Align L-2-aminoadipate aminotransferase monomer (EC 2.6.1.39) (characterized)
to candidate WP_076477443.1 BW971_RS04965 PLP-dependent aminotransferase family protein
Query= metacyc::MONOMER-6727 (397 letters) >NCBI__GCF_900156495.1:WP_076477443.1 Length = 389 Score = 247 bits (630), Expect = 5e-70 Identities = 151/389 (38%), Positives = 218/389 (56%), Gaps = 19/389 (4%) Query: 12 KSAGRIQASTIRELLKLTQRPGILSFAGGLPAPELFPKEEAAEAAARILREKGEVALQYS 71 ++ I+ S IR+LL++T+RP +LS AGGLPA +L P + AEAA+R++ E ALQY+ Sbjct: 10 RALSSIRGSAIRDLLRVTERPDVLSMAGGLPATDLIPSDRIAEAASRVISEAS--ALQYT 67 Query: 72 PTEGYAPLRAFVAEWIGVRPEEVLITTGSQQALDLVGKVFLDEGSPVLLEAPSYMGAIQA 131 + G PLR VA+ G PE VLIT GSQQAL L + LD G V+++ P Y+GA+Q Sbjct: 68 VSAGVRPLREVVADRDGTHPERVLITHGSQQALFLSAQALLDPGDTVIVDDPVYVGALQV 127 Query: 132 FRLQGPRFLTVPAGEEGPDLDALEEVLK-RERPRFLYLIPSFQNPTGGLTPLPARKRLLQ 190 F+ + +P EG D+D LE +L RPR ++ + +F NP G R+RL + Sbjct: 128 FQSVRAEIVALPITAEGTDVDRLERLLSDGVRPRIVHTVSNFHNPAGVTASARTRRRLAE 187 Query: 191 MVMERGLVVVEDDAYRELYFGEARLPSLFELAREAGYPG--VIYLGSFSKVLSPGLRVAF 248 + + G ++EDD Y +L F + + PG VI LGS SK+L+P LRV + Sbjct: 188 LAADHGFWIIEDDPYGQLRFAGRSMDPI---------PGDRVIRLGSASKILAPALRVGW 238 Query: 249 AVAHPEALQKLVQAKQGADLHTPMLNQMLVHELLKEG--FSERLERVRRVYREKAQAMLH 306 A P+ ++ + +QGADL Q++ +LL + + + +RR Y +A A+ Sbjct: 239 LQASPDVVELVELLRQGADLCGSTFAQLMTADLLGDSDFMTAHVSDLRREYARRAAALTG 298 Query: 307 AL--DREVPKEVRYTRPKGGMFVWMELPKGLSAEGLFRRALEENVAFVPGGPFFANGGGE 364 AL D V + P+GGMF W+ LP GL L A+ VAFVPG F + G Sbjct: 299 ALRTDLGAVCGVEFIEPEGGMFCWLRLP-GLDTAILLDHAVRAGVAFVPGAAFAVDAGLG 357 Query: 365 NTLRLSYATLDREGIAEGVRRLGRALKGL 393 + LRLS+ATL + + E VRRL A+ L Sbjct: 358 DRLRLSFATLSPDQLTEAVRRLATAVHDL 386 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: 339 Number of extensions: 18 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: 389 Length adjustment: 31 Effective length of query: 366 Effective length of database: 358 Effective search space: 131028 Effective search space used: 131028 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 24 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