Align Beta-phosphoglucomutase; Beta-PGM; EC 5.4.2.6 (characterized)
to candidate CA265_RS08325 CA265_RS08325 haloacid dehalogenase
Query= SwissProt::O06995 (226 letters) >FitnessBrowser__Pedo557:CA265_RS08325 Length = 223 Score = 77.4 bits (189), Expect = 2e-19 Identities = 61/185 (32%), Positives = 90/185 (48%), Gaps = 9/185 (4%) Query: 2 KAVIFDLDGVITDTAEYHFLAWKHI-AEQIDIPFDRDMNERLKGISREESLESILIFGGA 60 KA +FDL+G + + EYH LAW I E + D + ++ E LE + FG Sbjct: 9 KAFLFDLNGTMINDMEYHTLAWYSIMTEDLGAKLDYESVKKEMYGKNHEVLERV--FG-- 64 Query: 61 ETKYTNAEKQELMHRKNRDYQMLISKLTPEDLLPGIGRLLCQLKNENIK--IGLASSSRN 118 + K+ E + L K + YQ L L+ G+ L + K +I IG A+ N Sbjct: 65 KDKFNAEEIERLSIDKEKRYQE--GYLPHLALIEGLDVFLERTKQAHIPMAIGSAAIPFN 122 Query: 119 APKILRRLAIIDDFHAIVDPTTLAKGKPDPDIFLTAAAMLDVSPADCAAIEDAEAGISAI 178 ++ L I AIV + KPDP+ FL AAA L+++PA+C EDA G+ + Sbjct: 123 IDFVIDGLNIRHYLDAIVSADDVKTSKPDPETFLKAAAALNIAPANCLVFEDAPKGVESA 182 Query: 179 KSAGM 183 +AGM Sbjct: 183 LNAGM 187 Lambda K H 0.319 0.136 0.390 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: 120 Number of extensions: 6 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: 226 Length of database: 223 Length adjustment: 22 Effective length of query: 204 Effective length of database: 201 Effective search space: 41004 Effective search space used: 41004 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: 46 (22.3 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