Align Valine--pyruvate aminotransferase; Alanine--valine transaminase; EC 2.6.1.66 (characterized)
to candidate WP_012400027.1 BPHY_RS03085 pyridoxal phosphate-dependent aminotransferase
Query= SwissProt::P96847 (388 letters) >NCBI__GCF_000020045.1:WP_012400027.1 Length = 397 Score = 262 bits (669), Expect = 1e-74 Identities = 148/376 (39%), Positives = 208/376 (55%), Gaps = 7/376 (1%) Query: 11 VPPFYVMDVWLAAAERQRTHGDLVNLSAGQPSAGAPEPVRAAAAAALHLNQLGYSVALGI 70 + PFYVM++ AA +R D++++ G+P APEPV AAA AL Y+ ALGI Sbjct: 18 IQPFYVMELAKEAALLERAGRDIIHMGIGEPDFTAPEPVIEAAARALRSGATQYTGALGI 77 Query: 71 PELRDAIAADYQRRHGITVEPDAVVITTGSSGGFLLAFLACFDAGDRVAMASPGYPCYRN 130 LR+AIA Y+ +G+ ++P +V+T G+S LLA A D D V M P YPC R+ Sbjct: 78 HPLREAIAGHYKHTYGLEIDPARIVVTAGASAALLLACAALVDRDDEVLMPDPSYPCNRH 137 Query: 131 ILSALGCEVVEIPCGPQTRFQPTAQMLAEI-DPPLRGVVVASPANPTGTVIPPEELAAIA 189 ++A + V +P GP RFQ TA + + + RGV++ASP+NPTGT I P+EL I Sbjct: 138 FVAAAEGKPVLVPSGPAERFQLTANDVERLWNANTRGVLLASPSNPTGTSIEPDELRRIV 197 Query: 190 SWCDASDVRLISDEVYHGLVYQGAPQTSCAWQTSRNAVVVNSFSKYYAMTGWRLGWLLVP 249 A I DE+Y GL Y P ++ ++ + V VNSFSKY+ MTGWRLGWL+VP Sbjct: 198 EAVRARGGFTIVDEIYQGLSYDAPPVSALSF--GEDVVTVNSFSKYFNMTGWRLGWLVVP 255 Query: 250 TVLRRAVDCLTGNFTICPPVLSQIAAVSAFTPEATAEADGNLASYAINRSLLLDGLRRIG 309 L A + L N IC L+Q AA++ F P+ A + + R + L +G Sbjct: 256 PALVGAFEKLAQNLFICASALAQHAALACFEPDTLAIYEARRLEFKRRRDFIAPALESLG 315 Query: 310 IDRLAPTDGAFYVYADVSDF----TSDSLAFCSKLLADTGVAIAPGIDFDTARGGSFVRI 365 DGAFYVYAD DS A +L D GV + PG+DF + + ++R+ Sbjct: 316 FSVPVMPDGAFYVYADCRSIAHPAAGDSAALTRAMLHDAGVVLVPGMDFGSYQPREYIRL 375 Query: 366 SFAGPSGDIEEALRRI 381 S+A +EEA+ R+ Sbjct: 376 SYATAYSKLEEAVERL 391 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: 413 Number of extensions: 18 Number of successful extensions: 4 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