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.
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:
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