Align Succinylornithine transaminase (EC 2.6.1.81) (characterized)
to candidate WP_013819183.1 METME_RS12875 acetylornithine transaminase
Query= reanno::Koxy:BWI76_RS11670 (406 letters) >NCBI__GCF_000214665.1:WP_013819183.1 Length = 390 Score = 296 bits (758), Expect = 7e-85 Identities = 162/376 (43%), Positives = 227/376 (60%), Gaps = 7/376 (1%) Query: 14 MMPVYAPAAFIPVRGEGSRLWDQQGKEYIDFAGGIAVNALGHAHPRLVKALTEQAGKFWH 73 +MP YA RGEG+ LWD GK Y+D GIAV LGHAHP + +AL +Q+ H Sbjct: 5 IMPTYARQTVTFDRGEGAWLWDSNGKRYLDALAGIAVCNLGHAHPAVHQALCKQSQTLIH 64 Query: 74 TGNGYTNEPVLRLAKQLIDATFADRVFFCNSGAEANEAALKLARKYAHDRFGSEKSGIVA 133 T N Y + LA +L + D VFFCNSGAEANEAA+K+ARKY H++ G + I+ Sbjct: 65 TSNLYGVKLQAELADKLCRLSGMDNVFFCNSGAEANEAAIKIARKYGHEQ-GIDAPVILT 123 Query: 134 FKNAFHGRTLFTVSAGGQPAYSQDFAPLPPQIQHAIYNDLDSAKALI--DDNTCAVIVEP 191 +FHGRT+ +SA G Q FAPL P H YN++D+ + I D N A++VEP Sbjct: 124 MDKSFHGRTMGALSATGNTKIKQGFAPLLPGFVHVPYNNIDAIISAIHADKNIVAILVEP 183 Query: 192 MQGEGGVVPADADFLRGLRELCDAHNALLIFDEVQTGVGRTGELYAYMHYGVTPDLLSTA 251 +QGEGGV DAD+L +R LCD H LL+ DE+QTG+GRTGE AY + PD+ + A Sbjct: 184 VQGEGGVNIPDADYLNRIRALCDEHQLLLMLDEIQTGIGRTGEFLAYQRNQILPDVCTLA 243 Query: 252 KALGGGFPIGALLASERCASVMTVGTHGTTYGGNPLACAVAGEVFATINTREVLNGVKQR 311 KALG G PIGA +A + A+++T G HG+T+GGNPLAC+ A V T+ + +++ ++ Sbjct: 244 KALGNGVPIGACMARGKAAAILTAGNHGSTFGGNPLACSAALAVLDTLCSTDLIADADRK 303 Query: 312 HQWFCERLNAINARYGLFKEIRGLGLLIGCVLKDEYAGKAKAISNQAAEEGLMILIAGAN 371 + C+ + IR LGL+IG L D G+ + +A E+GL+I + N Sbjct: 304 GKRICDAVTRQLEGNPHIVSIRHLGLMIGIEL-DAPCGE---LVGKALEQGLLINVTADN 359 Query: 372 VVRFAPALIISEDEVN 387 +R P L+I + +++ Sbjct: 360 TIRLLPPLLIDDAQID 375 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: 422 Number of extensions: 17 Number of successful extensions: 3 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: 390 Length adjustment: 31 Effective length of query: 375 Effective length of database: 359 Effective search space: 134625 Effective search space used: 134625 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 10 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