Align Valine--pyruvate aminotransferase; Alanine--valine transaminase; EC 2.6.1.66 (characterized)
to candidate PP_4692 PP_4692 putative aspartate/tyrosine/aromatic aminotransferase
Query= SwissProt::P96847 (388 letters) >FitnessBrowser__Putida:PP_4692 Length = 390 Score = 259 bits (661), Expect = 1e-73 Identities = 149/379 (39%), Positives = 203/379 (53%), Gaps = 5/379 (1%) Query: 11 VPPFYVMDVWLAAAERQRTHGDLVNLSAGQPSAGAPEPVRAAAAAALHLNQLGYSVALGI 70 + PF+VM + A E Q D+++L G+P P+ AA AAL Y+ A G+ Sbjct: 12 IEPFHVMALLARANELQAAGHDVIHLEIGEPDFTTAAPIVAAGQAALAAGHTRYTAARGL 71 Query: 71 PELRDAIAADYQRRHGITVEPDAVVITTGSSGGFLLAFLACFDAGDRVAMASPGYPCYRN 130 P LR+AIA Y +R+G+ ++P+ ++IT G SG LLA D G +A PGYPC R+ Sbjct: 72 PALREAIAGFYGQRYGLNIDPERILITPGGSGALLLASSLLVDPGKHWLLADPGYPCNRH 131 Query: 131 ILSALGCEVVEIPCGPQTRFQPTAQMLAEI-DPPLRGVVVASPANPTGTVIPPEELAAIA 189 L + +P GP +Q TA ++ D G +VASPANPTGTV+ E LA +A Sbjct: 132 FLRLVEGGAQLVPVGPDVNYQLTADLVERYWDKDTVGALVASPANPTGTVLGREALACLA 191 Query: 190 SWCDASDVRLISDEVYHGLVY-QGAPQTSCAWQTSRNAVVVNSFSKYYAMTGWRLGWLLV 248 L+ DE+YHGL Y AP + +A V+NSFSKY+ MTGWRLGWL+ Sbjct: 192 RTTHERHGHLVVDEIYHGLTYGMDAPSVL---EVDDSAFVLNSFSKYFGMTGWRLGWLVA 248 Query: 249 PTVLRRAVDCLTGNFTICPPVLSQIAAVSAFTPEATAEADGNLASYAINRSLLLDGLRRI 308 P ++ L N I P ++Q AA++ F PEA A + A +A R LL LR + Sbjct: 249 PPGAVADLEKLAQNLYISAPSMAQHAALACFQPEALAIFEERRAEFARRRDYLLPALREL 308 Query: 309 GIDRLAPTDGAFYVYADVSDFTSDSLAFCSKLLADTGVAIAPGIDFDTARGGSFVRISFA 368 G GAFY+YAD+S F D+ AFC L VA PG+DF G VR ++ Sbjct: 309 GFRIAVEPQGAFYLYADISAFGGDAFAFCRHFLETQHVAFTPGLDFGRHLAGHHVRFAYT 368 Query: 369 GPSGDIEEALRRIGSWLPS 387 +EEA++RI L S Sbjct: 369 QSLPRLEEAVQRIARGLQS 387 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: 429 Number of extensions: 21 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: 390 Length adjustment: 30 Effective length of query: 358 Effective length of database: 360 Effective search space: 128880 Effective search space used: 128880 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 09 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