Align acetylornithine/N-succinyldiaminopimelate aminotransferase [EC:2.6.1.11 2.6.1.17] (characterized)
to candidate WP_011612205.1 TERY_RS12675 aspartate aminotransferase family protein
Query= reanno::azobra:AZOBR_RS19025 (389 letters) >NCBI__GCF_000014265.1:WP_011612205.1 Length = 423 Score = 311 bits (796), Expect = 3e-89 Identities = 173/395 (43%), Positives = 238/395 (60%), Gaps = 11/395 (2%) Query: 5 VMPTYARADIVFERGEGPYLYATDGRRFLDFAAGVAVNVLGHANPYLVEALTAQAHKLWH 64 VM TY R I ERGEG ++ T+G+ +LDF AG+A LGHA+P ++ ++ Q +L H Sbjct: 29 VMNTYGRFPIAIERGEGCRVWDTEGKEYLDFVAGIATCTLGHAHPVMMATVSEQIKRLHH 88 Query: 65 TSNLFRVAGQESLAKRLTEATFADTVFFTNSGAEAWECGAKLIRKYHYEKGDKARTRIIT 124 SNL+ + Q LA+ L + + AD FF NSGAEA E KL RKY +EK + I+T Sbjct: 89 VSNLYYIPVQGELAQWLIQHSCADKAFFCNSGAEANEGAIKLARKYAHEKLNIENPTILT 148 Query: 125 FEQAFHGRTLAAVSAAQQEKLIKGFGPLLDGFDLVPFGDLEAVRNAVTD------ETAGI 178 +FHGRTLA ++A Q K KGF PL+ GF VP+ D+ A+ +A+ + + A I Sbjct: 149 AHASFHGRTLATMTATGQPKYHKGFSPLMPGFYYVPYNDIAAIESAIEELDKDKRQVAAI 208 Query: 179 CLEPIQGEGGIRAGSVEFLRGLREICDEHGLLLFLDEIQCGMGRTGKLFAHEWAGITPDV 238 LE +QGEGGIR G + + + +REIC+E G+LL LDE+Q GMGR+GK++ +E GI PD+ Sbjct: 209 MLEALQGEGGIRPGDMTYFKRIREICNEKGILLILDEVQAGMGRSGKIWGYENLGIEPDI 268 Query: 239 MAVAKGIGGGFPLGACLATEKAASGMTAGTHGSTYGGNPLATAVGNAVLDKVLEPGFLDH 298 AKG+GGG P+GA L + G+H ST+GGNP A AV AV + + L + Sbjct: 269 FTSAKGLGGGIPIGAMLC-KSHCDVFEPGSHASTFGGNPFACAVALAVCHTLEQENLLAN 327 Query: 299 VQRIGGLLQDRLAGLVAENPAVFKGVRGKGLMLGLACGPAVG----DVVVALRANGLLSV 354 VQ+ G L+ L + + P +F VRG GL+ GL D+V A GLL V Sbjct: 328 VQQRGDELRIELKAIADKYPNLFSEVRGWGLINGLELNATATLTSIDIVKAAMNEGLLIV 387 Query: 355 PAGDNVVRLLPPLNIGEAEVEEAVAILAKTAKELV 389 PAG V+R +PPL + E EV+EA+ +LAK V Sbjct: 388 PAGPKVLRFVPPLIVTETEVKEAMDLLAKAIANTV 422 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: 428 Number of extensions: 21 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: 423 Length adjustment: 31 Effective length of query: 358 Effective length of database: 392 Effective search space: 140336 Effective search space used: 140336 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