Align acetylornithine/N-succinyldiaminopimelate aminotransferase [EC:2.6.1.11 2.6.1.17] (characterized)
to candidate WP_074200793.1 BUQ81_RS02435 aspartate aminotransferase family protein
Query= reanno::azobra:AZOBR_RS19025 (389 letters) >NCBI__GCF_900141795.1:WP_074200793.1 Length = 387 Score = 296 bits (757), Expect = 9e-85 Identities = 167/377 (44%), Positives = 234/377 (62%), Gaps = 6/377 (1%) Query: 5 VMPTYARADIVFERGEGPYLYATDGRRFLDFAAGVAVNVLGHANPYLVEALTAQAHKLWH 64 +M TYAR + F +G+G +LY R +LD +G+AV LGHANP + +AL QA+ L H Sbjct: 4 LMNTYARLPVAFVKGDGAWLYDESNRAYLDAISGIAVCSLGHANPEIAQALCDQANTLVH 63 Query: 65 TSNLFRVAGQESLAKRLTEATFADTVFFTNSGAEAWECGAKLIRKYHYEKGDKARTRIIT 124 TSNL+ + Q L +RL +A+ D VFF NSGAEA E KL R++ + +G + T I+ Sbjct: 64 TSNLYEIPLQTQLGERLCDASGMDKVFFCNSGAEANETAIKLARRWGHSRGIETPT-IVV 122 Query: 125 FEQAFHGRTLAAVSAAQQEKLIKGFGPLLDGFDLVPFGDLEAVRNAVTDET--AGICLEP 182 +FHGRTLAA+SA K GF PL++GF VP+ DL AV A++D + +EP Sbjct: 123 MNNSFHGRTLAALSATGNPKAQAGFEPLVEGFIPVPYDDLAAVE-ALSDNPNIVAVLVEP 181 Query: 183 IQGEGGIRAGSVEFLRGLREICDEHGLLLFLDEIQCGMGRTGKLFAHEWAGITPDVMAVA 242 +QGEGG+ + +L GLR +CD + LL +DE+Q GMGRTGKLFA + + I PDVM +A Sbjct: 182 VQGEGGVHIPADTYLPGLRALCDRNNWLLMVDEVQTGMGRTGKLFAFQHSDIQPDVMTLA 241 Query: 243 KGIGGGFPLGACLATEKAASGMTAGTHGSTYGGNPLATAVGNAVLDKVLEPGFLDHVQRI 302 K +G G P+GACLA +AA + G+HG+T+GGNPLA G VL+ + + V + Sbjct: 242 KALGNGVPIGACLARGEAADVLVPGSHGTTFGGNPLACRAGLTVLNIMQRDDWPARVAEM 301 Query: 303 GGLLQDRLAGLVAENPAVFKGVRGKGLMLGLACGPAVGDVVV-ALRANGLLSVPAGDNVV 361 G L+++ +A+NP V + +R KGLM+G+ G++V AL LL D VV Sbjct: 302 GKRLREQFEARLADNPNV-RAIRVKGLMIGIELDRPAGELVKRALEDYQLLINVTRDTVV 360 Query: 362 RLLPPLNIGEAEVEEAV 378 RLLPP I +E ++ V Sbjct: 361 RLLPPFVINASEQQQIV 377 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: 398 Number of extensions: 23 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: 389 Length of database: 387 Length adjustment: 30 Effective length of query: 359 Effective length of database: 357 Effective search space: 128163 Effective search space used: 128163 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