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 (SalA) (EC 3.2.1.21) (characterized)
to candidate RR42_RS30175 RR42_RS30175 beta-glucosidase

Query= CAZy::AAF21798.1
         (732 letters)



>FitnessBrowser__Cup4G11:RR42_RS30175
          Length = 708

 Score =  677 bits (1746), Expect = 0.0
 Identities = 360/688 (52%), Positives = 460/688 (66%), Gaps = 7/688 (1%)

Query: 39  PDERARLLDAELTLDERISLLHGPMPLPFPGSPPIPEGPSLVPVI---FPGVPRLGIPAL 95
           PD  AR  +A +T DER S+L+  M   F  S   P  P+ VP +     GVPRLGIP L
Sbjct: 13  PDALARDTEARMTDDERFSMLYSLMVRVFGTSAREPRVPADVPAVAGYVKGVPRLGIPPL 72

Query: 96  KETDASLGVTNPMNVRPGDTATALPSGLALASTFNPKLSYDGGAAIAKEAASKGFNVLLA 155
           K  DASLG+ +     P D ATALP+GLA+ +TFNP L+   G  I KEA ++ FNV L 
Sbjct: 73  KLADASLGLRHTDG--PDDCATALPAGLAIGATFNPSLARTIGNLIGKEARARDFNVALG 130

Query: 156 GGANLARDPRNGRNFEYLGEDPLLAGILAGESIRGIQSQNIISTVKHFSLNGQETNRHWG 215
           GG NL RD RNGRNFEY+ EDPLL+G++  E + G Q + +I+ +KH SLN  ETN+ + 
Sbjct: 131 GGINLVRDVRNGRNFEYISEDPLLSGLIGAEIVSGTQEEGVIAVLKHVSLNASETNKFFL 190

Query: 216 NSVIDEAAHRESDLLAFQIAIERGQPGSVMCAYNLVNGAYSCGNDHLLNKVLKGDWGYKG 275
           +++ID AAHRESDLLAFQIAIE+ QPG++M AYNLVNGAY+CGN  +L + +K   G+KG
Sbjct: 191 DAIIDPAAHRESDLLAFQIAIEKSQPGALMGAYNLVNGAYACGNRAILQETIKDAMGFKG 250

Query: 276 WVMSDWGAVPATDFALKGLDQQSGQQLDEKIWFGDLLKEAAAAGTIPAERLSDMSRRILR 335
           WVMSDW AV   +FAL GLDQ +G QLD++ WF   L++A   G +P ER+SDM RR+LR
Sbjct: 251 WVMSDWLAVYGWEFALSGLDQHAGAQLDKQEWFNGPLRQAYEQGKVPKERISDMVRRMLR 310

Query: 336 SMFAAGFFDGKPGKPVVDLDAHAAIAKQVADEGIVLLANDKGLLPLAAGSQKIAVIGGFA 395
           S +A G    +   PV D  AH A+A Q A EGIVLL N+   LPLAAG Q+IA+IGG+A
Sbjct: 311 SYYAIGIDQQRAAAPV-DFAAHNAVALQAAREGIVLLKNEGQALPLAAGRQRIAIIGGYA 369

Query: 396 DQGVLSGAGSSQVTSVGGNPVVIPVGGEGMLAAFLRQAYHNSSPLKALKERLPNATIRFN 455
             GVLSG GSSQV    G    +P+    +L   + + +  SSPL AL+++LP A I F+
Sbjct: 370 QTGVLSGDGSSQVMPTSGYAAQVPLRSHPLLGTTVMRLF-GSSPLAALRKQLPEAIIEFD 428

Query: 456 DGRYSAAAAALARQSDIVILFANQWMSEGMDAYDLKLPQGQDALIEAVAEANPNAVIVLQ 515
            G + A A A+A+++DIV++FA +  +E  D+ D+ LP GQDALIEAVA  N N ++VLQ
Sbjct: 429 CGAHIADAVAMAKRADIVVMFAYRHEAERFDSPDMTLPFGQDALIEAVANENRNLIVVLQ 488

Query: 516 TGGPVLMPWKDKVGAIVSAWYSGQKGGEAIADILVGKTNPSGRLPSTFPASADQYPHPEV 575
           TG PV MPW+DK  AIV AW+ GQ G +AIA++L GK NPSGRLP +FP    Q PHP +
Sbjct: 489 TGNPVAMPWRDKARAIVQAWFPGQLGAQAIAEVLTGKINPSGRLPISFPFDVGQTPHPTL 548

Query: 576 PGWNLPEKQQFDVVYEEGSDVGYRRFAAKGMKPLFPFGHGLSYTTFAYDKLKVKGGETLE 635
           PG ++       V Y EG++VGYR FA  G +PLF FGHGLSY TFAY  L+V   E+L 
Sbjct: 549 PGSDVELGTPIKVHYHEGAEVGYRWFAKTGRQPLFGFGHGLSYATFAYRDLEVVDAESLT 608

Query: 636 VSFQVTNTGKLQGKDAPQIYLAGANGQKLQRLIGFEKIDLKPGERRTVTIKADPRLLARF 695
           V+F VTNTG  QG D PQ+YL  A G    RL+GFE++ L+PGE   V I ADPRLLA F
Sbjct: 609 VAFTVTNTGARQGDDVPQVYLTDAAGDWRMRLLGFERVSLRPGESARVRITADPRLLACF 668

Query: 696 DEQGHQWRIDGGDYDVVVGRSATMTVLS 723
             +   WR++ G Y + +GRSA    LS
Sbjct: 669 QSELGCWRMEAGQYRIALGRSAQDLELS 696


Lambda     K      H
   0.316    0.135    0.401 

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: 1313
Number of extensions: 57
Number of successful extensions: 5
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: 732
Length of database: 708
Length adjustment: 40
Effective length of query: 692
Effective length of database: 668
Effective search space:   462256
Effective search space used:   462256
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