Align Valine--pyruvate aminotransferase; Alanine--valine transaminase; EC 2.6.1.66 (characterized)
to candidate WP_092481937.1 BM299_RS02765 aminotransferase class I/II-fold pyridoxal phosphate-dependent enzyme
Query= SwissProt::P96847 (388 letters) >NCBI__GCF_900115975.1:WP_092481937.1 Length = 414 Score = 155 bits (393), Expect = 2e-42 Identities = 123/391 (31%), Positives = 188/391 (48%), Gaps = 17/391 (4%) Query: 2 TDRV--ALRAGVPPFYVMDVWLAAAERQRTHGDLVNLSAGQPSAGAPEPVRAAAAAALHL 59 +DR+ A+R+ VPP + + AE T G +++L G+P P +R A +L Sbjct: 7 SDRINPAVRS-VPPSGIRRFFDLVAE---TRG-VISLGVGEPDFVTPWHIREACIYSLEK 61 Query: 60 NQLGYSVALGIPELRDAIAADYQRRHGITVEP-DAVVITTGSSGGFLLAFLACFDAGDRV 118 Y+ G+ ELR+A+AAD +R + + P + ++IT G S LA A GD V Sbjct: 62 GYTMYTSNWGLLELREAVAADLERTYNVKYNPKNEILITVGVSEALDLAMRALLVPGDEV 121 Query: 119 AMASPGYPCYRNILSALGCEVVEIPCGPQTRFQPTA-QMLAEIDPPLRGVVVASPANPTG 177 + P Y Y + G V +P + F+ +A Q+ + I P + +++ P NPTG Sbjct: 122 LIPEPSYVSYAPCTTLAGGVPVFMPTSMENNFRISADQVRSAITPRTKVLLLCYPNNPTG 181 Query: 178 TVIPPEELAAIASWCDASDVRLISDEVYHGLVYQGAPQTSCAWQ---TSRNAVVVNSFSK 234 V+ EELA IA D+ +ISDE+Y L Y G + +C V++N FSK Sbjct: 182 AVMEREELAKIAEVAVEHDLIVISDEIYDRLTYVG--EHTCLASLPGMQERTVLLNGFSK 239 Query: 235 YYAMTGWRLGWLLVPTVLRRAVDCLTGNFTICPPVLSQIAAVSAFTPEATAEADGNLASY 294 YAMTGWR+G+ A+ + +C P+ Q+AA+ A + Y Sbjct: 240 AYAMTGWRVGYAAGNPDFIGAMTKIHQYSMLCTPITGQMAALEAL-KNGQPGMRRMVGHY 298 Query: 295 AINRSLLLDGLRRIGIDRLAPTDGAFYVYADVSDFTSDSLAFCSKLLADTGVAIAPGIDF 354 R L++ R +G+ P GAFY + VS S F +LL VA+ PG F Sbjct: 299 NRRRHLVVQAFRDMGVPCFEP-GGAFYAFPQVSVTGLGSEEFAEELLKQEQVALVPGNAF 357 Query: 355 DTARGGSFVRISFAGPSGDIEEALRRIGSWL 385 + G F R+S+A D+ EA RR+ ++ Sbjct: 358 GRS-GEGFARVSYAASLDDLSEAFRRMARFV 387 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: 407 Number of extensions: 21 Number of successful extensions: 6 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: 414 Length adjustment: 31 Effective length of query: 357 Effective length of database: 383 Effective search space: 136731 Effective search space used: 136731 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