Align [amino group carrier protein]-gamma-(L-lysyl)-L-glutamate aminotransferase (EC 2.6.1.118) (characterized)
to candidate 7023380 Shewana3_0610 bifunctional N-succinyldiaminopimelate-aminotransferase/acetylornithine transaminase protein (RefSeq)
Query= BRENDA::Q93R93 (395 letters) >FitnessBrowser__ANA3:7023380 Length = 405 Score = 248 bits (634), Expect = 2e-70 Identities = 151/380 (39%), Positives = 212/380 (55%), Gaps = 22/380 (5%) Query: 32 VRGQGARVWDAEGNEYIDCVGGYGVANLGHGNPEVVEAVKRQAETLMAMPQTLPTPMRGE 91 VRG+G+RVWD EGNE+ID GG V LGH +P +V A+K Q E L + + E Sbjct: 28 VRGEGSRVWDQEGNEFIDFAGGIAVNCLGHCHPALVNALKTQGEKLWHLSNVMTNEPALE 87 Query: 92 FYRTLTAILPPELNRVFPVNSGTEANEAALKFARAHTGRK------KFVAAMRGFSGRTM 145 L E RV+ NSG EANEAALK AR + K + +A + F GRT Sbjct: 88 LATKLVNSTFAE--RVYFANSGAEANEAALKLARRYALEKFGVEKDEIIAFDKAFHGRTF 145 Query: 146 GSLSVTWEPKYREPFLPLVEPVEFIPYNDVEALKRAVDEETAAVILEPVQGEGGVRPATP 205 ++SV + Y + F P + + +PYNDV AL+ AV ++T A++LEP+QGEGG+ A P Sbjct: 146 FTVSVGGQAAYSDGFGPKPQSITHLPYNDVAALEAAVSDKTCAIMLEPLQGEGGIIDADP 205 Query: 206 EFLRAAREITQEKGALLILDEIQTGMGRTGKRFAFEHFGIVPDILTLAKALGGGVPLGVA 265 FL+A RE+ + AL+I DE+QTG+GRTG+ +A+ IVPDILT AKALGGG P+ Sbjct: 206 AFLKAVRELANKHNALVIFDEVQTGVGRTGELYAYMGTDIVPDILTTAKALGGGFPIAAM 265 Query: 266 VMREEVARSMPKGGHGTTFGGNPLAMAAGVAAIRYLERTRLWERAAELGPWFMEKLRAIP 325 + E+A + G HG+T+GGNPLA A G A + + + + L I Sbjct: 266 LTTAEIAEHLKVGTHGSTYGGNPLACAIGNAVLDVVNTPEVLNGVKHREQLLRDGLNKIN 325 Query: 326 SP--KIREVRGMGLMVGLELKE----KAAPYIARLEKEHRVLALQAGPTVIRFLPPLVIE 379 E+RG GL++G L E ++ ++ E +++L AG V+RF P LVI Sbjct: 326 EKYHVFSEIRGKGLLLGAVLNEQYQGRSRDFLVASVAE-GLMSLMAGANVVRFAPSLVIP 384 Query: 380 KEDL-------ERVVEAVRA 392 + D+ ER V ++ A Sbjct: 385 EADIAEGLARFERAVASIAA 404 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: 396 Number of extensions: 20 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: 405 Length adjustment: 31 Effective length of query: 364 Effective length of database: 374 Effective search space: 136136 Effective search space used: 136136 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