Align Valine--pyruvate aminotransferase; Alanine--valine transaminase; EC 2.6.1.66 (characterized)
to candidate WP_089322527.1 CHB58_RS02505 aminotransferase
Query= SwissProt::P96847 (388 letters) >NCBI__GCF_900188395.1:WP_089322527.1 Length = 371 Score = 223 bits (568), Expect = 7e-63 Identities = 128/376 (34%), Positives = 201/376 (53%), Gaps = 11/376 (2%) Query: 10 GVPPFYVMDVWLAAAERQRTHGDLVNLSAGQPSAGAPEPVRAAAAAALHLNQLGYSVALG 69 GV PF VMD+ A + + D ++ GQP P V A A+ ++ Y+ +LG Sbjct: 6 GVTPFIVMDIVRDAQKYE----DTIHFEVGQPDLQPPHQVWEFAQKAVKEHRTEYTESLG 61 Query: 70 IPELRDAIAADYQRRHGITVEPDAVVITTGSSGGFLLAFLACFDAGDRVAMASPGYPCYR 129 + LR+ IA Y +++G+ + P + IT+G+SG FL+A+ D +++ + P YPCY+ Sbjct: 62 LIALREKIAEFYYKKYGVNISPGRIAITSGTSGAFLVAYSVLLDFKEKILLTDPSYPCYK 121 Query: 130 NILSALGCEVVEIPCGPQTRFQPTAQMLAEIDPPLRGVVVASPANPTGTVIPPEELAAIA 189 N L E V P T +Q T L + ++ V ++SP+NP G V E ++ Sbjct: 122 NFAKVLDIEPVFEPIDSSTNYQLTPGKLKK-HKKIKAVHISSPSNPIGNVYDRENFKSLI 180 Query: 190 SWCDASDVRLISDEVYHGLVYQGAPQTSCAWQTSRNAVVVNSFSKYYAMTGWRLGWLLVP 249 + S + ISDE+YHGLVY T A + S NA+V+N FSKY+ M G+RLGW+++P Sbjct: 181 ETAENSGIYFISDEIYHGLVYDKKEHT--ALEFSDNAIVINGFSKYFCMPGFRLGWIILP 238 Query: 250 TVLRRAVDCLTGNFTICPPVLSQIAAVSAFTPEATAEADGNLASYAINRSLLLDGLRRIG 309 L R + + NF I P +SQ AA+ AF E + + R LL L I Sbjct: 239 EKLVRKAEIVLQNFFISAPTISQYAALGAFDFE---HLNKTTQVFKERRDFLLKELSEI- 294 Query: 310 IDRLAPTDGAFYVYADVSDFTSDSLAFCSKLLADTGVAIAPGIDFDTARGGSFVRISFAG 369 + A +GAFY++A++S + +DS F +LL + VA+ PG+DF R ++R ++ Sbjct: 295 FEIDARPEGAFYIWANISKYHNDSFTFAKELLENIHVAVTPGVDFGENRTREYIRFAYTR 354 Query: 370 PSGDIEEALRRIGSWL 385 ++E RI ++L Sbjct: 355 NIKHLKEGAERIKNYL 370 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: 325 Number of extensions: 15 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: 371 Length adjustment: 30 Effective length of query: 358 Effective length of database: 341 Effective search space: 122078 Effective search space used: 122078 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