Align succinylornithine transaminase (EC 2.6.1.81) (characterized)
to candidate AO356_18725 AO356_18725 acetylornithine aminotransferase
Query= BRENDA::O30508 (406 letters) >FitnessBrowser__pseudo5_N2C3_1:AO356_18725 Length = 406 Score = 658 bits (1698), Expect = 0.0 Identities = 321/405 (79%), Positives = 358/405 (88%) Query: 1 MSAPHAQVERADFDRYMVPNYAPAAFIPVRGEGSRVWDQSGRELIDFAGGIAVTSLGHAH 60 MS A V+RADFD+ MVPNYAPAAFIPVRG GSRVWDQSGRELIDFAGGIAV LGHAH Sbjct: 1 MSVEQAAVQRADFDQVMVPNYAPAAFIPVRGAGSRVWDQSGRELIDFAGGIAVNVLGHAH 60 Query: 61 PALVKALTEQAQRIWHVSNVFTNEPALRLARKLVDATFAERVFLANSGAEANEAAFKLAR 120 PALV ALTEQA ++WHVSNVFTNEPALRLA KLV+ATFAER F NSGAEANEAAFKLAR Sbjct: 61 PALVGALTEQANKLWHVSNVFTNEPALRLAHKLVNATFAERAFFCNSGAEANEAAFKLAR 120 Query: 121 RYANDVYGPQKYEIIAASNSFHGRTLFTVNVGGQPKYSDGFGPKFEGITHVPYNDLEALK 180 R A D +G +KYEIIAA NSFHGRTLFTVNVGGQ KYSDGFGPK GITHVPYNDL ALK Sbjct: 121 RVAFDRFGSEKYEIIAALNSFHGRTLFTVNVGGQSKYSDGFGPKITGITHVPYNDLAALK 180 Query: 181 AAISDKTCAVVLEPIQGEGGVLPAQQAYLEGARKLCDEHNALLVFDEVQSGMGRVGELFA 240 AA+SDKTCAVVLEPIQGEGGVLPA+QAYL+GAR LCD H+ALLVFDEVQ+GMGR G LFA Sbjct: 181 AAVSDKTCAVVLEPIQGEGGVLPAEQAYLQGARDLCDAHDALLVFDEVQTGMGRSGHLFA 240 Query: 241 YMHYGVVPDILSSAKSLGGGFPIGAMLTTGEIAKHLSVGTHGTTYGGNPLASAVAEAALD 300 YMHYGVVPDIL+SAKSLGGGFPI AMLTT +AKHL VGTHGTTYGGNPLA AVAEA +D Sbjct: 241 YMHYGVVPDILTSAKSLGGGFPIAAMLTTEALAKHLVVGTHGTTYGGNPLACAVAEAVID 300 Query: 301 VINTPEVLDGVKAKHERFKSRLQKIGQEYGIFDEIRGMGLLIGAALTDEWKGKARDVLNA 360 V+NTPEVL GVK KH +FK+RL++IG++YG+F ++RG+GLLIG L D WKGKA+D+ NA Sbjct: 301 VVNTPEVLGGVKTKHAKFKARLEQIGEKYGLFTQVRGLGLLIGCVLNDAWKGKAKDIFNA 360 Query: 361 AEKEAVMVLQASPDVVRFAPSLVIDDAEIDEGLERFERAVAKLVR 405 AE+E +M+LQA PDV+RFAPSLV++DA+ID GL+RFERA AKL + Sbjct: 361 AEQEGLMILQAGPDVIRFAPSLVVEDADIDAGLDRFERAAAKLTQ 405 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: 603 Number of extensions: 17 Number of successful extensions: 1 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: 406 Length adjustment: 31 Effective length of query: 375 Effective length of database: 375 Effective search space: 140625 Effective search space used: 140625 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 Aug 03 2021. The underlying query database was built on Aug 03 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