Align Beta-phosphoglucomutase; Beta-PGM; EC 5.4.2.6 (characterized)
to candidate GFF2879 PGA1_c29250 putative haloacid dehalogenase-like hydrolase
Query= SwissProt::P77366 (219 letters) >FitnessBrowser__Phaeo:GFF2879 Length = 222 Score = 54.7 bits (130), Expect = 1e-12 Identities = 56/212 (26%), Positives = 90/212 (42%), Gaps = 22/212 (10%) Query: 6 VIFDLDGVITDTAHLHFQAWQQIAAEIGISIDAQFNESLKGISRDESLRRILQHGGKEGD 65 VIFD DGV+ D+ L Q + G+ + L + + + Q G + Sbjct: 11 VIFDCDGVLVDSETLSNQVLVENLGRHGLQLSLADCMDLFVGGTMQGVMKKAQELGADLP 70 Query: 66 FNSQERAQLAYRKNLLYVHSLRELTVNA-VLPGIRSLLADLRAQQISVGLAS-------- 116 N + +Y + L ++PGI LLA L+A+ I+ +AS Sbjct: 71 ANWVDE---------VYGETYARLRQGVDLVPGIPDLLALLQARGIAFCVASNGSEDKMR 121 Query: 117 VSLNAPTILAALELREFFTFCADASQLKNSKPDPEIFLAACAGLGVPPQACIGIEDAQAG 176 ++L + + F+ A LK KPDP++FLAA V + C+ IED++ G Sbjct: 122 ITLGQNGLWDQFHPQAMFS----AHTLKTGKPDPDLFLAAACHFDVQARDCLVIEDSENG 177 Query: 177 IDAINASGMRSVGIGAGLTGAQLLLPSTESLT 208 A +GMR +G G +L + E +T Sbjct: 178 AIAAARAGMRCLGFDPHGKGTRLKRHNAEHIT 209 Lambda K H 0.320 0.135 0.392 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: 115 Number of extensions: 6 Number of successful extensions: 3 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 219 Length of database: 222 Length adjustment: 22 Effective length of query: 197 Effective length of database: 200 Effective search space: 39400 Effective search space used: 39400 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 (21.8 bits) S2: 45 (21.9 bits)
This GapMind analysis is from Sep 17 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