Align Phosphoglycerate mutase (characterized, see rationale)
to candidate WP_106712249.1 CU102_RS16835 histidine phosphatase family protein
Query= uniprot:P72649 (349 letters) >NCBI__GCF_003010955.1:WP_106712249.1 Length = 192 Score = 65.1 bits (157), Expect = 1e-15 Identities = 58/195 (29%), Positives = 89/195 (45%), Gaps = 15/195 (7%) Query: 133 LLLIRHGETQWNREGRFQGIRDIPLNDNGRHQAQKAAEFLKDVPINLGISSPMARPKETA 192 + L+RHGET+W+ G+ G DIPL G A+K A L + + SSP R TA Sbjct: 7 IYLVRHGETEWSASGKHTGRTDIPLTAAGEEAARKLAGRLDGIAYSAVWSSPSQRAANTA 66 Query: 193 EIILQYHPSIELDLQPELAEICHGLWEGKLETEIEAEYPGLLQQWKDAPATVQMPEGENL 252 ++ + P+ E + ELAE +G +EG +I AE P + Q ++D P GE Sbjct: 67 -VLAGFGPATE--KKAELAEWDYGAYEGITTKQILAERP-VWQLFRDG-----CPNGEAA 117 Query: 253 QQVWDRAIACWQDRVKFYSQGDGSTVGIVVAHDAINKVILAYLLGLTPAHFWQVKQGNGG 312 V RA D + + +TV ++ + +V+ A LG H Sbjct: 118 LDVGLRA-----DIIIGQLRSANNTV-LIFSSSHFLRVLAARWLGSPAEHGAHFVLDTAS 171 Query: 313 VSVIDYPQGLDKPPV 327 +SV+ Y L +P + Sbjct: 172 ISVLGYEHDLTEPVI 186 Score = 26.6 bits (57), Expect = 6e-04 Identities = 15/53 (28%), Positives = 24/53 (45%) Query: 54 AAGQTLLIVAHNGINRCLLMSAIGMPASHYQRLQQSNCNINVLNFSGGWGDPV 106 +A T+LI + + R L +G PA H +I+VL + +PV Sbjct: 133 SANNTVLIFSSSHFLRVLAARWLGSPAEHGAHFVLDTASISVLGYEHDLTEPV 185 Lambda K H 0.319 0.136 0.424 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: 209 Number of extensions: 13 Number of successful extensions: 3 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 349 Length of database: 192 Length adjustment: 24 Effective length of query: 325 Effective length of database: 168 Effective search space: 54600 Effective search space used: 54600 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: 47 (22.7 bits)
This GapMind analysis is from Jul 26 2024. The underlying query database was built on Jul 25 2024.
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