Align Succinylornithine transaminase (EC 2.6.1.81) (characterized)
to candidate Dsui_0023 Dsui_0023 acetylornithine/succinylornithine aminotransferase
Query= reanno::Koxy:BWI76_RS11670 (406 letters) >FitnessBrowser__PS:Dsui_0023 Length = 396 Score = 296 bits (759), Expect = 5e-85 Identities = 164/363 (45%), Positives = 218/363 (60%), Gaps = 3/363 (0%) Query: 28 GEGSRLWDQQGKEYIDFAGGIAVNALGHAHPRLVKALTEQAGKFWHTGNGYTNEPVLRLA 87 G GS L DQQGK Y+DF G AVN LGH HP +V+AL QAGK + + NEP L+LA Sbjct: 28 GRGSWLVDQQGKRYLDFVQGWAVNCLGHGHPAIVEALASQAGKLINPSPAFYNEPSLKLA 87 Query: 88 KQLIDATFADRVFFCNSGAEANEAALKLARKYAHDRFGSEKSGIVAFKNAFHGRTLFTVS 147 L + DRVFF ++GAEANE A+KLARK+ G I+ F FHGRTL T+S Sbjct: 88 AGLAAHSCFDRVFFASTGAEANEGAIKLARKWGQKHKGGAHE-IITFAGGFHGRTLATMS 146 Query: 148 AGGQPAYSQDFAPLPPQIQHAIYNDLDSAKALIDDNTCAVIVEPMQGEGGVVPADADFLR 207 A G+P + FAP P A NDLDS ALI++ T A+++EP+QGEGGVVPA A+FL+ Sbjct: 147 ASGKPGWDTLFAPQVPGFPKAQLNDLDSVAALINERTVAIMLEPIQGEGGVVPASAEFLQ 206 Query: 208 GLRELCDAHNALLIFDEVQTGVGRTGELYAYMHYGVTPDLLSTAKALGGGFPIGALLASE 267 LR++CD LLI DEVQTG+GRTG+L+A+ H G+ PD+++ K +GGG P+ ALLA E Sbjct: 207 LLRQICDDRGLLLIVDEVQTGMGRTGKLFAHQHAGIEPDIMTLGKGIGGGVPLSALLAKE 266 Query: 268 RCASVMTVGTHGTTYGGNPLACAVAGEVFATINTREVLNGVKQRHQWFCERLNAINARYG 327 G G TY GNPL AV V + L V + ++ L ++ R G Sbjct: 267 -SVCCFEAGDQGGTYNGNPLMTAVGAAVLEVLTAPGFLAEVAAKGEYLGAGLQRLSDRLG 325 Query: 328 LFKEIRGLGLLIGCVLKDEYAGKAKAISNQAAEEGLMILIAGANVVRFAPALIISEDEVN 387 L E RG GLL +L DE + + EGL++ +++RF P+L +S +E++ Sbjct: 326 LRGE-RGQGLLRALLLADERGPAIVEAARERGPEGLLLNAPRPHLLRFMPSLTVSREEID 384 Query: 388 SGL 390 L Sbjct: 385 QML 387 Lambda K H 0.321 0.137 0.412 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: 452 Number of extensions: 24 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: 406 Length of database: 396 Length adjustment: 31 Effective length of query: 375 Effective length of database: 365 Effective search space: 136875 Effective search space used: 136875 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 09 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