Align succinylornithine transaminase (EC 2.6.1.81) (characterized)
to candidate 8502443 DvMF_3149 acetylornithine aminotransferase (RefSeq)
Query= BRENDA::O30508 (406 letters) >FitnessBrowser__Miya:8502443 Length = 402 Score = 297 bits (760), Expect = 4e-85 Identities = 158/369 (42%), Positives = 218/369 (59%), Gaps = 5/369 (1%) Query: 30 RGEGSRVWDQSGRELIDFAGGIAVTSLGHAHPALVKALTEQAQRIWHVSNVFTNEPALRL 89 RG+GSR+WD GRE +D GIAVTSLGH H L + QA+++ HVSN+F E L L Sbjct: 29 RGQGSRLWDVDGREYVDLLSGIAVTSLGHCHEELAEVAAAQARKLVHVSNLFYQEEQLDL 88 Query: 90 ARKLVDATFAERVFLANSGAEANEAAFKLARRYANDVYGPQKYEIIAASNSFHGRTLFTV 149 A +L+ + + F NSGAEANEAA KLARRY V G + YEII + +FHGRTL TV Sbjct: 89 AERLLSTSHCTKAFFCNSGAEANEAAIKLARRYMQRVQGREAYEIITLTGAFHGRTLATV 148 Query: 150 NVGGQPKYSDGFGPKFEGITHVPYNDLEALKAAISDKTCAVVLEPIQGEGGVLPAQQAYL 209 GQ K+ DGF P EG VP D+EAL+AAI +T V++E +QGEGGV P Y Sbjct: 149 AATGQAKFQDGFYPMPEGFRQVPSGDIEALRAAIGPQTAGVLVEVVQGEGGVCPLDPDYA 208 Query: 210 EGARKLCDEHNALLVFDEVQSGMGRVGELFAYMHYGVVPDILSSAKSLGGGFPIGAMLTT 269 + LC E L + DE+Q+GM R G +++ +YG+ PDI+S AK+L G P+GAM+TT Sbjct: 209 RAVQALCREKGVLFMTDEIQAGMCRTGRFWSFQNYGLEPDIVSCAKALANGLPMGAMMTT 268 Query: 270 GEIAKHLSVGTHGTTYGGNPLASAVAEAALDVINTPEVLDGVKAKHERFKSRLQKIGQEY 329 E+A+ G+H TT+G L SAVA ++++ ++ + R R + +GQ+ Sbjct: 269 DEVARGFVAGSHATTFGAGALVSAVASRTVEIMLRDDLAGRAATEGARIMDRFRAMGQKL 328 Query: 330 -GIFDEIRGMGLLIGAALTDEWKGKARDVLNAAEKEAVMVLQASPDVVRFAPSLVIDDAE 388 G D +RG+GL+IG L + GK +V A + V+R P+L I A+ Sbjct: 329 PGTIDHVRGLGLMIGVVLA--FPGK--EVWQALIDRGFICNLTQDCVLRLLPALTIPRAD 384 Query: 389 IDEGLERFE 397 +D + E Sbjct: 385 LDAFADALE 393 Lambda K H 0.318 0.135 0.394 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: 390 Number of extensions: 13 Number of successful extensions: 2 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: 406 Length of database: 402 Length adjustment: 31 Effective length of query: 375 Effective length of database: 371 Effective search space: 139125 Effective search space used: 139125 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 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