Align L-2-aminoadipate aminotransferase monomer (EC 2.6.1.39) (characterized)
to candidate BPHYT_RS05965 BPHYT_RS05965 2-aminoadipate aminotransferase
Query= metacyc::MONOMER-6727 (397 letters) >FitnessBrowser__BFirm:BPHYT_RS05965 Length = 398 Score = 337 bits (864), Expect = 4e-97 Identities = 182/397 (45%), Positives = 255/397 (64%), Gaps = 13/397 (3%) Query: 1 MKPLSWSEAFGKSAGRIQASTIRELLKLTQRPGILSFAGGLPAPELFPKEEAAEAAARIL 60 +K +W + A ++ +S IRE+LK+T+RP ++SFAGGLP+P FP E A+ RIL Sbjct: 6 LKAPTWQ--LSERARKLTSSAIREILKVTERPEVISFAGGLPSPATFPAERMRAASDRIL 63 Query: 61 REKGEVALQYSPTEGYAPLRAFVAEWIGV-----RPEEVLITTGSQQALDLVGKVFLDEG 115 R++ ALQYS TEG+ PLR ++A+ V RP +VLITTGSQQALDL+GKV + Sbjct: 64 RDEPAAALQYSATEGFLPLREWIAKRYSVNGAQIRPTQVLITTGSQQALDLLGKVLVCPD 123 Query: 116 SPVLLEAPSYMGAIQAFRLQGPRFLTVPAGEEGPDLDALEEVLKRERPRFLYLIPSFQNP 175 SPVL+E P+Y+GA+Q+F + PR++ VP E G + L L R LY P+FQNP Sbjct: 124 SPVLVETPTYLGALQSFSMYEPRYVQVPTDEHGLVPEGLTPELTAGA-RLLYAQPNFQNP 182 Query: 176 TGGLTPLPARKRLLQMVMERGLVVVEDDAYRELYFGEARLPSLFELAREAGYPGVIYLGS 235 TG P+ R+ L V+EDD Y L + LP++ +A + +++LGS Sbjct: 183 TGRRLPIERRRALAAFAKTAPFPVIEDDPYGALDYAGEPLPTMLSMAPDH----IVHLGS 238 Query: 236 FSKVLSPGLRVAFAVAHPEALQKLVQAKQGADLHTPMLNQMLVHELLKEGFSE-RLERVR 294 FSKVL+PGLRV + +A E + KLVQAKQ DLHTP Q +V+E++K+GF + + +R Sbjct: 239 FSKVLAPGLRVGYIIAPEELIFKLVQAKQATDLHTPSFTQRIVYEVIKDGFLDTHVPTIR 298 Query: 295 RVYREKAQAMLHALDREVPKEVRYTRPKGGMFVWMELPKGLSAEGLFRRALEENVAFVPG 354 +YR++ AML +L+R +P+ V + RP+GGMFVW+ LP + + L A+ +NVAFVPG Sbjct: 299 ELYRDQCAAMLASLERYMPEGVSWNRPEGGMFVWVNLPAQIDSMKLLEEAVAQNVAFVPG 358 Query: 355 GPFFANGGGENTLRLSYATLDREGIAEGVRRLGRALK 391 GPFFAN NTLRLS+ T+ I EGV RLG ++ Sbjct: 359 GPFFANEAQHNTLRLSFVTVPPARIDEGVSRLGALIR 395 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: 508 Number of extensions: 19 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: 398 Length adjustment: 31 Effective length of query: 366 Effective length of database: 367 Effective search space: 134322 Effective search space used: 134322 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 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