Align Valine--pyruvate aminotransferase; Alanine--valine transaminase; EC 2.6.1.66 (characterized)
to candidate WP_035238275.1 Q366_RS09090 pyridoxal phosphate-dependent aminotransferase
Query= SwissProt::P96847 (388 letters) >NCBI__GCF_000745975.1:WP_035238275.1 Length = 385 Score = 210 bits (535), Expect = 5e-59 Identities = 123/374 (32%), Positives = 196/374 (52%), Gaps = 5/374 (1%) Query: 13 PFYVMDVWLAAAERQRTHGDLVNLSAGQPSAGAPEPVRAAAAAALHLNQLGYSVALGIPE 72 PF MDV + D++++ G+P PE V AL N+ Y+ +LG Sbjct: 12 PFIAMDVMEKIHNMEARGVDVIHMEIGEPDFNVPECVNRVCGEALAQNETCYTHSLGDLR 71 Query: 73 LRDAIAADYQRRHGITVEPDAVVITTGSSGGFLLAFLACFDAGDRVAMASPGYPCYRNIL 132 LR AI+ ++R +G TV+P +++T+G+S LL F A D GD V ++ P Y CY N + Sbjct: 72 LRQAISDYHKRIYGTTVDPGQILVTSGTSPAMLLVFSALIDPGDEVIVSDPHYACYANFI 131 Query: 133 SALGCEVVEIPCGPQTRFQPTAQ-MLAEIDPPLRGVVVASPANPTGTVIPPEELAAIASW 191 + E V + + F T Q +L +I P + + V SP+NPTG+VIP + I Sbjct: 132 RYVQGEPVFVKVYEKDGFVYTPQAILEKITPKTKAIFVNSPSNPTGSVIPEARMRQIVDL 191 Query: 192 CDASDVRLISDEVYHGLVYQGAPQTSCAWQTSRNAVVVNSFSKYYAMTGWRLGWLLVPTV 251 + ++SDE+YHGL Y+G + + + A V+N FSK +AMTG RLG+L+ P Sbjct: 192 AREHGLYIVSDEIYHGLTYEGKDHS--IMEFTDQAFVLNGFSKLFAMTGLRLGYLIAPPK 249 Query: 252 LRRAVDCLTGNFTICPPVLSQIAAVSAFTPEATAEADGNLASYAINRSLLLDGLRRIGID 311 RA+ L NF IC ++Q+A A T +A E +Y R ++ L+ +G+ Sbjct: 250 FIRALQVLQQNFFICANSITQLAGAVALT-DAGRETQAMRDTYNERRIFMIRRLKEMGLS 308 Query: 312 RLAPTDGAFYVYADVSDFTSDSLAFCSKLLADTGVAIAPGIDFDTARGGSFVRISFAGPS 371 + GAFYV+ + ++DS A +L + + PGIDF A G ++R S+A Sbjct: 309 MMVEPTGAFYVFVNFKHISTDSYALAFDILEKAHIGVTPGIDFG-ANGEGYLRFSYANSL 367 Query: 372 GDIEEALRRIGSWL 385 +++ + R+ ++L Sbjct: 368 DNLKIGMDRLENYL 381 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: 364 Number of extensions: 14 Number of successful extensions: 5 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: 385 Length adjustment: 30 Effective length of query: 358 Effective length of database: 355 Effective search space: 127090 Effective search space used: 127090 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