Align Succinylornithine transaminase; SOAT; EC 2.6.1.81; Succinylornithine aminotransferase (uncharacterized)
to candidate WP_109969430.1 DK846_RS13185 aspartate aminotransferase family protein
Query= curated2:Q3Z295 (406 letters) >NCBI__GCF_003173355.1:WP_109969430.1 Length = 400 Score = 253 bits (647), Expect = 5e-72 Identities = 149/387 (38%), Positives = 217/387 (56%), Gaps = 15/387 (3%) Query: 11 DEWMIPVYAPAPFIPVRGEGSRLWDQQGKEYIDFAGGIAVNALGHAHPELREALNEQASK 70 D + IP +G+G +WD+ GK+Y+DF G V +GHA+P + EAL Q+ K Sbjct: 12 DSYYIPFADKTHLSIEKGDGVYVWDENGKQYLDFTSGWGVTCIGHANPIITEALCNQSKK 71 Query: 71 FWHTGN-GYTNEP----VLRLAKKLIDATFADRVFFCNSGAEANEAALKLARKFAHDRYG 125 N G T P +++L +++ R+FF NSGAEAN+AA+KLARK Sbjct: 72 IIQNPNSGATYSPARSRLIQLFHEILPKHLT-RIFFANSGAEANDAAIKLARKV------ 124 Query: 126 SHKSGIVAFKNAFHGRTLFTVSAGGQPAYSQDFAPLPPDIRHAAYNDINSASALIDDATC 185 + K I++ + +FHGRT+ TVSA GQ + F PL P +NDI++ +ID Sbjct: 125 TGKKNIISTEMSFHGRTISTVSATGQDVHRNKFNPLMPGYFFVPFNDISAVKEIIDQDVA 184 Query: 186 AVIVEPIQGEGGVVPASNAFLQGLRELCDRHNALLIFDEVQTGVGRTGELYAYMHYGVTP 245 AVIVEPIQGEGGV S ++L L E+C H L I DE+QTG RTG L+ + G P Sbjct: 185 AVIVEPIQGEGGVNIPSESYLLELSEVCREHGVLFIADEIQTGFFRTGPLFYSISKGAKP 244 Query: 246 DLLTTAKALGGGFPVGALLTTEECASVMTVGTHGTTYGGNPLASAVAGKVLELINTPEML 305 D++T AK + GGFP A T+E + + G HG TY GNPL AV+ V+ + ++ Sbjct: 245 DIITMAKGIAGGFPFSAFAVTDEVVNGIQKGDHGGTYNGNPLGCAVSEAVIRYLIDSDIE 304 Query: 306 NGVKQRHDWFVERLNTINHRY-GLFSEVRGLGLLIGCVLNADYAGQAKQISQEAAKAGVM 364 + V ++RLN +Y +EVRG GLLI L D ++ +I G++ Sbjct: 305 SHVSDLGIDTIKRLNGWKEKYPKAITEVRGQGLLIALELTDDL--KSAEIVTRCLDNGLI 362 Query: 365 VLIAGGNVVRFAPALNVSEEEVTTGLD 391 + + G+++R PAL ++++E+ TGLD Sbjct: 363 LNLKHGHIIRIFPALTITKQEMQTGLD 389 Lambda K H 0.319 0.136 0.408 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: 382 Number of extensions: 19 Number of successful extensions: 5 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: 400 Length adjustment: 31 Effective length of query: 375 Effective length of database: 369 Effective search space: 138375 Effective search space used: 138375 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 Sep 24 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