQHLQFN 479
           L   +    G W       + VSL  G+KN + +Q  L + +G              +  
Sbjct: 411 LGKSEKDMQGFWSIAWEKDNLVSLYQGLKNKVGNQTELLYAKG-------------CEVA 457

Query: 480 EKDLTGIDQAVELAEKSDVVVLALGENCFQTGEGRSQTEIGLKGVQQQLLEAVYAANKNM 539
           +    G  +AV +A+++DVV++A+GE    +GE +S+  I + GVQ+ L++A+ A  K +
Sbjct: 458 DSSKAGFAEAVAVAKQADVVIMAVGETLDMSGEAKSKANIHMPGVQEDLIKAIQATGKPV 517

Query: 540 VVVLMNGRPLVIDWMAERVPAIVEAWHLGSEAGNAIADVLFGDYNPSGKLPVSFPRSVGQ 599
           VV++M GRPL+ +W A+ VPAI+  W LGSEAGNA+A+VL+GDYNP+GKLP++FPR  GQ
Sbjct: 518 VVLIMAGRPLIFNWTADHVPAIMNTWWLGSEAGNAMANVLYGDYNPAGKLPMTFPRDEGQ 577

Query: 600 CPIYYNHKNTGRPI--DTGTVFWSHYTDQSNEPLFPFGYGLSYTTFEYADLKLSSSEIRP 657
            P+YYN+ +TGRP   D  T + S Y D  N P F FGYGLSYTTF+Y DL LS ++I+ 
Sbjct: 578 IPLYYNYLSTGRPAKNDKDTRYRSAYLDMPNSPKFAFGYGLSYTTFDYTDLTLSKTQIKQ 637

Query: 658 GEKLKISVNLKNTGKLSGAEVVQLYIRDLYGSVTRPVKELKGFKKISLNPGESRVVEFEI 717
            EK+ +S  LKNTGK +G EVVQLY++D + SV RPVKELK F+K+ L  GE + + F I
Sbjct: 638 DEKITVSFTLKNTGKYAGEEVVQLYLQDKFASVVRPVKELKDFQKVMLTAGERKTITFTI 697

Query: 718 SVRDLAFYTADGEWKAEPGHFHLWVGTNSNE-GLKGGFSLKN 758
               L+FY    +W AE G F L +GT SN   L+  F+L N
Sbjct: 698 DKEKLSFYNQQLKWAAEAGDFKLMIGTASNNIKLEKDFTLLN 739


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: 1454
Number of extensions: 59
Number of successful extensions: 6
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: 739
Length adjustment: 40
Effective length of query: 718
Effective length of database: 699
Effective search space:   501882
Effective search space used:   501882
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.

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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