Align Beta-phosphoglucomutase; Beta-PGM; EC 5.4.2.6 (characterized)
to candidate 7024893 Shewana3_2067 HAD family hydrolase (RefSeq)
Query= SwissProt::P77366 (219 letters) >FitnessBrowser__ANA3:7024893 Length = 202 Score = 87.0 bits (214), Expect = 2e-22 Identities = 61/198 (30%), Positives = 95/198 (47%), Gaps = 15/198 (7%) Query: 2 KLQGVIFDLDGVITDTAHLHFQAWQQIAAEIGISIDAQFNESLKGISRDESLRRILQHGG 61 + G+IFD+DG + D+ LH QAW+Q GI ++ SL G+ +L ++ H G Sbjct: 4 EFDGIIFDMDGTLVDSGQLHEQAWRQTLNHFGIPVEPALMRSLAGVPTIGTLEILIAHFG 63 Query: 62 KEGDFNSQERAQLAYRKNLLYVHSLRELTVNAVLPGIRSLLADLRAQQ-----ISVGLAS 116 + + A Y++ L+ R+ V P + LA+ Q ++VG + Sbjct: 64 VTPTASCE--AMNEYKEALV-----RDTMHLYVKP---TALAEFAKQNQGKRPMAVGTGA 113 Query: 117 VSLNAPTILAALELREFFTFCADASQLKNSKPDPEIFLAACAGLGVPPQACIGIEDAQAG 176 + A IL L E + A Q+ + KP P+ FL +G+ P+ CI EDA+AG Sbjct: 114 YTEEAIQILTLCGLLELVDYVVGADQVASPKPAPDTFLRCAELMGIAPERCIVFEDAKAG 173 Query: 177 IDAINASGMRSVGIGAGL 194 I A A+GM V + A L Sbjct: 174 IQAAEAAGMFVVDVHAEL 191 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: 106 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: 219 Length of database: 202 Length adjustment: 21 Effective length of query: 198 Effective length of database: 181 Effective search space: 35838 Effective search space used: 35838 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