Align Valine--pyruvate aminotransferase; Alanine--valine transaminase; EC 2.6.1.66 (characterized)
to candidate GFF973 Psest_1004 Aspartate/tyrosine/aromatic aminotransferase
Query= SwissProt::P96847 (388 letters) >FitnessBrowser__psRCH2:GFF973 Length = 390 Score = 255 bits (652), Expect = 1e-72 Identities = 144/389 (37%), Positives = 211/389 (54%), Gaps = 4/389 (1%) Query: 1 MTDRVALRA-GVPPFYVMDVWLAAAERQRTHGDLVNLSAGQPSAGAPEPVRAAAAAALHL 59 MT + R+ + PF+VM + A + Q D+++L G+P P+ AA AAL Sbjct: 1 MTSSYSARSRAIEPFHVMALLERANQLQVQGHDVIHLEIGEPDFTTAAPIVAAGQAALAA 60 Query: 60 NQLGYSVALGIPELRDAIAADYQRRHGITVEPDAVVITTGSSGGFLLAFLACFDAGDRVA 119 Y+ A G+P+LR+AIAA Y +R+G++++P ++IT G SG LLA D G Sbjct: 61 GHTRYTPARGLPQLREAIAAFYAQRYGLSIDPGRILITPGGSGALLLAASLLVDPGKHWL 120 Query: 120 MASPGYPCYRNILSALGCEVVEIPCGPQTRFQPTAQMLAEI-DPPLRGVVVASPANPTGT 178 +A PGYPC R+ L + +P GP R+Q T +++ D G +VASPANPTGT Sbjct: 121 LADPGYPCNRHFLRLVEGAAQLVPVGPDVRYQLTPELVERYWDRDSVGALVASPANPTGT 180 Query: 179 VIPPEELAAIASWCDASDVRLISDEVYHGLVYQGAPQTSCAWQTSRNAVVVNSFSKYYAM 238 ++ +ELA +++ L+ DE+YHGL Y + + +A V+NSFSKY+ M Sbjct: 181 LLERDELARLSAALKERGGHLVVDEIYHGLTY--GVDAASVLEVDDDAFVLNSFSKYFGM 238 Query: 239 TGWRLGWLLVPTVLRRAVDCLTGNFTICPPVLSQIAAVSAFTPEATAEADGNLASYAINR 298 TGWRLGWL+ P ++ L N I P ++Q AA++ F P + A +A R Sbjct: 239 TGWRLGWLVAPPTAVPELEKLAQNLYISAPSMAQHAALACFEPATLEILEARRAEFARRR 298 Query: 299 SLLLDGLRRIGIDRLAPTDGAFYVYADVSDFTSDSLAFCSKLLADTGVAIAPGIDFDTAR 358 LL LR +G GAFY+YAD+S F D+ AFC +L VAI PG+DF + Sbjct: 299 DFLLPALRELGFGIAVEPQGAFYLYADISAFGGDAYAFCQHMLETEFVAITPGLDFGRFQ 358 Query: 359 GGSFVRISFAGPSGDIEEALRRIGSWLPS 387 G VR ++ +++A+ RI L S Sbjct: 359 AGHHVRFAYTQDLPRLQQAVERIARGLRS 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: 427 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: 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