Align Valine--pyruvate aminotransferase; Alanine--valine transaminase; EC 2.6.1.66 (characterized)
to candidate WP_011996059.1 XAUT_RS02030 pyridoxal phosphate-dependent aminotransferase
Query= SwissProt::P96847 (388 letters) >NCBI__GCF_000017645.1:WP_011996059.1 Length = 395 Score = 183 bits (464), Expect = 8e-51 Identities = 124/358 (34%), Positives = 186/358 (51%), Gaps = 7/358 (1%) Query: 33 LVNLSAGQPSAGAPEPVRAAAAAALHLNQLGYSVALGIPELRDAIAADYQRRHGITVEPD 92 ++NL GQP P+ + AA AL Q GY+ ++GI LR+A+AAD RR+G+ V+PD Sbjct: 33 ILNLGIGQPDFRTPDHIVEAAVKALRDGQHGYTPSVGILPLREAVAADLNRRYGVEVDPD 92 Query: 93 AVVITTGSSGGFLLAFLACFDAGDRVAMASPGYPCYRNILSALGCEVVEIPCGPQTRFQP 152 V+I G A + G + PG+P YR+++ G V +P + F Sbjct: 93 LVMIMPGGKVTMYAAIRLFGEPGAEILYPDPGFPIYRSMIEHTGATPVPVPIREENGFAF 152 Query: 153 TA-QMLAEIDPPLRGVVVASPANPTGTVIPPEELAAIASWCDA-SDVRLISDEVYHGLVY 210 +A + LA I P R +++ SPANPTG V P E+ + A V L+SDE+Y ++ Sbjct: 153 SAEETLALITPKTRLLIINSPANPTGGVTPAAEIDKLVKGLAAHPHVALMSDEIYDRFLF 212 Query: 211 QGAP-QTSCAWQTSRN-AVVVNSFSKYYAMTGWRLGWLLVPTVLRRAVDCLTGNFTICPP 268 G +T A+ R+ +++N +SK YAMTGWRLG+ + P L V L N C Sbjct: 213 DGEEHRTLLAYPQIRDRLILLNGWSKTYAMTGWRLGYSIWPKDLYDKVRKLAVNCWSCVN 272 Query: 269 VLSQIAAVSAFTPEATAEADGNLASYAINRSLLLDGLRRIGIDRLAPTDGAFYVYADVSD 328 +Q A ++A A D A + R +++DGL + R A GAFY + +VS Sbjct: 273 AATQYAGIAALEGPQDA-VDAMTAEFDARRRIVVDGLNALPGVRCATPKGAFYAFPNVSG 331 Query: 329 F-TSDSLAFCSKLLADTGVAIAPGIDFDTARGGSFVRISFAGPSGDIEEALRRIGSWL 385 S++ S LL + GVA+ G DF G ++R+S+A +I AL R+G +L Sbjct: 332 TGWSEAKKLASALLEEAGVAVIGGPDFG-VYGEGYLRLSYATSRENIAAALARMGDFL 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: 420 Number of extensions: 18 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: 395 Length adjustment: 31 Effective length of query: 357 Effective length of database: 364 Effective search space: 129948 Effective search space used: 129948 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 09 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