GapMind for catabolism of small carbon sources

 

Alignments for a candidate for pgmA in Stenotrophomonas chelatiphaga DSM 21508

Align phosphoglucomutase (alpha-D-glucose-1,6-bisphosphate-dependent) (EC 5.4.2.2) (characterized)
to candidate WP_057508397.1 ABB28_RS09500 phosphomannomutase/phosphoglucomutase

Query= BRENDA::Q8PGN7
         (450 letters)



>NCBI__GCF_001431535.1:WP_057508397.1
          Length = 448

 Score =  756 bits (1951), Expect = 0.0
 Identities = 372/447 (83%), Positives = 404/447 (90%)

Query: 3   MTLPAFKAYDIRGRVPDELNEDLARRIGVALAAQLDQGPVVLGHDVRLASPALQEALSAG 62
           M LPAFKAYDIRGRVPDELNEDLARRIGVAL+ QL+ G VV+GHDVRL S ALQ+AL  G
Sbjct: 1   MPLPAFKAYDIRGRVPDELNEDLARRIGVALSDQLEPGTVVVGHDVRLTSAALQDALVVG 60

Query: 63  LRASGRDVIDIGLCGTEEVYFQTDYLKAAGGVMVTASHNPMDYNGMKLVREQARPISSDT 122
           LR +GR+VIDIGLCGTEEVYFQTD+L AAGGVMVTASHNPMDYNGMKLVRE ARPISSDT
Sbjct: 61  LRGAGREVIDIGLCGTEEVYFQTDHLGAAGGVMVTASHNPMDYNGMKLVRENARPISSDT 120

Query: 123 GLFAIRDTVAADTAAPGEPTASEQSRTDKTAYLEHLLSYVDRSTLKPLKLVVNAGNGGAG 182
           GLFAI D VAADTAA   P A +  + DK+AY+ HLLSYVD + LKPLK+VVNAGNGGAG
Sbjct: 121 GLFAISDAVAADTAAALPPKAGQSEQHDKSAYIAHLLSYVDAAALKPLKVVVNAGNGGAG 180

Query: 183 LIVDLLAPHLPFEFVRVFHEPDGNFPNGIPNPLLPENRDATAKAVKDNGADFGIAWDGDF 242
            IVDLLAPHLP +F+RV HEPDGNFPNGIPNPLLPENR ATA+AV+++GADFGIAWDGDF
Sbjct: 181 AIVDLLAPHLPLQFIRVNHEPDGNFPNGIPNPLLPENRAATAEAVREHGADFGIAWDGDF 240

Query: 243 DRCFFFDHTGRFIEGYYLVGLLAQAILAKQPGGKVVHDPRLTWNTVEQVEEAGGIPVLCK 302
           DRCFFFDHTGRFIEGYYLVGLLAQA L + PGGKVVHDPRL WNTVE VE+AGGIPVLCK
Sbjct: 241 DRCFFFDHTGRFIEGYYLVGLLAQAALKRHPGGKVVHDPRLVWNTVEMVEQAGGIPVLCK 300

Query: 303 SGHAFIKEKMRSENAVYGGEMSAHHYFREFAYADSGMIPWLLIAELVSQSGRSLADLVEA 362
           SGHAFIKEKMR+E+AVYGGEMSAHHYFREFAYADSGMIPWLLIA LVS+SGRSLAD VE 
Sbjct: 301 SGHAFIKEKMRAEDAVYGGEMSAHHYFREFAYADSGMIPWLLIAALVSESGRSLADWVED 360

Query: 363 RMQKFPCSGEINFKVADAKASVARVMEHYASLSPELDYTDGISADFGQWRFNLRSSNTEP 422
           RM  +PCSGEINFKVADAK SVARVMEH+AS +P LD+TDGISADFG WRFNLRSSNTEP
Sbjct: 361 RMAAYPCSGEINFKVADAKVSVARVMEHFASHAPALDHTDGISADFGDWRFNLRSSNTEP 420

Query: 423 LLRLNVETRGDAALLETRTQEISNLLR 449
           LLRLNVETRGDAALL++RT EIS+LL+
Sbjct: 421 LLRLNVETRGDAALLQSRTDEISSLLQ 447


Lambda     K      H
   0.319    0.136    0.404 

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: 702
Number of extensions: 18
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: 450
Length of database: 448
Length adjustment: 33
Effective length of query: 417
Effective length of database: 415
Effective search space:   173055
Effective search space used:   173055
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 51 (24.3 bits)

This GapMind analysis is from Sep 24 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:

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:

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:

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:

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