Align acetylornithine/N-succinyldiaminopimelate aminotransferase [EC:2.6.1.11 2.6.1.17] (characterized)
to candidate PfGW456L13_1158 Acetylornithine aminotransferase (EC 2.6.1.11)
Query= reanno::azobra:AZOBR_RS19025 (389 letters) >FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_1158 Length = 427 Score = 247 bits (630), Expect = 5e-70 Identities = 155/384 (40%), Positives = 209/384 (54%), Gaps = 13/384 (3%) Query: 5 VMPTYARADIVFERGEGPYLYATDGRRFLDFAAGVAVNVLGHANPYLVEALTAQAHKLWH 64 +MP+ R VF RG+G +L+ +D R +LDF+ G N LGH+ LV A+TAQA L + Sbjct: 34 LMPSVERPKQVFVRGQGSWLWDSDDRAYLDFSQGGGANSLGHSPSVLVNAITAQAQSLIN 93 Query: 65 TSNLFRVAGQESLAKRLTEATFADTVFFTNSGAEAWECGAKLIRKYHYEKGDKARTRIIT 124 G SLA+ L +T +D + N+G+EA E KL RK+ A +RII Sbjct: 94 PGFGLHNRGMLSLAEHLCASTGSDQAYLLNTGSEACEAAIKLARKWGQRHRGGA-SRIIV 152 Query: 125 FEQAFHGRTLAAVSAAQQEKLIKGFGPLLDGFDLVPFGDLEAVRNAVTDETAGICLEPIQ 184 HGR+LA +SA+ L F P L GF VPF DL A+ AV + T I LEPIQ Sbjct: 153 ANNGCHGRSLATISASDSSTLANRFEPQLPGFSRVPFNDLPALHAAVDERTVAIMLEPIQ 212 Query: 185 GEGGIRAGSVEFLRGLREICDEHGLLLFLDEIQCGMGRTGKLFAHEWAGITPDVMAVAKG 244 E G+ +V +L+G+ +C E G+LL DE+Q G+GR G L A + G+T D++ + KG Sbjct: 213 SEAGVVPATVHYLKGVERLCRELGILLIFDEVQTGIGRCGSLLAEQSCGVTADIVVLGKG 272 Query: 245 IGGGFPLGACLATEKAAS---GMTAGTHGSTYGGNPLATAVGNAVLDKVLEPGFLDHVQR 301 +GGG PL A LA KA G AGTH GN L TA G +VLD V + FL HV Sbjct: 273 LGGGVPLAALLARGKACCFDIGELAGTH----HGNALMTAAGLSVLDTVQDKAFLKHVAE 328 Query: 302 IGGLLQDRLAGLVAENPAVFKGVRGKGLMLGLACGPAVGDVVV--ALRANGLLSVPAGDN 359 G L++ L L + +RG+GL+ GL D VV AL LL+ P D Sbjct: 329 AGQHLREGLGRLA--HRYGHGELRGQGLLWGLTLSDDSADAVVKAALYEGLLLNAPQAD- 385 Query: 360 VVRLLPPLNIGEAEVEEAVAILAK 383 +R P LN+ A ++E + LA+ Sbjct: 386 CLRFTPALNVSNANIDEMLLRLAR 409 Lambda K H 0.321 0.139 0.414 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: 432 Number of extensions: 26 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: 389 Length of database: 427 Length adjustment: 31 Effective length of query: 358 Effective length of database: 396 Effective search space: 141768 Effective search space used: 141768 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