Align Valine--pyruvate aminotransferase; Alanine--valine transaminase; EC 2.6.1.66 (characterized)
to candidate WP_057506846.1 ABB28_RS01035 pyridoxal phosphate-dependent aminotransferase
Query= SwissProt::P96847 (388 letters) >NCBI__GCF_001431535.1:WP_057506846.1 Length = 382 Score = 134 bits (338), Expect = 3e-36 Identities = 108/361 (29%), Positives = 159/361 (44%), Gaps = 15/361 (4%) Query: 30 HGDLVNLSAGQPSAGAPEPVRAAAAAALHLNQLGYSVALGIPELRDAIAADYQRRHGITV 89 HG VNL G P AP+ + A AA+ Y G+ LR AIA +G V Sbjct: 25 HG-AVNLGQGFPDFSAPQRLIDATTAAMADGLNQYPPMTGVAPLRQAIAQKSLDLYGAQV 83 Query: 90 EPDA-VVITTGSSGGFLLAFLACFDAGDRVAMASPGYPCYRNILSALGCEVVEIPCGPQT 148 +PD + +T+G++ A A AG+ V + P Y CY + G V +P PQT Sbjct: 84 DPDTEITVTSGATEAIFNAIHAVVRAGEEVIVLDPAYDCYEPAIDLAGARAVHVPLDPQT 143 Query: 149 RFQPTAQMLAEIDPPLRGVVVASPANPTGTVIPPEELAAIASWCDASDVRLISDEVYHGL 208 ++ A I P R ++V +P NP+G ++ +L A+A +D+ LISDEVY + Sbjct: 144 FAVDWDRVRAAITPRTRLLMVNTPHNPSGAMLAEADLQALADLLRGTDIYLISDEVYEHI 203 Query: 209 VYQGAPQTSCAW--QTSRNAVVVNSFSKYYAMTGWRLGWLLVPTVLRRAVDCL--TGNFT 264 +Y G S + A V++SF K Y TGW++G+ + P L + FT Sbjct: 204 IYDGRRHESALRHPELRARAFVISSFGKTYHCTGWKIGYAIAPPALSAEFRKVHQYNTFT 263 Query: 265 ICPPVLSQIAAVSAFTPEATAEADGNLASYAINRSLLLDGLRRIGIDRLAPTDGAFYV-- 322 P AA+ P+ E A Y R + L + + LA G F + Sbjct: 264 SFGPAQYGFAAMIRDEPQHHLELG---AFYQAKRDRFREQLAQTRLVPLAVPGGYFQLVD 320 Query: 323 YADVSDFTSDSLAFCSKLLADTGVAIAPGIDFDTAR--GGSFVRISFAGPSGDIEEALRR 380 Y+ +SD F L + GVA P F A G VR+ FA ++ A+ R Sbjct: 321 YSAISDLPDHE--FVKWLTIEKGVAAIPLSPFYEAPPVGQRIVRLCFAKNEATLDAAIER 378 Query: 381 I 381 + Sbjct: 379 L 379 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: 369 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