Align [amino group carrier protein]-C-terminal-L-glutamyl-γ-L-lysine aminotransferase (EC 2.6.1.118; EC 2.6.1.124) (characterized)
to candidate 353284 BT3758 acetylornithine aminotransferase (NCBI ptt file)
Query= metacyc::MONOMER-18314 (387 letters) >FitnessBrowser__Btheta:353284 Length = 373 Score = 224 bits (571), Expect = 3e-63 Identities = 134/372 (36%), Positives = 210/372 (56%), Gaps = 12/372 (3%) Query: 1 MKLIQLYGDRGLTIVKGEAQYVWDIEGRRYLDFHTGIGVAFLGHRNPIILEYLKNQLENI 60 MKL +Y + IVKG+ VWD G YLD + G V +GH +P +E + NQ+ + Sbjct: 1 MKLFDVYPLYDINIVKGQGCKVWDENGTEYLDLYGGHAVISIGHAHPHYVEMISNQVATL 60 Query: 61 SILSTSFSTPIKDEMLQALDKVKPDKMDNAMLLNSGTEAVEAALKTARKITGRKKIIAFK 120 S S ++ ++ + L K+ + + L+NSG EA E ALK A GR K+I+F Sbjct: 61 GFYSNSVINKLQQQVAERLGKISGYEDYSLFLINSGAEANENALKLASFYNGRTKVISFS 120 Query: 121 NAFHGRTAGSLSVTWNKKYREPFEPLVGPVEFLTFNNIEDLSK--IDNETAAVIVEPIQG 178 AFHGRT+ ++ T N P G V +L N+IE + + + AVI+E IQG Sbjct: 121 KAFHGRTSLAVEATNNPTIIAPINN-NGHVTYLPLNDIEAMKQELAKGDVCAVIIEGIQG 179 Query: 179 ESGVIPANIEFMKALKEKTENTGSLLIFDEIQTGFGRTGKLWAYKHYNIVPDILTAGKAI 238 G+ EFM+ L++ TG++LI DEIQ+G+GR+GK +A+++ +I PDI+T K I Sbjct: 180 VGGIKIPTTEFMQELRKVCTETGTILILDEIQSGYGRSGKFFAHQYNHIQPDIITVAKGI 239 Query: 239 GGGFPVSVVFLPDHIANKLEEGDHGSTYGGNPMAMAAVTAACKVIEKENVVEQANQKGQQ 298 G GFP++ V + K G G+T+GGN +A +A A VIE++N+VE A G Sbjct: 240 GNGFPMAGVLISPMF--KPVYGQLGTTFGGNHLACSAALAVMDVIEQDNLVENAKAVG-- 295 Query: 299 FSNILVKNLADLKVVREVRGKGLMIGIDIRFQPGQVL--KYLQEKGILAVKAGSTVIRFL 356 + L++ L ++EVRG+GLMIG++ +P + L + + ++ + +G+ V+R L Sbjct: 296 --DYLLEELKKFPQIKEVRGRGLMIGLEFE-EPIKELRSRLIYDEHVFTGASGTNVLRLL 352 Query: 357 PSYLITYENMEE 368 P ++ E +E Sbjct: 353 PPLCLSMEEADE 364 Lambda K H 0.317 0.136 0.385 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: 390 Number of extensions: 17 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: 387 Length of database: 373 Length adjustment: 30 Effective length of query: 357 Effective length of database: 343 Effective search space: 122451 Effective search space used: 122451 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.6 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