Align Valine--pyruvate aminotransferase; Alanine--valine transaminase; EC 2.6.1.66 (characterized)
to candidate WP_078717089.1 B5D49_RS07615 pyridoxal phosphate-dependent aminotransferase
Query= SwissProt::P96847 (388 letters) >NCBI__GCF_900167125.1:WP_078717089.1 Length = 385 Score = 153 bits (387), Expect = 7e-42 Identities = 108/355 (30%), Positives = 159/355 (44%), Gaps = 6/355 (1%) Query: 32 DLVNLSAGQPSAGAPEPVRAAAAAALHLNQLGYSVALGIPELRDAIAADYQRRHGITVEP 91 D +NL+ G PEPV A A+ + Y+ G+PE R AIA +R G+ ++P Sbjct: 28 DGINLAQGVCDLDVPEPVLHGAEQAMRQGKNVYTRFDGLPEFRQAIARHQRRFQGLDLDP 87 Query: 92 DA-VVITTGSSGGFLLAFLACFDAGDRVAMASPGYPCYRNILSALGCEVVEIPCGPQTRF 150 ++ +V++ G++G F A FD GD + + P Y + N L ++ + Sbjct: 88 ESNIVVSVGATGAFQATCAAMFDPGDEILLFEPFYGYHVNTLRSMDLTPTFVSLRQPDWS 147 Query: 151 QPTAQMLAEIDPPLRGVVVASPANPTGTVIPPEELAAIASWCDASDVRLISDEVYHGLVY 210 + A P LRGVV+ +P NP G V EEL +A +C D+ L+SDE+Y VY Sbjct: 148 FTDDDLDAAASPKLRGVVLNTPLNPCGKVFTQEELERVARFCRKHDLMLLSDEIYEHFVY 207 Query: 211 QGAPQTSCAW--QTSRNAVVVNSFSKYYAMTGWRLGWLLVPTVLRRAVDCLTGNFTICPP 268 G S A V ++ SK +A+TGWRLGW + + + + +CPP Sbjct: 208 DGHRHISPATLPGMEERVVSISGVSKVFAVTGWRLGWAVCHSRWHEPIGHFNDLYYVCPP 267 Query: 269 VLSQIAAVSAFTPEATAEADGNLASYAINRSLLLDGLRRIGIDRLAPTDGAFYVYADVSD 328 Q+ A + + R L R G+ P DGA+Y A + Sbjct: 268 APLQMGAANGLDQLGDDYYQELAEDHRRKRDRFCLALTRAGLKPHVP-DGAYYALARIDH 326 Query: 329 FTS-DSLAFCSKLLADTGVAIAPGIDF-DTARGGSFVRISFAGPSGDIEEALRRI 381 DS LL +TGVA PG F + G R FA ++EEA RR+ Sbjct: 327 LPGRDSHERAMHLLRETGVACVPGRAFWNDPLGQGLARFCFAKRWPELEEACRRL 381 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: 387 Number of extensions: 21 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: 385 Length adjustment: 30 Effective length of query: 358 Effective length of database: 355 Effective search space: 127090 Effective search space used: 127090 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