Align acetylornithine/N-succinyldiaminopimelate aminotransferase [EC:2.6.1.11 2.6.1.17] (characterized)
to candidate Echvi_3848 Echvi_3848 Ornithine/acetylornithine aminotransferase
Query= reanno::Marino:GFF3099 (404 letters) >FitnessBrowser__Cola:Echvi_3848 Length = 381 Score = 214 bits (544), Expect = 4e-60 Identities = 143/380 (37%), Positives = 200/380 (52%), Gaps = 20/380 (5%) Query: 24 IIPVRGEGSRIWDQEGREFIDLQGGIAVTCLGHSHPGLVGALHDQAEKIWHLSNVMTNEP 83 + PV+ GS IWD +G E++DL GG AV +GHSHP + +Q + I SN + Sbjct: 12 VTPVKASGSTIWDDQGNEYLDLYGGHAVISIGHSHPHYTKRIKEQLDNIAFYSNSVQIPI 71 Query: 84 ALRLAKTLCDLTFAER--VFFANSGAEANEAAFKLARRYAWEHHGKEKNEIISFKNSFHG 141 LA L L+ +F NSGAEANE A KLA K I+F FHG Sbjct: 72 QKELATKLGQLSGYPDYDLFLCNSGAEANENALKLAS------FETGKKGFIAFTKGFHG 125 Query: 142 RTLFTVSVGGQPKYLEGFEPAPGGIHHAEFNDLESVKKLISKEKTCAIVVEPIQGEGGVM 201 RT V++ PK + F A G+H FNDLE+V+K ++ ++VE IQG GG+ Sbjct: 126 RTSGAVALTDNPKIIAPFN-AHEGVHILPFNDLEAVEKQLATGTIAGVIVEGIQGVGGIQ 184 Query: 202 PGDQAFLQGLRDLCDENDALLVFDEVQSGVGRSGHFYAYQ-MYGVVPDILSSAKGLGGGF 260 D AFL GL L + A L+ DEVQSG RSG F+A+Q + G+ PD+++ AKG+G GF Sbjct: 185 VPDPAFLLGLSALTKQYGAKLILDEVQSGYARSGKFFAHQWVEGLKPDLITVAKGMGNGF 244 Query: 261 PVAAMLTTAKVAASLGVGTHGSTYGGNALACAVAQRVVDTVSQPEILKGVKARSDKLRKG 320 P+ +L + + AS G+ G+T+GGN LACA A V++ + + ++ K Sbjct: 245 PIGGVLISPEFKASHGL--LGTTFGGNHLACAAALAVLEVIDEENLITAAAENG----KA 298 Query: 321 MMDIGERYGVFTEVRGAGLLLGCVL-TEKWQGKAKDFLNAGLEEGVMVLVAGANVIRLAP 379 +M E+ TEVRG GL++G L TE +A + G G + IRL P Sbjct: 299 IMAALEKVAGVTEVRGKGLMIGFDLATEAGPVRAALIHEHKIFTG---SAGGKHTIRLLP 355 Query: 380 SLIIPEPDIELALERFEAAV 399 L I + L LE+ E + Sbjct: 356 PLNIEPKALTLFLEKLETVL 375 Lambda K H 0.318 0.137 0.406 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: 406 Number of extensions: 37 Number of successful extensions: 8 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: 404 Length of database: 381 Length adjustment: 31 Effective length of query: 373 Effective length of database: 350 Effective search space: 130550 Effective search space used: 130550 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 (21.7 bits) S2: 50 (23.9 bits)
This GapMind analysis is from Sep 17 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