Align Valine--pyruvate aminotransferase; Alanine--valine transaminase; EC 2.6.1.66 (characterized)
to candidate WP_068461763.1 APY04_RS08820 pyridoxal phosphate-dependent aminotransferase
Query= SwissProt::P96847 (388 letters) >NCBI__GCF_001541235.1:WP_068461763.1 Length = 400 Score = 142 bits (357), Expect = 2e-38 Identities = 113/386 (29%), Positives = 178/386 (46%), Gaps = 19/386 (4%) Query: 11 VPPFYVMDVWLAAAERQRTHGDLVNLSAGQPSAGAPEPVRAAAAAALHLNQLGYSVALGI 70 + P + V A E + D+++LSAG+P PE ++ AA AL Q Y+ G Sbjct: 11 IQPSATIAVTTKARELKAAGRDVISLSAGEPDFDTPENIKQAAVKALADGQTKYTDVDGT 70 Query: 71 PELRDAIAADYQRRHGITVEPDAVVITTGSSGGFLLAFLACFDAGDRVAMASPGYPCYRN 130 P L+ AI ++R +G+ +P+ + + TG A +A + GD V + +P + Y + Sbjct: 71 PALKAAIVRKFKRENGLEYKPEQISVGTGGKQVIYNALMATLNPGDEVILPAPCWVSYAD 130 Query: 131 ILSALGCEVVEIPCGPQTRFQPTAQML-AEIDPPLRGVVVASPANPTGTVIPPEELAAIA 189 I+ + V + + ++ TA L A I P + ++ SP+NP+G +E+ A+ Sbjct: 131 IVMLADAKPVFVETKLEDGYRLTAAALEAAITPKTKWLIFNSPSNPSGAAYSRDEIKALT 190 Query: 190 S-WCDASDVRLISDEVYHGLVYQGAPQTSCAW---QTSRNAVVVNSFSKYYAMTGWRLGW 245 V +++D++Y L+Y G + A Q + +N SK Y MTGWRLG+ Sbjct: 191 DVLLKHPHVWIMTDDIYEHLLYDGLEFHTIAAVEPQLFDRTLTINGLSKAYCMTGWRLGY 250 Query: 246 LLVPTVLRRAVDCLTGNFTICPPVLSQIAAVSAFTPEATAEADGNLASYAINRSLLLDGL 305 P L A+ L T P ++Q AAV A A N A + R L++ L Sbjct: 251 AGGPVQLINAMRKLQSQSTSNPCSITQAAAVEALDGPQDFIAANN-AKFVERRDLVVSML 309 Query: 306 RRIGIDRLAPTDGAFYVYADVSDFTSDSLA----------FCSKLLADTGVAIAPGIDFD 355 + +GAFYVY + + A F + LL + GVA+ G F Sbjct: 310 NQASGITCPKPEGAFYVYPSCAGVIGKTSASGKKIETDEDFATALLEEEGVAVVHGAAF- 368 Query: 356 TARGGSFVRISFAGPSGDIEEALRRI 381 A +F RIS+A +EEA RRI Sbjct: 369 -AFSPAF-RISYATSKDVLEEACRRI 392 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: 385 Number of extensions: 16 Number of successful extensions: 5 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: 400 Length adjustment: 31 Effective length of query: 357 Effective length of database: 369 Effective search space: 131733 Effective search space used: 131733 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