Align Valine--pyruvate aminotransferase; Alanine--valine transaminase; EC 2.6.1.66 (characterized)
to candidate WP_012169089.1 AZC_RS02835 pyridoxal phosphate-dependent aminotransferase
Query= SwissProt::P96847 (388 letters) >NCBI__GCF_000010525.1:WP_012169089.1 Length = 394 Score = 183 bits (465), Expect = 6e-51 Identities = 126/361 (34%), Positives = 189/361 (52%), Gaps = 11/361 (3%) Query: 32 DLVNLSAGQPSAGAPEPVRAAAAAALHLNQLGYSVALGIPELRDAIAADYQRRHGITVEP 91 D++NL GQP PE + AA AL Q GY+ ++GI LR+A+A D +R + V+P Sbjct: 32 DIINLGIGQPDFRTPEHIVEAAVKALKDGQHGYTPSVGIQPLREAVARDLHKRFDVEVDP 91 Query: 92 DAVVITTGSSGGFLLAFLACFDAGDRVAMASPGYPCYRNILSALGCEVVEIPCGPQTRFQ 151 V+I G A L + G + PG+P YR+++ G + +P + F Sbjct: 92 GLVMIMPGGKVTMYAAILLFGEPGAEILYPDPGFPIYRSMIEYTGATPIPVPIREENGFA 151 Query: 152 PTA-QMLAEIDPPLRGVVVASPANPTGTVIPPEEL-AAIASWCDASDVRLISDEVYHGLV 209 +A + LA I P R +++ SPANPTG V P E+ + D V L+SDE+Y + Sbjct: 152 FSAEETLALITPKTRLLIINSPANPTGGVTPKAEIDKLVKGLADHPHVALMSDEIYDQFL 211 Query: 210 YQG-APQTSCAWQTSRN-AVVVNSFSKYYAMTGWRLGWLLVPTVLRRAVDCLTGNFTICP 267 + G QT A+ R+ +++N +SK YAMTGWRLG+ + P L V L+ N C Sbjct: 212 FDGERHQTLLAYPEIRDRLILLNGWSKTYAMTGWRLGYSIWPQALYDKVRKLSVNAWSCV 271 Query: 268 PVLSQIAAVSAFT-PEATAEADGNLASYAINRSLLLDGLRRIGIDRLAPTDGAFYVYADV 326 +Q A ++A P+ A LA + R L+++GL + A GAFY + +V Sbjct: 272 NAATQYAGIAALEGPQEPVAA--MLAEFDKRRRLVVEGLNALPGVTCAKPKGAFYAFPNV 329 Query: 327 S--DFTSDSLAFCSKLLADTGVAIAPGIDFDTARGGSFVRISFAGPSGDIEEALRRIGSW 384 S +TS + A S LL D GVA G DF G ++R+S+A + +I AL R+G++ Sbjct: 330 SRTGWTS-AKALASALLEDAGVATIGGPDFG-VHGEGYIRLSYANSAENIARALERMGAF 387 Query: 385 L 385 L Sbjct: 388 L 388 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: 412 Number of extensions: 23 Number of successful extensions: 8 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: 394 Length adjustment: 31 Effective length of query: 357 Effective length of database: 363 Effective search space: 129591 Effective search space used: 129591 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