Align acetylornithine/N-succinyldiaminopimelate aminotransferase [EC:2.6.1.11 2.6.1.17] (characterized)
to candidate Ga0059261_3205 Ga0059261_3205 transaminase, acetylornithine/succinylornithine family
Query= reanno::azobra:AZOBR_RS19025 (389 letters) >FitnessBrowser__Korea:Ga0059261_3205 Length = 398 Score = 424 bits (1090), Expect = e-123 Identities = 218/391 (55%), Positives = 274/391 (70%), Gaps = 3/391 (0%) Query: 2 IPVVMPTYARADIVFERGEGPYLYATDGRRFLDFAAGVAVNVLGHANPYLVEALTAQAHK 61 I +MP Y R ++ RGEG YL G R+LDFAAG+AVN LGH +P +A+ QA Sbjct: 3 ITPLMPVYPRCEVRPVRGEGCYLIGERGERYLDFAAGIAVNALGHGHPQFTKAIAEQAAT 62 Query: 62 LWHTSNLFRVAGQESLAKRLTEATFADTVFFTNSGAEAWECGAKLIRKYHYEKGDKARTR 121 L H SNL+ E+LA+R+ + +FADTVFFTNSG EA EC K R+YHY G+ R + Sbjct: 63 LMHVSNLYGSPQGEALAQRIVDNSFADTVFFTNSGVEAIECAIKTARRYHYVNGNPQRHK 122 Query: 122 IITFEQAFHGRTLAAVSAAQQEKLIKGFGPLLDGFDLVPFGDLEAVRNAVTDETAGICLE 181 +ITF+ AFHGR++ A+SA Q K+ GF PLL GFD V F DLE + DETAG +E Sbjct: 123 LITFKNAFHGRSIGAISATDQPKMRDGFEPLLPGFDYVKFNDLEGAIAKIDDETAGFLVE 182 Query: 182 PIQGEGGIRAGSVEFLRGLREICDEHGLLLFLDEIQCGMGRTGKLFAHEWAGITPDVMAV 241 +QGEGG+ AG+VEF++GLR+ CDEHGLLL LDEIQCG GRTGK++A+E GITPD++ Sbjct: 183 TVQGEGGMTAGTVEFIQGLRKACDEHGLLLILDEIQCGYGRTGKMWAYEHYGITPDILTA 242 Query: 242 AKGIGGGFPLGACLATEKAASGMTAGTHGSTYGGNPLATAVGNAVLDKVLEPGFLDHVQR 301 AKGIG GFPLGACLATE+AA GMT GTHGSTYGGNPLA A G AVLD +LEPGF +HV++ Sbjct: 243 AKGIGNGFPLGACLATEEAAKGMTFGTHGSTYGGNPLAMAAGQAVLDVMLEPGFFEHVEK 302 Query: 302 IGGLLQDRLAGLVAENPAVFKGVRGKGLMLGLAC-GPAVG-DVVVALRAN-GLLSVPAGD 358 +G L+ L+ + +F +RGKGLMLG+ PAV D V LR N GLL+V AG+ Sbjct: 303 MGERLRAGFEQLIPNHDHLFDEIRGKGLMLGIKLKEPAVSRDFVAHLRENHGLLTVAAGE 362 Query: 359 NVVRLLPPLNIGEAEVEEAVAILAKTAKELV 389 NV R+LPPL I E+ + E + L+ A+ V Sbjct: 363 NVFRVLPPLVIEESHIAECIEKLSAGARSYV 393 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: 535 Number of extensions: 22 Number of successful extensions: 2 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: 398 Length adjustment: 31 Effective length of query: 358 Effective length of database: 367 Effective search space: 131386 Effective search space used: 131386 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