Align L-2-aminoadipate aminotransferase monomer (EC 2.6.1.39) (characterized)
to candidate WP_012465060.1 CLIM_RS00365 PLP-dependent aminotransferase family protein
Query= metacyc::MONOMER-6727 (397 letters) >NCBI__GCF_000020465.1:WP_012465060.1 Length = 397 Score = 243 bits (619), Expect = 9e-69 Identities = 143/393 (36%), Positives = 215/393 (54%), Gaps = 14/393 (3%) Query: 10 FGKSAGRIQASTIRELLKLTQRPGILSFAGGLPAPELFPKEEAAEAAARILREKGEVALQ 69 F +S +++S IREL+ L RP I+SFAGG+P +LFP EE E + + + A Q Sbjct: 4 FSQSVSALRSSAIRELMSLASRPDIISFAGGMPGNDLFPVEEVEELFQNLDPKTKQTAFQ 63 Query: 70 YSPTEGYAPLRAFVAEWIG-----VRPEEVLITTGSQQALDLVGKVFLDEGSPVLLEAPS 124 Y PT G L ++ ++ V+ ++ITTGSQQAL ++ + F+D G VL E P Sbjct: 64 YGPTPGLPSLLESLSGYLERKGLPVQKNRLMITTGSQQALSILARAFIDPGDQVLSEYPC 123 Query: 125 YMGAIQAFRLQGPRFLTVPAGEEGPDLDALEEVLKRERP-RFLYLIPSFQNPTGGLTPLP 183 ++GAI AF+ G +++P EEG D+ L R P + LYL P F NP G L Sbjct: 124 FIGAIAAFKACGADIVSIPVDEEGIDIGMLRHEAGRPSPAKLLYLTPYFHNPAGMLYTTR 183 Query: 184 ARKRLLQMVMERGLVVVEDDAYRELYFGE---ARLPSLFELAREAGYPGVIYLGSFSKVL 240 +++L++++ R + ++EDDAY +L+F E RL L + E + Y GSFSK+L Sbjct: 184 RKRQLIEVMQGRDIPIIEDDAYGDLWFSEEDRERLQPLKSIDPEG--IDLCYTGSFSKIL 241 Query: 241 SPGLRVAFAVAHPEAL-QKLVQAKQGADLHTPMLNQMLVHELLKEG-FSERLERVRRVYR 298 PGLR+ + +A PEA+ +K KQ AD +P Q++ ++ G + VR YR Sbjct: 242 GPGLRLGWLLA-PEAIHEKCELIKQSADACSPSFTQVIADAFIRSGRIDSYIASVRNEYR 300 Query: 299 EKAQAMLHALDREVPKEVRYTRPKGGMFVWMELPKGLSAEGLFRRALEENVAFVPGGPFF 358 +A M AL +P V++ PKGG ++W+ LP+G A + + A+E FV G F Sbjct: 301 CRAACMTAALGSLLPDYVQWNEPKGGFYIWLTLPEGADATEILKHAIEGGAVFVAGSTFD 360 Query: 359 ANGGGENTLRLSYATLDREGIAEGVRRLGRALK 391 G N +RLSY E I G+ + RA++ Sbjct: 361 PEGRRNNAIRLSYCNNTPEEIERGIPIVARAIR 393 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: 462 Number of extensions: 24 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: 397 Length adjustment: 31 Effective length of query: 366 Effective length of database: 366 Effective search space: 133956 Effective search space used: 133956 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 10 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