Align Valine--pyruvate aminotransferase; Alanine--valine transaminase; EC 2.6.1.66 (characterized)
to candidate WP_106719584.1 CU100_RS26240 aminotransferase class I/II-fold pyridoxal phosphate-dependent enzyme
Query= SwissProt::P96847 (388 letters) >NCBI__GCF_003010935.1:WP_106719584.1 Length = 400 Score = 158 bits (399), Expect = 3e-43 Identities = 114/366 (31%), Positives = 181/366 (49%), Gaps = 14/366 (3%) Query: 24 AERQRTHGDLVNLSAGQPSAGAPEPVRAAAAAALHLNQLGYSVALGIPELRDAIAADYQR 83 A+R R D+V L G+ P + AA AAL Y+ +LG+P LR A+ +DY Sbjct: 35 ADRGRDDPDVVKLWIGEGDLPTPPYIVEAAEAALRAGHTRYTYSLGLPRLRQAL-SDYHF 93 Query: 84 RH-GITVEPDAVVITTGSSGGFLLAFLACFDAGDRVAMASPGYPCYRNILSALGCEVVEI 142 RH + + + +T G + + A D GD + + +P +P + G V + Sbjct: 94 RHWNVRLPVERFTVTVGGMNALMQSAQAVLDPGDEIIVPTPAWPNLIESMRLAGGTPVLV 153 Query: 143 PCGPQTRFQPTA---QMLAEIDPPLRGVVVASPANPTGTVIPPEELAAIASWCDASDVRL 199 P G Q+ + +LA I P + +++ SP+NPTG V+P E++ +++ + Sbjct: 154 PYGIQSDGRLALNIDDVLAAITPKTKAILINSPSNPTGWVMPREDMEKFVDLSRQTNIWI 213 Query: 200 ISDEVYHGLVYQGAPQTSCAWQTSRN--AVVVNSFSKYYAMTGWRLGWLLVPTVLRRAVD 257 I+DEVY Y G+ S T N +V N+FSK +AMTGWR+GW +VP L + Sbjct: 214 IADEVYAQFKYDGSVAPSFLQITDENDKVIVTNTFSKNWAMTGWRIGWAVVPRGLDKFYA 273 Query: 258 CLTGNFTICPPVLSQIAAVSAFTPEATAEADGNLASYAINRSLLLDGLRRIGIDRLAPTD 317 L+ T P Q AA++A + ++ A R + +DGL +I + P D Sbjct: 274 KLSEYNTTGVPTFVQHAAIAAL-DQGDEFIRQMVSRCAETRKIFVDGLSQIEGVTVLPPD 332 Query: 318 GAFYVYADVSDFTSD--SLAFCSKLLADTGVAIAPGIDFDTARGGSFVRISFAGPSGDIE 375 GAFY+ + F D SL ++LA+ V +APG F +A G ++R+ FA Sbjct: 333 GAFYL---MVGFPGDETSLDVAIRMLAEAKVGVAPGTAFGSA-GQGYLRLCFAISPKLAR 388 Query: 376 EALRRI 381 EA++R+ Sbjct: 389 EAVKRL 394 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: 428 Number of extensions: 20 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: 400 Length adjustment: 31 Effective length of query: 357 Effective length of database: 369 Effective search space: 131733 Effective search space used: 131733 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 Jul 26 2024. The underlying query database was built on Jul 25 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