Align [amino group carrier protein]-gamma-(L-lysyl)-L-glutamate aminotransferase (EC 2.6.1.118) (characterized)
to candidate AO353_03025 AO353_03025 acetylornithine aminotransferase
Query= BRENDA::Q93R93 (395 letters) >FitnessBrowser__pseudo3_N2E3:AO353_03025 Length = 406 Score = 265 bits (678), Expect = 1e-75 Identities = 157/377 (41%), Positives = 221/377 (58%), Gaps = 17/377 (4%) Query: 32 VRGQGARVWDAEGNEYIDCVGGYGVANLGHGNPEVVEAVKRQAETLMAMPQTLPT-PMRG 90 VRG G+RVWD G E ID GG V LGH +P +V A+ QA L + P Sbjct: 29 VRGAGSRVWDQSGRELIDFAGGIAVNVLGHAHPALVGALTEQANKLWHVSNVFTNEPALR 88 Query: 91 EFYRTLTAILPPELNRVFPVNSGTEANEAALKFAR--AHT--GRKKF--VAAMRGFSGRT 144 ++ + A +RVF NSG EANEAA K AR AH G +K+ +AA+ F GRT Sbjct: 89 LAHKLIDATFA---DRVFFCNSGAEANEAAFKLARRVAHDRFGSEKYEIIAALNSFHGRT 145 Query: 145 MGSLSVTWEPKYREPFLPLVEPVEFIPYNDVEALKRAVDEETAAVILEPVQGEGGVRPAT 204 + +++V + KY + F P + + + +ND++ALK A+ ++T AV+LEP+QGEGGV PA Sbjct: 146 LFTVNVGGQSKYSDGFGPKITGITHVKFNDLDALKAAISDKTCAVVLEPIQGEGGVLPAD 205 Query: 205 PEFLRAAREITQEKGALLILDEIQTGMGRTGKRFAFEHFGIVPDILTLAKALGGGVPLGV 264 +L+ ARE+ + ALLI DE+QTGMGR+G+ FA++H+G+ PDILT AK+LGGG P+ Sbjct: 206 LAYLQGARELCTQHNALLIFDEVQTGMGRSGELFAYQHYGVTPDILTSAKSLGGGFPIAA 265 Query: 265 AVMREEVARSMPKGGHGTTFGGNPLAMAAGVAAIRYLERTRLWERAAELGPWFMEKLRAI 324 + E++A+ + G HGTT+GGNPLA A A I + + F +L I Sbjct: 266 MLTTEDLAKHLVVGTHGTTYGGNPLACAVAEAVIDVVNTPEVLNGVKAKHDLFKTRLEQI 325 Query: 325 PSP--KIREVRGMGLMVGLELKE----KAAPYIARLEKEHRVLALQAGPTVIRFLPPLVI 378 + +VRG+GL++G L E KA E+E ++ LQAGP VIRF P LV+ Sbjct: 326 GAKYGLFTQVRGLGLLLGCVLSEAWKGKAKDVFNAAERE-GLMILQAGPDVIRFAPSLVV 384 Query: 379 EKEDLERVVEAVRAVLA 395 E D+E +E +A Sbjct: 385 EDADIEEGLERFERAVA 401 Lambda K H 0.319 0.137 0.403 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: 385 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: 395 Length of database: 406 Length adjustment: 31 Effective length of query: 364 Effective length of database: 375 Effective search space: 136500 Effective search space used: 136500 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 (21.7 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