Align L-2-aminoadipate aminotransferase monomer (EC 2.6.1.39) (characterized)
to candidate HSERO_RS09050 HSERO_RS09050 2-aminoadipate aminotransferase
Query= metacyc::MONOMER-6727 (397 letters) >FitnessBrowser__HerbieS:HSERO_RS09050 Length = 398 Score = 337 bits (865), Expect = 3e-97 Identities = 181/399 (45%), Positives = 256/399 (64%), Gaps = 15/399 (3%) Query: 3 PLSWSEAFGKSAGRIQASTIRELLKLTQRPGILSFAGGLPAPELFPKEEAAEAAARILRE 62 PL W F + A +++S IRE+LK+T RP I SFAGGLP+P FP E A R+L + Sbjct: 8 PLQWQ--FSQRADAMKSSAIREILKVTMRPDITSFAGGLPSPLTFPVEHMKTAFDRVLSQ 65 Query: 63 KGEVALQYSPTEGYAPLRAFVAEWIG-----VRPEEVLITTGSQQALDLVGKVFLDEGSP 117 +G++ALQY PT+GY PLR ++A + + E+VL+ +GSQQ LDL+GKV +DEGS Sbjct: 66 QGKMALQYGPTDGYLPLREWIAASLSTNGAQISAEQVLMVSGSQQGLDLLGKVLIDEGSK 125 Query: 118 VLLEAPSYMGAIQAFRLQGPRFLTVPAGEEGPDLDALEEVLKRERPRFLYLIPSFQNPTG 177 VL+E PSY+GA+QAF L G +F +VP+ E G + +E + R LY +P+FQNPTG Sbjct: 126 VLVETPSYLGALQAFALYGAKFESVPSDEFGLQPETIEAI--AGGARMLYSLPNFQNPTG 183 Query: 178 GLTPLPARKRLLQMVMERGLVVVEDDAYRELYFGEARLPSLFELAREAGYPGVIYLGSFS 237 P R +L++ GL ++EDD Y L + A LP + + GVIY+GSFS Sbjct: 184 RTLPTERRFKLVETCARLGLPLIEDDPYGALSYQNAPLPKMLSM----NPSGVIYMGSFS 239 Query: 238 KVLSPGLRVAFAVAHPEALQKLVQAKQGADLHTPMLNQMLVHELLKEGF-SERLERVRRV 296 KVL+PG+R+ + VA + K+ QAKQ DLHT L QM+V+E +K+GF + + +R++ Sbjct: 240 KVLTPGIRLGYVVAPRPLILKMEQAKQATDLHTAQLTQMVVYEAIKDGFLDQHVPTIRKL 299 Query: 297 YREKAQAMLHALDREVPKEVRYTRPKGGMFVWMELPKGLSAEGLFRRALE-ENVAFVPGG 355 Y ++ QAML AL + P +++P+GGMF+W+ LP+ + A L A+E E VAFVPG Sbjct: 300 YGDQCQAMLDALQQYFPASCSWSKPEGGMFIWVTLPEHIDAGALLNEAVEQEKVAFVPGA 359 Query: 356 PFFANGGGENTLRLSYATLDREGIAEGVRRLGRALKGLL 394 PF+AN +NTLRLS+ T+ E I GV RLG+ + L Sbjct: 360 PFYANVAQKNTLRLSFVTVPPEQIRAGVERLGKLIASKL 398 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: 485 Number of extensions: 28 Number of successful extensions: 6 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