Align Valine--pyruvate aminotransferase; Alanine--valine transaminase; EC 2.6.1.66 (characterized)
to candidate WP_090448311.1 BLS63_RS23945 pyridoxal phosphate-dependent aminotransferase
Query= SwissProt::P96847 (388 letters) >NCBI__GCF_900100495.1:WP_090448311.1 Length = 393 Score = 249 bits (637), Expect = 7e-71 Identities = 138/381 (36%), Positives = 202/381 (53%), Gaps = 7/381 (1%) Query: 11 VPPFYVMDVWLAAAERQRTHGDLVNLSAGQPSAGAPEPVRAAAAAALHLNQLGYSVALGI 70 + PF+VM + A + Q D+++L G+P P+ AA AAL Y+ A G+ Sbjct: 12 IEPFHVMALLARANQLQAAGFDVIHLEIGEPDFTTAAPIVAAGQAALAAGHTRYTAARGL 71 Query: 71 PELRDAIAADYQRRHGITVEPDAVVITTGSSGGFLLAFLACFDAGDRVAMASPGYPCYRN 130 P LR+AIA Y +R+ ++++P+ ++IT G SG LL D G +A PGYPC R+ Sbjct: 72 PALREAIAGFYAQRYRLSIDPERILITPGGSGALLLTSALLVDPGKNWLLADPGYPCNRH 131 Query: 131 ILSALGCEVVEIPCGPQTRFQPTAQMLAEI-DPPLRGVVVASPANPTGTVIPPEELAAIA 189 L + +P GP+ R+Q T +++A D G +VASPANPTGT++ +ELA ++ Sbjct: 132 FLRLIEGAAQLVPVGPEVRYQLTPELIARHWDKDSVGALVASPANPTGTLLHRDELAGLS 191 Query: 190 SWCDASDVRLISDEVYHGLVYQGAPQTSCAWQTSRNAVVVNSFSKYYAMTGWRLGWLLVP 249 L+ DE+YHGL Y S + +A V+NSFSKY+ MTGWRLGWL+ P Sbjct: 192 RALKERGGHLVVDEIYHGLTY--GVDASSVLEVDDDAFVLNSFSKYFGMTGWRLGWLVAP 249 Query: 250 TVLRRAVDCLTGNFTICPPVLSQIAAVSAFTPEATAEADGNLASYAINRSLLLDGLRRIG 309 ++ L N I P ++Q AA++ F P+ A + + R LL LR +G Sbjct: 250 PAAVAELEKLAQNLYISAPSMAQHAALACFEPQTLAILEQRRHEFQRRRDYLLPALRELG 309 Query: 310 IDRLAPTDGAFYVYADVSDFTSDSLAFCSKLLADTGVAIAPGIDFDTARGGSFVRISFAG 369 +GAFY+YAD+S F D+ AFC L VA PG+DF VR ++ Sbjct: 310 FKIAVEPEGAFYLYADISAFGGDAFAFCQHFLETEHVAFTPGLDFGRHLASQHVRFAYTQ 369 Query: 370 PSGDIEEALRRIG----SWLP 386 +++A+ RI SW P Sbjct: 370 DLPRLQQAVERIARGLKSWRP 390 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: 426 Number of extensions: 26 Number of successful extensions: 3 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: 393 Length adjustment: 31 Effective length of query: 357 Effective length of database: 362 Effective search space: 129234 Effective search space used: 129234 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