Align phosphoglucomutase (alpha-D-glucose-1,6-bisphosphate-dependent) (EC 5.4.2.2) (characterized)
to candidate WP_028489260.1 Q394_RS0110510 phosphomannomutase
Query= BRENDA::Q8PGN7 (450 letters) >NCBI__GCF_000621325.1:WP_028489260.1 Length = 454 Score = 529 bits (1362), Expect = e-155 Identities = 266/448 (59%), Positives = 326/448 (72%), Gaps = 7/448 (1%) Query: 5 LPAFKAYDIRGRVPDELNEDLARRIGVALAAQLDQGP-VVLGHDVRLASPALQEALSAGL 63 L FKAYDIRG++ +ELN+D+A RIG A + G VV+G DVRL S L+ AL+ GL Sbjct: 4 LTCFKAYDIRGKLGEELNDDVAYRIGRAYGEFVGSGKRVVVGGDVRLTSETLKLALANGL 63 Query: 64 RASGRDVIDIGLCGTEEVYFQTDYLKAAGGVMVTASHNPMDYNGMKLVREQARPISSDTG 123 + +G DVIDIG+ GTEE+YF T +L GG+ VTASHNPMDYNGMKLVRE +RPIS DTG Sbjct: 64 QDAGVDVIDIGMTGTEEIYFATFHLGVDGGIEVTASHNPMDYNGMKLVREGSRPISGDTG 123 Query: 124 LFAIRDTVAADTAAPGEPTASEQSRTDKTAYLEHLLSYVDRSTLKPLKLVVNAGNGGAGL 183 L I+ + S ++ Y++HLL Y+D +KPL LVVNAGNG AG Sbjct: 124 LKDIQRMAEENNFPAVTQRGSLTQQSCLADYVQHLLGYIDLKAIKPLTLVVNAGNGAAGH 183 Query: 184 IVDLLAP-----HLPFEFVRVFHEPDGNFPNGIPNPLLPENRDATAKAVKDNGADFGIAW 238 +VD L H+P F++V +EPDG FP+GIPNPLLPENR T AV + AD GIAW Sbjct: 184 VVDALEAEFTRLHVPIRFIKVHNEPDGTFPHGIPNPLLPENRADTRDAVLAHNADMGIAW 243 Query: 239 DGDFDRCFFFDHTGRFIEGYYLVGLLAQAILAKQPGGKVVHDPRLTWNTVEQVEEAGGIP 298 DGDFDRCF FD TG FIEGYY+VGLLA+A L PG ++HDPRLTWNTV+ VE AGG P Sbjct: 244 DGDFDRCFLFDETGEFIEGYYIVGLLAEAFLQLHPGSNIIHDPRLTWNTVDVVESAGGKP 303 Query: 299 VLCKSGHAFIKEKMRSENAVYGGEMSAHHYFREFAYADSGMIPWLLIAELVSQSGRSLAD 358 + K+GHAFIKE+MR E+A+YGGEMSAHHYFR+FAY DSGMIPWLL+A+L+S G+SL+ Sbjct: 304 IQSKTGHAFIKERMRLEDAIYGGEMSAHHYFRDFAYCDSGMIPWLLVAQLMSVKGQSLSS 363 Query: 359 LVEARMQKFPCSGEINFKVADAKASVARVMEHYASLSP-ELDYTDGISADFGQWRFNLRS 417 LV R+ KFPCSGEINF V D KA +A V EH+ +L P +D TDG+S +F +WRFNLR Sbjct: 364 LVNERIAKFPCSGEINFHVNDVKACIAAVREHFTALQPLVIDTTDGLSMEFAEWRFNLRG 423 Query: 418 SNTEPLLRLNVETRGDAALLETRTQEIS 445 SNTEP+LRLNVE+R D AL++ + IS Sbjct: 424 SNTEPVLRLNVESRQDMALVQEQVTNIS 451 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: 29 Number of successful extensions: 5 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: 454 Length adjustment: 33 Effective length of query: 417 Effective length of database: 421 Effective search space: 175557 Effective search space used: 175557 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