Align Valine--pyruvate aminotransferase; Alanine--valine transaminase; EC 2.6.1.66 (characterized)
to candidate WP_073035829.1 BUB04_RS00280 pyridoxal phosphate-dependent aminotransferase
Query= SwissProt::P96847 (388 letters) >NCBI__GCF_900129305.1:WP_073035829.1 Length = 382 Score = 222 bits (566), Expect = 1e-62 Identities = 135/378 (35%), Positives = 208/378 (55%), Gaps = 10/378 (2%) Query: 11 VPPFYVMDVWLAAAERQRTHGDLVNLSAGQPSAGAPEPVRAAAAAALHLNQLGYSVALGI 70 + PF VMDV A +R +++L G+P APE VR AA AL Q Y+ + GI Sbjct: 9 IKPFLVMDVLEKAQAMERAGESVIHLEVGEPDFDAPEAVRRAAVEALDKGQTHYTHSQGI 68 Query: 71 PELRDAIAADYQRRHGIT-VEPDAVVITTGSSGGFLLAFLACFDAGDRVAMASPGYPCYR 129 P+LR+AI Y +G+ +EPD +++T+GSS FL+A + G+ V ++ P Y CY Sbjct: 69 PQLREAICRYYADTYGVRHLEPDQIMVTSGSSPAFLVALSTILNCGEEVILSDPHYACYP 128 Query: 130 NILSALGCEVVEIPCGPQTRFQPTAQMLAE-IDPPLRGVVVASPANPTGTVIPPEELAAI 188 + + L +P + FQ + + + + P + +++ SPANPTGT++ E L AI Sbjct: 129 SFVHFLEGVPKPVPVFEEEGFQFRPEAIRKAVGPNTKAILINSPANPTGTLLDRERLEAI 188 Query: 189 ASWCDASDVRLISDEVYHGLVYQGAPQTSCAWQTSRNAVVVNSFSKYYAMTGWRLGWLLV 248 A + ++SDE+YHGLVY+G ++ + + +V N FSK +AMTG+RLG+L+V Sbjct: 189 AD----LGLWVLSDEIYHGLVYEGRARS--ILEFTDKCIVFNGFSKLFAMTGFRLGYLIV 242 Query: 249 PTVLRRAVDCLTGNFTICPPVLSQIAAVSAFT-PEATAEADGNLASYAINRSLLLDGLRR 307 P L R + L NF I +SQ A ++A T P + + +Y R ++ LR Sbjct: 243 PKDLVRPMQALMQNFFISANSVSQWAGLAALTDPTVQEDVERMRRTYDERRRFMIRRLRE 302 Query: 308 IGIDRLAPTDGAFYVYADVSDFTSDSLAFCSKLLADTGVAIAPGIDFDTARGGSFVRISF 367 +G GAFYV+A+ F +SL F ++L V I PG+DF A+G +VR S+ Sbjct: 303 MGFGISVEPTGAFYVFANARRFCDNSLEFAFQVLERAKVGITPGVDFG-AQGEGYVRFSY 361 Query: 368 AGPSGDIEEALRRIGSWL 385 A G+I E + R+ +L Sbjct: 362 ANSLGNIAEGMDRLEKFL 379 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: 381 Number of extensions: 21 Number of successful extensions: 7 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: 382 Length adjustment: 30 Effective length of query: 358 Effective length of database: 352 Effective search space: 126016 Effective search space used: 126016 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