Align Valine--pyruvate aminotransferase; Alanine--valine transaminase; EC 2.6.1.66 (characterized)
to candidate WP_086510442.1 BZY95_RS13490 aminotransferase class V-fold PLP-dependent enzyme
Query= SwissProt::P96847 (388 letters) >NCBI__GCF_002151265.1:WP_086510442.1 Length = 386 Score = 272 bits (696), Expect = 1e-77 Identities = 156/379 (41%), Positives = 212/379 (55%), Gaps = 3/379 (0%) Query: 11 VPPFYVMDVWLAAAERQRTHGDLVNLSAGQPSAGAPEPVRAAAAAALHLNQLGYSVALGI 70 V PF VM + AA R+ D+++L G+P PEPV AA AAL YS A G+ Sbjct: 10 VAPFRVMSLLEAAQAREAAGHDVIHLEVGEPDFATPEPVVAAGQAALAAGLTRYSPAAGL 69 Query: 71 PELRDAIAADYQRRHGITVEPDAVVITTGSSGGFLLAFLACFDAGDRVAMASPGYPCYRN 130 P LR+AIA Y G V+P V++T G+SG LLA GDRV MA P YPC R+ Sbjct: 70 PALREAIAGHYGEHFGADVDPRRVLVTPGASGALLLASQLLVGPGDRVLMADPNYPCNRH 129 Query: 131 ILSALGCEVVEIPCGPQTRFQPTAQMLAEI-DPPLRGVVVASPANPTGTVIPPEELAAIA 189 ++ G EV +P GPQ+ +Q A ++A R ++A+P+NPTG ++ +L A+A Sbjct: 130 FMALAGAEVDTVPIGPQSGWQLDANLVARHWQDATRLAMLATPSNPTGHMLDAAQLKAVA 189 Query: 190 SWCDASDVRLISDEVYHGLVYQGAPQTSCAWQTSRNAVVVNSFSKYYAMTGWRLGWLLVP 249 A L+ DE+Y GL Y AP + + + +A VVNSFSKY+ MTGWRLGWLL P Sbjct: 190 DTVAARGGHLLVDEIYQGLSYDIAPLSVAS--LTADAFVVNSFSKYFGMTGWRLGWLLAP 247 Query: 250 TVLRRAVDCLTGNFTICPPVLSQIAAVSAFTPEATAEADGNLASYAINRSLLLDGLRRIG 309 + L N + P +Q AA++AFTPE A + + R LL GL R+G Sbjct: 248 QAAVEPLTRLAQNVFLAAPTPAQHAALAAFTPECRALLEARRSELGRRRDALLAGLARLG 307 Query: 310 IDRLAPTDGAFYVYADVSDFTSDSLAFCSKLLADTGVAIAPGIDFDTARGGSFVRISFAG 369 + P GAFY++ D+S ++ DS AFC +LL + VAI PGIDF G VRI+F Sbjct: 308 LAPSLPPQGAFYLWLDISRYSRDSQAFCQRLLEEENVAITPGIDFAVTGGEYHVRIAFTT 367 Query: 370 PSGDIEEALRRIGSWLPSQ 388 +EEA+ R+ +L Q Sbjct: 368 GIERLEEAVSRLERFLARQ 386 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: 439 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: 386 Length adjustment: 30 Effective length of query: 358 Effective length of database: 356 Effective search space: 127448 Effective search space used: 127448 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