Align Valine--pyruvate aminotransferase; Alanine--valine transaminase; EC 2.6.1.66 (characterized)
to candidate WP_012334619.1 M446_RS23585 pyridoxal phosphate-dependent aminotransferase
Query= SwissProt::P96847 (388 letters) >NCBI__GCF_000019365.1:WP_012334619.1 Length = 392 Score = 185 bits (469), Expect = 2e-51 Identities = 127/359 (35%), Positives = 184/359 (51%), Gaps = 8/359 (2%) Query: 32 DLVNLSAGQPSAGAPEPVRAAAAAALHLNQLGYSVALGIPELRDAIAADYQRRHGITVEP 91 D++NL GQP P V AA AL GY+ A GI LR+A+A D RR + V P Sbjct: 32 DVINLGIGQPDMPTPPHVVEAAIKALRDGHHGYTPATGILPLREAVARDLHRRLEVEVSP 91 Query: 92 DAVVITTGSSGGFLLAFLACFDAGDRVAMASPGYPCYRNILSALGCEVVEIPCGPQTRFQ 151 D+V+I G A L + G + PG+P YR+++ G V IP F Sbjct: 92 DSVMIVPGGKVTMFAAILMFGEPGAEILYPDPGFPIYRSMIEFTGATPVPIPIREANGFA 151 Query: 152 PTA-QMLAEIDPPLRGVVVASPANPTGTVIPPEEL-AAIASWCDASDVRLISDEVYHGLV 209 +A + LA I P R ++V SPANPTG V P E+ +A DV ++SDE+Y + Sbjct: 152 FSAEETLALISPRTRLLIVNSPANPTGGVTPKAEIDRLVAGLAAHPDVAVLSDEIYGTMT 211 Query: 210 YQGA-PQTSCAWQTSRNAVV-VNSFSKYYAMTGWRLGWLLVPTVLRRAVDCLTGNFTICP 267 Y GA T A+ R+ ++ ++ SK YAMTGWRLGW + P L A L N C Sbjct: 212 YDGARHHTLLAYPEIRDRLIYLDGASKTYAMTGWRLGWSVWPAPLYEAARKLAVNSFSCV 271 Query: 268 PVLSQIAAVSAFTPEATAEADGNLASYAINRSLLLDGLRRI-GIDRLAPTDGAFYVYADV 326 +Q A ++A A A +A + R L+++GL R+ G+ + P GAFY + ++ Sbjct: 272 NAATQWAGIAALDGPQDAVA-AMMAEFDRRRLLVVEGLNRLPGVSCITP-KGAFYAFPNI 329 Query: 327 SDFTSDSLAFCSKLLADTGVAIAPGIDFDTARGGSFVRISFAGPSGDIEEALRRIGSWL 385 + + A S LL + G+A G DF G ++R+S+A + +I AL R+G +L Sbjct: 330 ARTGWKAKALASALLEEAGIAAIGGPDFG-VHGEGYLRLSYANSAENIARALERMGGFL 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: 453 Number of extensions: 27 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: 392 Length adjustment: 31 Effective length of query: 357 Effective length of database: 361 Effective search space: 128877 Effective search space used: 128877 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