Align Valine--pyruvate aminotransferase; Alanine--valine transaminase; EC 2.6.1.66 (characterized)
to candidate WP_143592272.1 B1A74_RS13915 aminotransferase class I/II-fold pyridoxal phosphate-dependent enzyme
Query= SwissProt::P96847 (388 letters) >NCBI__GCF_001995255.1:WP_143592272.1 Length = 227 Score = 133 bits (335), Expect = 4e-36 Identities = 80/210 (38%), Positives = 114/210 (54%), Gaps = 2/210 (0%) Query: 11 VPPFYVMDVWLAAAERQRTHGDLVNLSAGQPSAGAPEPVRAAAAAALHLNQLGYSVALGI 70 V PF VMD+ A +R D+++L G+P P V +A AL + Y+ A G Sbjct: 16 VEPFRVMDILDRAQAAERAGRDIIHLEVGEPDFVTPRGVVSAGEIALAAGETRYTPAHGR 75 Query: 71 PELRDAIAADYQRRHGITVEPDAVVITTGSSGGFLLAFLACFDAGDRVAMASPGYPCYRN 130 +LR AIA DY+ RH V+P+ VV+T+G+S LLA A + G+ V + PGY C R Sbjct: 76 EKLRRAIAQDYRNRHAAEVDPERVVVTSGASAAILLALAAGVNPGEGVLLPDPGYACNRQ 135 Query: 131 ILSALGCEVVEIPCGPQTRFQPTAQMLAEI-DPPLRGVVVASPANPTGTVIPPEELAAIA 189 ++A G + + +QPTA +A R V++ASPANPTGT + E LA I Sbjct: 136 FVAARGARPRPLVVSAEDAWQPTADAVAAAWSDTTRAVLLASPANPTGTCLSRETLAEIV 195 Query: 190 SWCDASDVRLISDEVYHGLVYQGAPQTSCA 219 + +A +I DE+Y LV+ G P+ S A Sbjct: 196 AVVEARGGLVIMDEIYGQLVF-GEPERSAA 224 Lambda K H 0.321 0.136 0.416 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: 263 Number of extensions: 14 Number of successful extensions: 2 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 1 Length of query: 388 Length of database: 227 Length adjustment: 26 Effective length of query: 362 Effective length of database: 201 Effective search space: 72762 Effective search space used: 72762 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 (21.9 bits) S2: 48 (23.1 bits)
This GapMind analysis is from Apr 09 2024. The underlying query database was built on Apr 09 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