Align Valine--pyruvate aminotransferase; Alanine--valine transaminase; EC 2.6.1.66 (characterized)
to candidate WP_057508908.1 ABB28_RS12185 pyridoxal phosphate-dependent aminotransferase
Query= SwissProt::P96847 (388 letters) >NCBI__GCF_001431535.1:WP_057508908.1 Length = 397 Score = 233 bits (595), Expect = 5e-66 Identities = 136/378 (35%), Positives = 201/378 (53%), Gaps = 7/378 (1%) Query: 11 VPPFYVMDVWLAAAERQRTHGDLVNLSAGQPSAGAPEPVRAAAAAALHLNQLGYSVALGI 70 + PF+VM + A ++ D+++L G+P PV A AAL Y+ A G+ Sbjct: 19 IAPFHVMSLLARAQALEQAGHDVIHLEIGEPDFTTAAPVVRAGQAALAAGHTRYTAARGL 78 Query: 71 PELRDAIAADYQRRHGITVEPDAVVITTGSSGGFLLAFLACFDAGDRVAMASPGYPCYRN 130 P LR+AIA Y+ + + ++P +++T G SG LLA D G +A PGYPC R+ Sbjct: 79 PALREAIAGFYRSHYLLDIDPQRILVTPGGSGALLLASSLLVDPGRHWLLADPGYPCNRH 138 Query: 131 ILSAL--GCEVVEIPCGPQTRFQPTAQMLAEI-DPPLRGVVVASPANPTGTVIPPEELAA 187 L + G ++V + G T +Q T +++A + G ++ASPANPTGTV+ EL+ Sbjct: 139 FLRLVEGGAQLVPVDAG--TAYQLTPELVARHWNEHSVGALLASPANPTGTVLSAAELSR 196 Query: 188 IASWCDASDVRLISDEVYHGLVYQGAPQTSCAWQTSRNAVVVNSFSKYYAMTGWRLGWLL 247 ++ A ++ DE+YHGL Y + Q +A V+NSFSKY+ MTGWRLGWL+ Sbjct: 197 LSQSLHARGGHMVVDEIYHGLTY--GMDAASVLQVDDSAFVLNSFSKYFGMTGWRLGWLV 254 Query: 248 VPTVLRRAVDCLTGNFTICPPVLSQIAAVSAFTPEATAEADGNLASYAINRSLLLDGLRR 307 P ++ L N I ++Q AA++ F EA A + ++ R LL LR Sbjct: 255 APPAAVPELEKLAQNLYISASSIAQHAALACFQDEAMAIFEQRREAFRQRRDFLLPALRE 314 Query: 308 IGIDRLAPTDGAFYVYADVSDFTSDSLAFCSKLLADTGVAIAPGIDFDTARGGSFVRISF 367 +G GAFY+YADVS FT D+ AFC+ L VA PG+DF R VR+++ Sbjct: 315 LGFRINVEPQGAFYLYADVSAFTDDAQAFCAHFLETEHVAFTPGLDFGFHRANQHVRLAY 374 Query: 368 AGPSGDIEEALRRIGSWL 385 ++EA+ RI L Sbjct: 375 TQEIPRLQEAVERIARGL 392 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: 403 Number of extensions: 18 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: 397 Length adjustment: 31 Effective length of query: 357 Effective length of database: 366 Effective search space: 130662 Effective search space used: 130662 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