Align Valine--pyruvate aminotransferase; Alanine--valine transaminase; EC 2.6.1.66 (characterized)
to candidate WP_024851889.1 N745_RS0109485 aminotransferase class I/II-fold pyridoxal phosphate-dependent enzyme
Query= SwissProt::P96847 (388 letters) >NCBI__GCF_000526715.1:WP_024851889.1 Length = 405 Score = 222 bits (566), Expect = 1e-62 Identities = 122/379 (32%), Positives = 206/379 (54%), Gaps = 2/379 (0%) Query: 11 VPPFYVMDVWLAAAERQRTHGDLVNLSAGQPSAGAPEPVRAAAAAALHLNQLGYSVALGI 70 V PF+VM + A + +++L G+P + V A A++ + Y+ LG+ Sbjct: 21 VEPFHVMKLLGEAKALEAQGKQMIHLEIGEPDFPSLTCVHDAVTEAINHGKTHYTPTLGL 80 Query: 71 PELRDAIAADYQRRHGITVEPDAVVITTGSSGGFLLAFLACFDAGDRVAMASPGYPCYRN 130 P LR+ ++ Y + V + +++T G+SG L A + D+V + P YPC R Sbjct: 81 PILREKLSQFYHDFYHADVPSERILLTPGASGALHLLLTAIINPSDKVMLCDPTYPCNRE 140 Query: 131 ILSALGCEVVEIPCGPQTRFQPTAQMLAEI-DPPLRGVVVASPANPTGTVIPPEELAAIA 189 ++ L +VV +P ++FQ T +++ + P ++ V+VA+P+NPTGT+I EL +IA Sbjct: 141 FVNLLHGKVVSVPVDESSQFQLTLELIQKHWHPDIKAVMVATPSNPTGTLIEQTELKSIA 200 Query: 190 SWCDASDVRLISDEVYHGLVYQGAPQTSCAWQTSR-NAVVVNSFSKYYAMTGWRLGWLLV 248 + + +V LI DE+Y GLVY+ ++ + + + N +V+NSFSK++ MTGWRLGW++ Sbjct: 201 DFLEEKEVYLIVDEIYQGLVYERPAESILSIRDLQANVIVINSFSKFFGMTGWRLGWIVA 260 Query: 249 PTVLRRAVDCLTGNFTICPPVLSQIAAVSAFTPEATAEADGNLASYAINRSLLLDGLRRI 308 P L +D L N + +Q A+ +A AE + ++ R+ L + + Sbjct: 261 PNFLIPTLDKLAQNLYLAASTPAQYGALRVLENDALAELENRRQTFETRRTQLYEAMIAA 320 Query: 309 GIDRLAPTDGAFYVYADVSDFTSDSLAFCSKLLADTGVAIAPGIDFDTARGGSFVRISFA 368 G + GAFY+Y DVSD T D+ AFC L+ TGV + PG DF R +RI++ Sbjct: 321 GFNIPCKPQGAFYLYWDVSDLTDDAEAFCKALMEHTGVVLTPGRDFGDFRSNHHIRIAYT 380 Query: 369 GPSGDIEEALRRIGSWLPS 387 + ++EA+ +I ++ S Sbjct: 381 VDNAYLKEAVTKIRFFVDS 399 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: 365 Number of extensions: 13 Number of successful extensions: 3 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: 388 Length of database: 405 Length adjustment: 31 Effective length of query: 357 Effective length of database: 374 Effective search space: 133518 Effective search space used: 133518 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: 50 (23.9 bits)
This GapMind analysis is from Apr 10 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