Align Valine--pyruvate aminotransferase; Alanine--valine transaminase; EC 2.6.1.66 (characterized)
to candidate WP_015948152.1 G491_RS0110270 pyridoxal phosphate-dependent aminotransferase
Query= SwissProt::P96847 (388 letters) >NCBI__GCF_000429905.1:WP_015948152.1 Length = 380 Score = 221 bits (563), Expect = 3e-62 Identities = 132/378 (34%), Positives = 202/378 (53%), Gaps = 9/378 (2%) Query: 11 VPPFYVMDVWLAAAERQRTHGDLVNLSAGQPSAGAPEPVRAAAAAALHLNQLGYSVALGI 70 + PF VM+V A +R ++V+L G+P PE + A AL Y+ +LGI Sbjct: 10 ITPFIVMEVLERAKAMERDGVNIVHLEVGEPDFDTPECITEAGIKALRDGYSHYTHSLGI 69 Query: 71 PELRDAIAADYQRRHGITVEPDAVVITTGSSGGFLLAFLACFDAGDRVAMASPGYPCYRN 130 ELR+AIA Y +G+ V PD +V+T G+S G + F A +AGD V ++ P Y CY N Sbjct: 70 LELREAIAEHYYNEYGVEVNPDHIVVTNGTSPGIFMTFAALLEAGDEVIVSDPHYACYPN 129 Query: 131 ILSALGCEVVEIPCGPQTRFQPTAQMLAE-IDPPLRGVVVASPANPTGTVIPPEELAAIA 189 + G + V++ + FQ A+ + + + + V++ SP+NPTG ++ PE + +A Sbjct: 130 FIEFAGAKPVKVAVTEEEGFQYRAEQIQKHMTDRTKAVMINSPSNPTGNLLSPERMQQVA 189 Query: 190 SWCDASDVRLISDEVYHGLVYQGAPQTSCAWQTSRNAVVVNSFSKYYAMTGWRLGWLLVP 249 D V ++SDE+YHGLVY+G ++ + + A V+N FSK YAMTGWRLG+L+ P Sbjct: 190 ---DLGKV-VVSDEIYHGLVYEGKERS--ILEFTDEAFVLNGFSKAYAMTGWRLGYLIAP 243 Query: 250 TVLRRAVDCLTGNFTICPPVLSQIAAVSAFTPEATAEADGNLASYAINRSLLLDGLRRIG 309 R + L NF I ++Q+A ++A EA + Y R ++ LR IG Sbjct: 244 KRFIRPLQKLQQNFFISANAMTQMAGIAAL-KEAGPDVARMREIYDQRRRFMIRRLREIG 302 Query: 310 IDRLAPTDGAFYVYADVSDFTSDSLAFCSKLLADTGVAIAPGIDFDTARGGSFVRISFAG 369 + GAFYV A+ SDS +L + V + PGIDF G ++R S+A Sbjct: 303 LGITVEPTGAFYVLANARHLGSDSYKMAFDILENAHVGVTPGIDFGQQAEG-YIRFSYAN 361 Query: 370 PSGDIEEALRRIGSWLPS 387 +IEE + R+ ++ S Sbjct: 362 SLENIEEGMNRLEKYINS 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: 348 Number of extensions: 14 Number of successful extensions: 6 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: 380 Length adjustment: 30 Effective length of query: 358 Effective length of database: 350 Effective search space: 125300 Effective search space used: 125300 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