Alignments for a candidate for bgl in Cupriavidus basilensis 4G11

GapMind for catabolism of small carbon sources

Alignments for a candidate for bgl in Cupriavidus basilensis 4G11

Align β-glucosidase (BglX;STM2166) (EC 3.2.1.21) (characterized)
to candidate RR42_RS26860 RR42_RS26860 beta-D-glucoside glucohydrolase

Query= CAZy::AAL21070.1
         (765 letters)



>FitnessBrowser__Cup4G11:RR42_RS26860
          Length = 762

 Score =  918 bits (2372), Expect = 0.0
 Identities = 451/764 (59%), Positives = 578/764 (75%), Gaps = 7/764 (0%)

Query: 4   LCSVGVAVSLAMQPALAENLFGNHPLTPEARDAFVTDLLKKMTVDEKIGQLRLISVGPDN 63
           L  + ++ SL   P LA    G  P     ++AFV DL+ +MT++EKIGQLRLIS+G D 
Sbjct: 2   LSLLALSASLVCSPVLA----GTAPAATGDKNAFVADLIGRMTLEEKIGQLRLISIGEDM 57

Query: 64  PKEAIREMIKDGQVGAIFNTVTRQDIRQMQDQVMALSRLKIPLFFAYDVVHGQRTVFPIS 123
           P+  + + I  G+VG  FN+VTR+D R MQ   +  SRLKIP+FFAYDVVHG RT+FPIS
Sbjct: 58  PQPQLLKEIAAGRVGGTFNSVTRKDNRPMQQAAVERSRLKIPIFFAYDVVHGHRTIFPIS 117

Query: 124 LGLASSFNLDAVRTVGRVSAYEAADDGLNMTWAPMVDVSRDPRWGRASEGFGEDTYLTSI 183
           LGLASS++++ V    R+SA EA+ DGL+MT+APMVD+SRDPRWGR SEGFGED YL S+
Sbjct: 118 LGLASSWDMETVAQSARISAIEASADGLDMTFAPMVDISRDPRWGRTSEGFGEDPYLVSL 177

Query: 184 MGETMVKAMQGKSPADRYSVMTSVKHFAAYGAVEGGKEYNTVDMSSQRLFNDYMPPYKAG 243
             +  V+  QG S A+  SVM  VKHFA YGAVEGG++YNTVDMS  R++ DY+PPY+AG
Sbjct: 178 CAQASVRGFQGTSLANADSVMAVVKHFALYGAVEGGRDYNTVDMSPLRMYQDYLPPYRAG 237

Query: 244 LDAGSGAVMVALNSLNGTPATSDSWLLKDVLRDEWGFKGITVSDHGAIKELIKHGTAADP 303
           +DAG G VM+ALNS+NG PATS++WLL+D+LR  WGFKGITVSDHGAI EL KHG A D 
Sbjct: 238 VDAGGGGVMIALNSINGVPATSNTWLLRDLLRKTWGFKGITVSDHGAIDELTKHGVAKDA 297

Query: 304 EDAVRVALKAGVDMSMADEYYSKYLPGLIKSGKVTMAELDDATRHVLNVKYDMGLFNDPY 363
            ++ ++A+ AGVDMSM D  Y  +LP L+KSG+V M  +DDA R +L  KYD+GLF DP+
Sbjct: 298 RESAKLAITAGVDMSMHDSAYRDHLPELVKSGEVPMRVIDDAVREILGAKYDLGLFQDPF 357

Query: 364 SHLGPKESDPVDTNAESRLHRKEAREVARESVVLLKNRLETLPLKKSGTIAVVGPLADSQ 423
             +G  E DP D +A  RLHR+ AR  AR+S+VLL+NR  TLPLKKSGT+AVVGPLAD+ 
Sbjct: 358 KRIGAAEQDPADVDAPGRLHREAARAAARQSLVLLENRERTLPLKKSGTVAVVGPLADAP 417

Query: 424 RDVMGSWSAAGVANQSVTVLAGIQNAVGDGAKILYAKGANITNDKGIV---DFLNLYEEA 480
            D MGSWSAAG + Q+VT+L G+++A+G   ++ YA+GAN+T+D G+V   +F+N  +  
Sbjct: 418 IDTMGSWSAAGKSGQTVTLLQGVRDALGGNGRVAYARGANVTDDAGVVRYLNFMNWDKPE 477

Query: 481 VKIDPRSPQAMIDEAVQAAKQADVVVAVVGESQGMAHEASSRTNITIPQSQRDLITALKA 540
           +  D R+P  MI EAV AA+ ADV+V  VGES+GM+HEASSRT +++P SQ  L+ ALK 
Sbjct: 478 IVQDKRAPGDMIAEAVAAARGADVIVVAVGESRGMSHEASSRTTLSLPGSQETLLKALKT 537

Query: 541 TGKPLVLVLMNGRPLALVKEDQQADAILETWFAGTEGGNAIADVLFGDYNPSGKLPISFP 600
           TGKP+V+VLMNGRPL +      ADA+LETW+AGTEGG+AIADVLFGDYNPSGKLP+SFP
Sbjct: 538 TGKPMVVVLMNGRPLTINWVKDNADAVLETWYAGTEGGHAIADVLFGDYNPSGKLPVSFP 597

Query: 601 RSVGQIPVYYSHLNTGRPYNPEKPNKYTSRYFDEANGPLYPFGYGLSYTTFTVSDVTLSS 660
           RS+GQIP YY+ L  GRP+ P +P  YTS+YF+E +GPLYPFGYGLSYT F VS +TLSS
Sbjct: 598 RSLGQIPTYYNQLRIGRPFVPGQPPNYTSQYFEETSGPLYPFGYGLSYTDFGVSGITLSS 657

Query: 661 PTMQRDGKVTASVEVTNTGKREGATVIQMYLQDVTASMSRPVKQLKGFEKITLKPGERKT 720
           PTM R G++ ASV V NTG+R+G TV+Q+Y+QDV AS+ RPVK+LK F K+ LK GE + 
Sbjct: 658 PTMPRGGRIEASVTVKNTGQRDGETVVQLYIQDVAASVVRPVKELKDFHKLMLKAGEERV 717

Query: 721 VSFPIDIEALKFWNQQMKYDAEPGKFNVFIGVDSARVKQGSFEL 764
           V F +D + LKF+N +++Y AEPG+F V IG+DS  V++  F L
Sbjct: 718 VRFSLDEDKLKFFNAKLEYAAEPGEFKVQIGLDSQAVREQGFVL 761


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: 53
Number of successful extensions: 2
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: 765
Length of database: 762
Length adjustment: 40
Effective length of query: 725
Effective length of database: 722
Effective search space:   523450
Effective search space used:   523450
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