Align [amino group carrier protein]-gamma-(L-lysyl)-L-glutamate aminotransferase (EC 2.6.1.118) (characterized)
to candidate N515DRAFT_3308 N515DRAFT_3308 acetylornithine/N-succinyldiaminopimelate aminotransferase
Query= BRENDA::Q93R93 (395 letters) >FitnessBrowser__Dyella79:N515DRAFT_3308 Length = 411 Score = 269 bits (688), Expect = 9e-77 Identities = 172/405 (42%), Positives = 225/405 (55%), Gaps = 28/405 (6%) Query: 11 ALLEAEKTLDSGVYNKHDLLIVRGQGARVWDAEGNEYIDCVGGYGVANLGHGNPEVVEAV 70 +L++ K VY ++++ G+GARVWD EG +Y+D G V LGH +P++V+A+ Sbjct: 9 SLIDLGKRYWLPVYRPREVVLDHGKGARVWDTEGRDYVDLGAGIAVNALGHQDPDLVDAL 68 Query: 71 KRQAETLMAMPQTLPTPMRGEFYRTLTAILPPEL-------NRVFPVNSGTEANEAALKF 123 QA L FY L EL RVF NSGTEANEAA+K Sbjct: 69 VTQARKLWHSSNV--------FYTEPPLHLAEELVQASGFAERVFLCNSGTEANEAAIKL 120 Query: 124 AR---AHTGR---KKFVAAMRG-FSGRTMGSLSVTWEPKYREPFLPLVEPVEFIPYNDVE 176 R A GR ++ + RG F GRT+ +++ T +PKY+E + PL ++ +NDV Sbjct: 121 VRKWAASKGRAPEQRVILTFRGSFHGRTLAAVTATAQPKYQENYEPLPGGFRYLDFNDVA 180 Query: 177 ALKRAVDE-ETAAVILEPVQGEGGVRPATPEFLRAAREITQEKGALLILDEIQTGMGRTG 235 L+ A + + AAV+LEPVQGEGGV PA+P F+R ARE+ ALL+LDEIQ GMGRTG Sbjct: 181 GLEAAFAQGDVAAVMLEPVQGEGGVLPASPAFIRRARELCDTHEALLVLDEIQCGMGRTG 240 Query: 236 KRFAFEHFGIVPDILTLAKALGGGVPLGVAVMREEVARSMPKGGHGTTFGGNPLAMAAGV 295 FA G+ PDI+TLAKALG G P+G + +VA M G HGTTFGGNP+A A Sbjct: 241 TLFAHAQDGVTPDIVTLAKALGCGFPIGAMLAGPKVAEVMQYGAHGTTFGGNPMAAAVAR 300 Query: 296 AAIRYLERTRLWERAAELGPWFMEKLRAIPS--PKIREVRGMGLMVGLELKEK---AAPY 350 A+R L L A+ + L AI EVRG GLM+G L E A Sbjct: 301 VALRKLASAELMANVAKQAQALRDGLAAIDGELKLFAEVRGRGLMLGAVLAEAYKGRAGE 360 Query: 351 IARLEKEHRVLALQAGPTVIRFLPPLVIEKEDLERVVEAVRAVLA 395 + H +L LQAGP V+RF+PPL I DL + +RA LA Sbjct: 361 VLDHAAAHGLLVLQAGPDVLRFVPPLNITDADLAEGLARLRAALA 405 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: 413 Number of extensions: 23 Number of successful extensions: 6 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: 411 Length adjustment: 31 Effective length of query: 364 Effective length of database: 380 Effective search space: 138320 Effective search space used: 138320 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