Align phosphoglucomutase (alpha-D-glucose-1,6-bisphosphate-dependent) (EC 5.4.2.2) (characterized)
to candidate WP_046009540.1 OLEAN_RS12770 phosphomannomutase/phosphoglucomutase
Query= BRENDA::Q8PGN7 (450 letters) >NCBI__GCF_000967895.1:WP_046009540.1 Length = 452 Score = 564 bits (1453), Expect = e-165 Identities = 273/448 (60%), Positives = 337/448 (75%), Gaps = 2/448 (0%) Query: 5 LPAFKAYDIRGRVPDELNEDLARRIGVALAAQLDQGPVVLGHDVRLASPALQEALSAGLR 64 L FKAYD+RGR+PDELNED+A IG A A L VV+G+D+RL S + + + GLR Sbjct: 5 LACFKAYDVRGRMPDELNEDIAYSIGRAFAQFLKPKTVVVGYDIRLTSKQMCDKVIEGLR 64 Query: 65 ASGRDVIDIGLCGTEEVYFQTDYLKAAGGVMVTASHNPMDYNGMKLVREQARPISSDTGL 124 +G +V++IG+CGTEEVYF T +LKA GG+ VTASHNP DYNGMK VRE +RPIS DTGL Sbjct: 65 DAGSNVLNIGMCGTEEVYFATAHLKADGGICVTASHNPKDYNGMKFVREGSRPISGDTGL 124 Query: 125 FAIRDTVAADT--AAPGEPTASEQSRTDKTAYLEHLLSYVDRSTLKPLKLVVNAGNGGAG 182 I A+ A S + + AY +HLL+YV+ LKPLK+V NAGNGG G Sbjct: 125 KDIEILAHANDFPAVDANERGSVEIVDTRPAYTQHLLTYVEADKLKPLKIVCNAGNGGGG 184 Query: 183 LIVDLLAPHLPFEFVRVFHEPDGNFPNGIPNPLLPENRDATAKAVKDNGADFGIAWDGDF 242 L +D + P LP E+V+V HE DGNFP+G+PNPLL ENR +T KA+ DN AD GIAWDGDF Sbjct: 185 LALDAIEPFLPIEWVKVHHEQDGNFPHGVPNPLLIENRASTIKAIADNKADLGIAWDGDF 244 Query: 243 DRCFFFDHTGRFIEGYYLVGLLAQAILAKQPGGKVVHDPRLTWNTVEQVEEAGGIPVLCK 302 DRCFFFD G FIEGYY+VGLLA+A L K PG +VHDPRLTWNT+E E AGG + K Sbjct: 245 DRCFFFDDKGTFIEGYYIVGLLAEAALLKNPGASIVHDPRLTWNTIEMAEAAGGKAIQSK 304 Query: 303 SGHAFIKEKMRSENAVYGGEMSAHHYFREFAYADSGMIPWLLIAELVSQSGRSLADLVEA 362 +GHAFIKE+MR E+AVYGGEMSAHHYF++F Y DSGMIPWLL+ EL+S++G+SL LVE Sbjct: 305 TGHAFIKERMRLEDAVYGGEMSAHHYFKDFFYCDSGMIPWLLVVELISKTGKSLTQLVEE 364 Query: 363 RMQKFPCSGEINFKVADAKASVARVMEHYASLSPELDYTDGISADFGQWRFNLRSSNTEP 422 RM KFPCSGEIN + DA A++ +V HYAS E+D+TDG+S +FG WRFNLR+SNTEP Sbjct: 365 RMAKFPCSGEINSVLEDAPATLVKVEAHYASSGAEIDHTDGLSMNFGDWRFNLRASNTEP 424 Query: 423 LLRLNVETRGDAALLETRTQEISNLLRG 450 ++RLNVE+RGD AL+E +T E+ L++G Sbjct: 425 VVRLNVESRGDQALMEAKTAELLKLMKG 452 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: 612 Number of extensions: 22 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: 450 Length of database: 452 Length adjustment: 33 Effective length of query: 417 Effective length of database: 419 Effective search space: 174723 Effective search space used: 174723 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