Align Valine--pyruvate aminotransferase; Alanine--valine transaminase; EC 2.6.1.66 (characterized)
to candidate WP_004303932.1 C665_RS07050 pyridoxal phosphate-dependent aminotransferase
Query= SwissProt::P96847 (388 letters) >NCBI__GCF_000310185.1:WP_004303932.1 Length = 400 Score = 239 bits (611), Expect = 8e-68 Identities = 142/378 (37%), Positives = 201/378 (53%), Gaps = 6/378 (1%) Query: 9 AGVPPFYVMDVWLAAAERQRTHGDLVNLSAGQPSAGAPEPVRAAAAAALHLNQLGYSVAL 68 A + PF+VM++ A E + D++++ G+P G P PV AA L + Y+ AL Sbjct: 17 ADIQPFHVMELLRRARELEAQGRDIIHMEVGEPDFGTPAPVVEAATRFLAGGDVHYTPAL 76 Query: 69 GIPELRDAIAADYQRRHGITVEPDAVVITTGSSGGFLLAFLACFDAGDRVAMASPGYPCY 128 G+P LR+AIA Y R G V P+ +V+T G+SG +LA A D GD + PGYP Sbjct: 77 GLPALREAIARFYHDRFGADVAPERIVVTAGASGALMLALAATTDPGDEWLLPDPGYPSN 136 Query: 129 RNILSALGCEVVEIPCGPQTRFQPTAQML-AEIDPPLRGVVVASPANPTGTVIPPEELAA 187 R+++ A + +R+QP + + A RG++VA+P+NPTGT++ E+AA Sbjct: 137 RHLIRAFEGVARALAVDAASRYQPRPEQVDAAWGERTRGLMVATPSNPTGTLLSVAEIAA 196 Query: 188 IASWCDASDVRLISDEVYHGLVYQGAPQTSCAWQTSRNAV----VVNSFSKYYAMTGWRL 243 + A L+ DE+Y GL Y G S NA VVNSFSKY+ MTGWRL Sbjct: 197 LHRRTRARGGVLLVDEIYQGLTY-GVESASALGDPVLNAADDVFVVNSFSKYFGMTGWRL 255 Query: 244 GWLLVPTVLRRAVDCLTGNFTICPPVLSQIAAVSAFTPEATAEADGNLASYAINRSLLLD 303 GWL+ P R ++ L +F I P +Q AA++AF P A + +A R +LL Sbjct: 256 GWLVAPAGFVRELEKLAQHFFISPSTPAQHAALAAFAPATIAILEERRHEFAQRRDVLLP 315 Query: 304 GLRRIGIDRLAPTDGAFYVYADVSDFTSDSLAFCSKLLADTGVAIAPGIDFDTARGGSFV 363 LR +G A GAFYVYADVS DS A +++ + GVA PG+DF + Sbjct: 316 ALRALGFGIAAEPQGAFYVYADVSALADDSEALARRMIEEAGVAATPGLDFGHHLPRRHL 375 Query: 364 RISFAGPSGDIEEALRRI 381 RI++ + EA RI Sbjct: 376 RIAYTTHGARLLEAAERI 393 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: 443 Number of extensions: 25 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: 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