Align beta-Phosphoglucomutase (EC 5.4.2.6) (characterized)
to candidate AO353_00950 AO353_00950 HAD family hydrolase
Query= BRENDA::P71447 (221 letters) >FitnessBrowser__pseudo3_N2E3:AO353_00950 Length = 230 Score = 90.5 bits (223), Expect = 2e-23 Identities = 65/192 (33%), Positives = 100/192 (52%), Gaps = 14/192 (7%) Query: 3 KAVLFDLDGVITDTAEYHFRAWKALAEEIGINGVDRQFNEQLKGVSREDSLQKILDLADK 62 KAV+FD+DG++ DT + + +AE G D + + G D + +++ + Sbjct: 11 KAVIFDMDGLLLDTEGIYTEVTQIIAERYG-RTFDWHIKQNIIGRGAGDLARYVVEALEL 69 Query: 63 KVSAEEFKELAKRKNDNYVKMIQDVSPADVYPGILQLLKDLRSNKIKIALASASKNGPFL 122 +SAEEF + + M + A PG +L++ L++N I IA+ ++S + F Sbjct: 70 PISAEEFLLIREPL------MRERFPRALAMPGARELVQHLKANNIPIAVGTSSSSQSFG 123 Query: 123 LEKMNLTG----YFDAI--ADPAEVAASKPAPDIFIAAAHAVGVAPSESIGLEDSQAGIQ 176 +K L G FD I AD EV A+KPAPDIF+ AA +GVAP + + EDS G+ Sbjct: 124 -QKTTLHGDWFALFDTIVTADDPEVGAAKPAPDIFLIAAQRLGVAPRDCLVFEDSPFGVT 182 Query: 177 AIKDSGALPIGV 188 A K +G I V Sbjct: 183 AAKAAGMTAIAV 194 Lambda K H 0.316 0.135 0.377 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: 113 Number of extensions: 9 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: 221 Length of database: 230 Length adjustment: 22 Effective length of query: 199 Effective length of database: 208 Effective search space: 41392 Effective search space used: 41392 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.6 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