Align acetylornithine/N-succinyldiaminopimelate aminotransferase [EC:2.6.1.11 2.6.1.17] (characterized)
to candidate WP_017599103.1 D471_RS0113530 aminotransferase class III-fold pyridoxal phosphate-dependent enzyme
Query= reanno::azobra:AZOBR_RS19025 (389 letters) >NCBI__GCF_000341125.1:WP_017599103.1 Length = 418 Score = 228 bits (580), Expect = 3e-64 Identities = 154/410 (37%), Positives = 213/410 (51%), Gaps = 45/410 (10%) Query: 14 IVFERGEGPYLYATDGRRFLDFAAGVAVNVLGHANPYLVEALTAQAHKLWH---TSNLFR 70 ++ RGEG YLY D RR+LDF AG+ V GH +P +V A Q L H T+ + R Sbjct: 14 VLAARGEGAYLYDEDDRRYLDFTAGIGVTSTGHCHPRVVAAAQEQVATLIHGQYTTVMHR 73 Query: 71 --VAGQESLAKRLTEATFADTVFFTNSGAEAWECGAKLIRKYHYEKGDKARTRIITFEQA 128 + E L L E D +F+ NSG+EA E +L R+ R I F+ + Sbjct: 74 PLLRLTERLGDVLPEGV--DRLFYVNSGSEAVEAALRLARQA------TGRQNAIVFQGS 125 Query: 129 FHGRTLAAVSAAQQE-KLIKGFGPLLDGFDLVPF--------GDLEAVRNAVTD------ 173 FHGRT+ A S K+ G GPL+ G + PF + +AV +A+ + Sbjct: 126 FHGRTMGAASLTTSGVKIRAGIGPLVPGVVVSPFPYAYRLGMAEEDAVAHALREFDYQLT 185 Query: 174 ------ETAGICLEPIQGEGGIRAGSVEFLRGLREICDEHGLLLFLDEIQCGMGRTGKLF 227 +TA + +EP+ GEGG FLRGLRE D+HG LL LDE+Q G GRTG + Sbjct: 186 TVSSPKDTAAVFIEPVLGEGGYVPVPDSFLRGLRERADQHGFLLVLDEVQTGFGRTGTFW 245 Query: 228 AHEWAGITPDVMAVAKGIGGGFPLGACLATEKAASGMTAGTHGSTYGGNPLATAVGNAVL 287 HE +G+ PD++ AKG+ GFPL A A E + G+ G TYGGN +A A A L Sbjct: 246 GHEPSGVRPDIVITAKGLASGFPLSAIAAPESIMAKAWPGSQGGTYGGNAVACAAAIATL 305 Query: 288 DKVLEPGFLDHVQRIGGLLQDRLAGLVAENPAVFKGVRGKGLMLG--LACGPAVGDVVVA 345 D + E G +++ R+G L+ L + +P V VRG+GLML D A Sbjct: 306 DVIQEEGLVENSARMGERLRQGLEKVAGAHP-VIGDVRGRGLMLANEFTAPDGSPDGATA 364 Query: 346 LRA------NGLLSVPAG--DNVVRLLPPLNIGEAEVEEAVAILAKTAKE 387 LRA NGLL + G NVVR++PPL + +V+ AV++ A + +E Sbjct: 365 LRAQQAAAGNGLLLLTCGPAGNVVRMIPPLVVNGEQVDTAVSLWAASVEE 414 Lambda K H 0.321 0.139 0.414 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: 500 Number of extensions: 36 Number of successful extensions: 4 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: 389 Length of database: 418 Length adjustment: 31 Effective length of query: 358 Effective length of database: 387 Effective search space: 138546 Effective search space used: 138546 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