Align phosphoglucomutase (alpha-D-glucose-1,6-bisphosphate-dependent) (EC 5.4.2.2) (characterized)
to candidate WP_072909216.1 BUB13_RS13075 phosphomannomutase
Query= BRENDA::Q8PGN7 (450 letters) >NCBI__GCF_900142125.1:WP_072909216.1 Length = 451 Score = 563 bits (1450), Expect = e-165 Identities = 274/448 (61%), Positives = 338/448 (75%) Query: 3 MTLPAFKAYDIRGRVPDELNEDLARRIGVALAAQLDQGPVVLGHDVRLASPALQEALSAG 62 M + FKAYDIRGR+PD+LNED+A RIG A A L VV+G DVRL+S +L AL+ G Sbjct: 1 MEITCFKAYDIRGRLPDQLNEDVAWRIGRAYAEFLKPKIVVVGRDVRLSSESLTNALAEG 60 Query: 63 LRASGRDVIDIGLCGTEEVYFQTDYLKAAGGVMVTASHNPMDYNGMKLVREQARPISSDT 122 L G DV+DIGLCGTEE+Y T K GG+MVTASHNP+DYNGMKLVRE+++PIS DT Sbjct: 61 LCQGGVDVLDIGLCGTEEIYHATFSQKTDGGIMVTASHNPIDYNGMKLVREESKPISGDT 120 Query: 123 GLFAIRDTVAADTAAPGEPTASEQSRTDKTAYLEHLLSYVDRSTLKPLKLVVNAGNGGAG 182 GL IR P + + + K Y+EHLLSY+D + +KP K+V NAGNG AG Sbjct: 121 GLNDIRALAEKGQFQPVDSPGAVTKVSFKAQYVEHLLSYLDPAAVKPFKVVFNAGNGCAG 180 Query: 183 LIVDLLAPHLPFEFVRVFHEPDGNFPNGIPNPLLPENRDATAKAVKDNGADFGIAWDGDF 242 IVDLL HLP E V++ H+PDG+FPNGIPNPLL ENR T AV N AD GIAWDGDF Sbjct: 181 PIVDLLEKHLPLEVVKICHQPDGSFPNGIPNPLLRENRSITRDAVLANNADLGIAWDGDF 240 Query: 243 DRCFFFDHTGRFIEGYYLVGLLAQAILAKQPGGKVVHDPRLTWNTVEQVEEAGGIPVLCK 302 DRCFFFD G FIEGYY+VGLL++A+L++ PG K++HDPRLTWNT++ V+ AGGIPV K Sbjct: 241 DRCFFFDEKGEFIEGYYIVGLLSEALLSRHPGEKIIHDPRLTWNTIDTVKNAGGIPVQSK 300 Query: 303 SGHAFIKEKMRSENAVYGGEMSAHHYFREFAYADSGMIPWLLIAELVSQSGRSLADLVEA 362 +GHAFIKE+MR ENAVYGGEMSAHHYFREFAY DSGMIPWL++ L+S SG+S+++LV Sbjct: 301 TGHAFIKERMRKENAVYGGEMSAHHYFREFAYCDSGMIPWLMVVALMSSSGKSMSELVAD 360 Query: 363 RMQKFPCSGEINFKVADAKASVARVMEHYASLSPELDYTDGISADFGQWRFNLRSSNTEP 422 + KFP SGEIN +VADA +A + E Y + + ++D+TDG+S D GQWR NLR SNTEP Sbjct: 361 CVAKFPASGEINRRVADASVVIADIKERYQADALDIDFTDGLSLDMGQWRLNLRESNTEP 420 Query: 423 LLRLNVETRGDAALLETRTQEISNLLRG 450 +LRLNVE+RGD +L+E +T E+ L+ G Sbjct: 421 VLRLNVESRGDMSLMEEKTAELLKLIGG 448 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: 639 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: 450 Length of database: 451 Length adjustment: 33 Effective length of query: 417 Effective length of database: 418 Effective search space: 174306 Effective search space used: 174306 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