Align L-2-aminoadipate aminotransferase monomer (EC 2.6.1.39) (characterized)
to candidate Ac3H11_1358 Valine--pyruvate aminotransferase (EC 2.6.1.66)
Query= metacyc::MONOMER-6727 (397 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_1358 Length = 401 Score = 317 bits (811), Expect = 5e-91 Identities = 180/393 (45%), Positives = 254/393 (64%), Gaps = 12/393 (3%) Query: 5 SWSEAFGKSAGRIQASTIRELLKLTQRPGILSFAGGLPAPELFPKEEAAEAAARILREKG 64 +W+ A + A R+ S IRE+LK+T++PGI+S AGGLP+P+ FP A A+A +L G Sbjct: 11 TWTLA--RRAERMNPSVIREILKVTEKPGIISLAGGLPSPKTFPVSAFAAASAAVLANDG 68 Query: 65 EVALQYSPTEGYAPLRAFVAEWI--GVRPEEVLITTGSQQALDLVGKVFLDEGSPVLLEA 122 ALQY+ +EGYAPLR +A+++ V +++LITTGSQQALDL+ KV +DE S VL+E Sbjct: 69 PAALQYAASEGYAPLRQAIADFLPWDVDADQILITTGSQQALDLIAKVLIDENSRVLVET 128 Query: 123 PSYMGAIQAFRLQGPRFLTVPAGEEGPDLDALEEVL--KRERPRFLYLIPSFQNPTGGLT 180 P+Y+GA+QAF P + V + +EG +D L+ + ++ RFLY++P+FQNPTG Sbjct: 129 PTYLGALQAFTPMEPSVVAVASDDEGVLIDDLKAKVGTGADKARFLYVLPNFQNPTGRTM 188 Query: 181 PLPARKRLLQMVMERGLVVVEDDAYRELYFGEARLPSLFELAREAGYPGVIYLGSFSKVL 240 R L++ E L +VED+ Y +L+F P AR G IY+GSFSKVL Sbjct: 189 TEARRAALVKAAAELNLPLVEDNPYGDLWFDNP--PPAPLTARNP--EGCIYMGSFSKVL 244 Query: 241 SPGLRVAFAVAHPEALQKLVQAKQGADLHTPMLNQMLVHELLKEGFSER-LERVRRVYRE 299 +PGLR+ F VA KL+QAKQ ADLHTP NQ LV E++K F +R + +R +Y++ Sbjct: 245 APGLRLGFVVAPKAVYPKLLQAKQAADLHTPGYNQRLVAEVMKGNFLDRHVPTIRALYKQ 304 Query: 300 KAQAMLHALDREVP-KEVRYTRPKGGMFVWMELPKGLSAEGLFRRALEENVAFVPGGPFF 358 + +AML AL +E+ V + RP GGMF+W+ LP+G+SA L +A+E NVAFVPG F+ Sbjct: 305 QCEAMLAALTQEMAGLGVEWNRPDGGMFLWVRLPEGMSAIELLPQAVERNVAFVPGAAFY 364 Query: 359 ANGGGENTLRLSYATLDREGIAEGVRRLGRALK 391 A+ TLRLS+ T E IA G+ L A++ Sbjct: 365 ADNADPRTLRLSFVTSTVEQIATGIAALAAAIR 397 Lambda K H 0.320 0.139 0.401 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: 439 Number of extensions: 16 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: 397 Length of database: 401 Length adjustment: 31 Effective length of query: 366 Effective length of database: 370 Effective search space: 135420 Effective search space used: 135420 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 (21.8 bits) S2: 50 (23.9 bits)
This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.
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