Align Valine--pyruvate aminotransferase; Alanine--valine transaminase; EC 2.6.1.66 (characterized)
to candidate YP_004142732.1 Mesci_3562 class I and II aminotransferase
Query= SwissProt::P96847 (388 letters) >NCBI__GCF_000185905.1:YP_004142732.1 Length = 382 Score = 334 bits (857), Expect = 2e-96 Identities = 186/386 (48%), Positives = 241/386 (62%), Gaps = 6/386 (1%) Query: 1 MTDRVALRAGVPPFYVMDVWLAAAERQRTHG-DLVNLSAGQPSAGAPEPVRAAAAAALHL 59 M ++ R V PF+ MD+ LA A R ++ G +V+++ GQPS AP VRAAAA AL Sbjct: 1 MVVSLSRRGNVEPFHAMDI-LAEANRLKSQGVPVVSMAVGQPSDPAPVLVRAAAAKALQD 59 Query: 60 NQLGYSVALGIPELRDAIAADYQRRHGITVEPDAVVITTGSSGGFLLAFLACFDAGDRVA 119 ++GY+ ALG+ LR AIA Y +G+ +EP + +TTGSS F LAFLA FD GDRVA Sbjct: 60 GRIGYTDALGLAGLRKAIAGHYADHYGLEIEPGRIAVTTGSSAAFNLAFLAMFDRGDRVA 119 Query: 120 MASPGYPCYRNILSALGCEVVEIPCGPQTRFQPTAQMLAEIDPPLRGVVVASPANPTGTV 179 +A+PGYP YRNI++ALG EVVEI G A + PL+GV+ ASPANPTG V Sbjct: 120 IAAPGYPAYRNIMAALGIEVVEIELGDAAYLHAGHLEAAHREKPLKGVLFASPANPTGAV 179 Query: 180 IPPEELAAIASWCDASDVRLISDEVYHGLVYQGAPQTSCAWQTSRNAVVVNSFSKYYAMT 239 IP +ELAA+ + +ISDE+YH L Y T+ A+ + V+NSFSKYY MT Sbjct: 180 IPADELAALVRTAQDLGIAVISDEIYHRLAYAAPDTTALAY--GGDVTVINSFSKYYCMT 237 Query: 240 GWRLGWLLVPTVLRRAVDCLTGNFTICPPVLSQIAAVSAFTPEATAEADGNLASYAINRS 299 GWR+GW+++P L R V+ + + I PP LSQIAA+ AF AT E + YA NR Sbjct: 238 GWRIGWMVLPQELVRPVERVAQSLYISPPELSQIAAIEAF--RATEELEAVKGRYAWNRE 295 Query: 300 LLLDGLRRIGIDRLAPTDGAFYVYADVSDFTSDSLAFCSKLLADTGVAIAPGIDFDTARG 359 LLL L +G AP DGAFY + DV+ T+DS+AF K+LA+ VA PG DFDT G Sbjct: 296 LLLKRLPELGFPLAAPMDGAFYAFCDVTRHTNDSMAFARKMLAEAHVAATPGRDFDTQAG 355 Query: 360 GSFVRISFAGPSGDIEEALRRIGSWL 385 +R S+AG D+ EA+ RI WL Sbjct: 356 HRTMRFSYAGSHDDMVEAMVRIERWL 381 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: 443 Number of extensions: 20 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: 382 Length adjustment: 30 Effective length of query: 358 Effective length of database: 352 Effective search space: 126016 Effective search space used: 126016 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