Align Beta-phosphoglucomutase; Beta-PGM; EC 5.4.2.6 (characterized)
to candidate AO356_20805 AO356_20805 HAD family hydrolase
Query= SwissProt::O06995 (226 letters) >FitnessBrowser__pseudo5_N2C3_1:AO356_20805 Length = 231 Score = 78.6 bits (192), Expect = 9e-20 Identities = 60/195 (30%), Positives = 94/195 (48%), Gaps = 17/195 (8%) Query: 1 MKAVIFDLDGVITDTAEYHFLAWKHIAEQIDIPFDRDMNERLKGISREESLESILIFGGA 60 +KAVIFD+DG++ DT + IAE+ FD + + + G + ++ Sbjct: 11 IKAVIFDMDGLLLDTEGIYTEVTSIIAERYGRTFDWSVKQNIIGRGATDLANYVV----- 65 Query: 61 ETKYTNAEKQELMHRKNRDYQMLISKLTPEDL-LPGIGRLLCQLKNENIKIGLASSSRNA 119 + QE + + + L+ + P L +PG L+ LK NI I + +SS ++ Sbjct: 66 QALELPITPQEFLVIR----EPLMRERFPHALGMPGAEELVRHLKAHNIPIAVGTSS-SS 120 Query: 120 PKILRRLAIIDDFHAIVDPTTLAK------GKPDPDIFLTAAAMLDVSPADCAAIEDAEA 173 P + + D+ A+ D A KP PDIFLTAA L V P DC ED+ Sbjct: 121 PTFALKTTLHRDWFALFDCIVTADDPEVGAAKPAPDIFLTAARRLGVEPRDCLVFEDSPF 180 Query: 174 GISAIKSAGMFAVGV 188 G++A K+AGM A+ + Sbjct: 181 GVTAAKAAGMTAIAI 195 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: 7 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: 231 Length adjustment: 23 Effective length of query: 203 Effective length of database: 208 Effective search space: 42224 Effective search space used: 42224 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