Align Beta-phosphoglucomutase; Beta-PGM; EC 5.4.2.6 (characterized)
to candidate Pf6N2E2_6049 hydrolase, haloacid dehalogenase-like family
Query= SwissProt::O06995 (226 letters) >FitnessBrowser__pseudo6_N2E2:Pf6N2E2_6049 Length = 231 Score = 79.3 bits (194), Expect = 6e-20 Identities = 60/194 (30%), Positives = 90/194 (46%), Gaps = 15/194 (7%) Query: 1 MKAVIFDLDGVITDTAEYHFLAWKHIAEQIDIPFDRDMNERLKGISREESLESILIFGGA 60 +KAVIFD+DG++ DT + IAE+ FD + + + G + ++ Sbjct: 11 IKAVIFDMDGLLLDTEGIYTEVTSIIAERYGRTFDWSVKQNIIGRGATDLANYVV--QAL 68 Query: 61 ETKYTNAEKQELMHRKNRDYQMLISKLTPEDL-LPGIGRLLCQLKNENIKIGLASSSRNA 119 E T E + + L+ + P L +PG L+ LK N+ I + +SS + Sbjct: 69 ELPITPEEFLVIR-------EPLMRERFPHALGMPGAEELVRHLKAHNVPIAVGTSSSSP 121 Query: 120 PKILRRLAIID-----DFHAIVDPTTLAKGKPDPDIFLTAAAMLDVSPADCAAIEDAEAG 174 L+ D DF D + KP PDIFLTAA L V P DC ED+ G Sbjct: 122 TFALKTTLHRDWFALFDFIVTADDPEVGAAKPAPDIFLTAARRLGVDPRDCLVFEDSPFG 181 Query: 175 ISAIKSAGMFAVGV 188 ++A K+AGM A+ + Sbjct: 182 VTAAKAAGMTAIAI 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: 152 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: 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