Align Beta-phosphoglucomutase; Beta-PGM; EC 5.4.2.6 (characterized)
to candidate GFF4129 PS417_21150 HAD family hydrolase
Query= SwissProt::O06995 (226 letters) >FitnessBrowser__WCS417:GFF4129 Length = 229 Score = 80.9 bits (198), Expect = 2e-20 Identities = 67/219 (30%), Positives = 107/219 (48%), Gaps = 19/219 (8%) Query: 1 MKAVIFDLDGVITDTAEYHFLAWKHIAEQIDIPFDRDMNERLKGISREESLESILIFGGA 60 +KAVIFD+DG++ DT + + IAE+ +D + + + G ++ + ++ Sbjct: 11 IKAVIFDMDGLLLDTEGIYTEVTQIIAERYGRTYDWGIKQHIIGRGAQDLADYVV--KAL 68 Query: 61 ETKYTNAEKQELMHRKNRDYQMLISKLTPEDL-LPGIGRLLCQLKNENIKIGLA-SSSRN 118 + T A+ E+ + L+S+ P+ L +PG L+ LK NI I + SSSRN Sbjct: 69 DLPITPAQFLEIR-------EPLMSERFPKALGMPGAEALVRHLKAHNIPIAVGTSSSRN 121 Query: 119 A----PKILRRLAIIDDFHAIVDPTTLAKGKPDPDIFLTAAAMLDVSPADCAAIEDAEAG 174 + + R + D D + KP PDIFLTAA L V+P DC ED+ G Sbjct: 122 SFGHKTTLHREWFGLFDTIVTADDPEVGAAKPAPDIFLTAARRLGVAPEDCLVFEDSPFG 181 Query: 175 ISAIKSAGMFAVGVGQ----GQPMLGADLVVRQTSDLTL 209 ++A K+A M A+ V AD ++R+ +D L Sbjct: 182 VTAAKAAHMTAIAVPDEAMADSKYHHADQIIRKLADFDL 220 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: 151 Number of extensions: 8 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: 229 Length adjustment: 22 Effective length of query: 204 Effective length of database: 207 Effective search space: 42228 Effective search space used: 42228 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