Aligments for a candidate for bglG in Escherichia coli BW25113

GapMind for catabolism of small carbon sources

Aligments for a candidate for bglG in Escherichia coli BW25113

Align PTS system arbutin-, cellobiose-, and salicin-specific EIIBC component; EIIBC-Asc; EII-Asc; EC 2.7.1.- (characterized)
to candidate 1936841 b2715 fused cellobiose/arbutin/salicin-specific PTS enzymes: IIB component/IC component (NCBI)

Query= SwissProt::P24241
         (485 letters)



>lcl|FitnessBrowser__Keio:1936841 b2715 fused
           cellobiose/arbutin/salicin-specific PTS enzymes: IIB
           component/IC component (NCBI)
          Length = 485

 Score =  930 bits (2404), Expect = 0.0
 Identities = 485/485 (100%), Positives = 485/485 (100%)

Query: 1   MAKNYAALARSVIAALGGVDNISAVTHCMTRLRFVIKDDALIDSPTLKTIPGVLGVVRSD 60
           MAKNYAALARSVIAALGGVDNISAVTHCMTRLRFVIKDDALIDSPTLKTIPGVLGVVRSD
Sbjct: 1   MAKNYAALARSVIAALGGVDNISAVTHCMTRLRFVIKDDALIDSPTLKTIPGVLGVVRSD 60

Query: 61  NQCQVIIGNTVSQAFQEVVSLLPGDMQPAQPVGKPKLTLRRIGAGILDALIGTMSPLIPA 120
           NQCQVIIGNTVSQAFQEVVSLLPGDMQPAQPVGKPKLTLRRIGAGILDALIGTMSPLIPA
Sbjct: 61  NQCQVIIGNTVSQAFQEVVSLLPGDMQPAQPVGKPKLTLRRIGAGILDALIGTMSPLIPA 120

Query: 121 IIGGSMVKLLAMILEMSGVLTKGSPTLTILNVIGDGAFFFLPLMVAASAAIKFKTNMSLA 180
           IIGGSMVKLLAMILEMSGVLTKGSPTLTILNVIGDGAFFFLPLMVAASAAIKFKTNMSLA
Sbjct: 121 IIGGSMVKLLAMILEMSGVLTKGSPTLTILNVIGDGAFFFLPLMVAASAAIKFKTNMSLA 180

Query: 181 IAIAGVLVHPSFIELMAKAAQGEHVEFALIPVTAVKYTYTVIPALVMTWCLSYIERWVDS 240
           IAIAGVLVHPSFIELMAKAAQGEHVEFALIPVTAVKYTYTVIPALVMTWCLSYIERWVDS
Sbjct: 181 IAIAGVLVHPSFIELMAKAAQGEHVEFALIPVTAVKYTYTVIPALVMTWCLSYIERWVDS 240

Query: 241 ITPAVTKNFLKPMLIVLIAAPLAILLIGPIGIWIGSAISALVYTIHGYLGWLSVAIMGAL 300
           ITPAVTKNFLKPMLIVLIAAPLAILLIGPIGIWIGSAISALVYTIHGYLGWLSVAIMGAL
Sbjct: 241 ITPAVTKNFLKPMLIVLIAAPLAILLIGPIGIWIGSAISALVYTIHGYLGWLSVAIMGAL 300

Query: 301 WPLLVMTGMHRVFTPTIIQTIAETGKEGMVMPSEIGANLSLGGSSLAVAWKTKNPELRQT 360
           WPLLVMTGMHRVFTPTIIQTIAETGKEGMVMPSEIGANLSLGGSSLAVAWKTKNPELRQT
Sbjct: 301 WPLLVMTGMHRVFTPTIIQTIAETGKEGMVMPSEIGANLSLGGSSLAVAWKTKNPELRQT 360

Query: 361 ALAAAASAIMAGISEPALYGVAIRLKRPLIASLISGFICGAVAGMAGLASHSMAAPGLFT 420
           ALAAAASAIMAGISEPALYGVAIRLKRPLIASLISGFICGAVAGMAGLASHSMAAPGLFT
Sbjct: 361 ALAAAASAIMAGISEPALYGVAIRLKRPLIASLISGFICGAVAGMAGLASHSMAAPGLFT 420

Query: 421 SVQFFDPANPMSIVWVFAVMALAVVLSFILTLLLGFEDIPVEEAAAQARKYQSVQPTVAK 480
           SVQFFDPANPMSIVWVFAVMALAVVLSFILTLLLGFEDIPVEEAAAQARKYQSVQPTVAK
Sbjct: 421 SVQFFDPANPMSIVWVFAVMALAVVLSFILTLLLGFEDIPVEEAAAQARKYQSVQPTVAK 480

Query: 481 EVSLN 485
           EVSLN
Sbjct: 481 EVSLN 485


Lambda     K      H
   0.324    0.137    0.397 

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: 975
Number of extensions: 23
Number of successful extensions: 1
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: 485
Length of database: 485
Length adjustment: 34
Effective length of query: 451
Effective length of database: 451
Effective search space:   203401
Effective search space used:   203401
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.5 bits)
S2: 52 (24.6 bits)

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

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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, or view the source code.

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