Align [amino group carrier protein]-gamma-(L-lysyl)-L-glutamate aminotransferase (EC 2.6.1.118) (characterized)
to candidate WP_013643724.1 METBO_RS00600 acetylornithine transaminase
Query= BRENDA::Q93R93 (395 letters) >NCBI__GCF_000191585.1:WP_013643724.1 Length = 390 Score = 303 bits (775), Expect = 7e-87 Identities = 156/386 (40%), Positives = 232/386 (60%), Gaps = 5/386 (1%) Query: 12 LLEAEKTLDSGVYNKHDLLIVRGQGARVWDAEGNEYIDCVGGYGVANLGHGNPEVVEAVK 71 ++E + Y +H + +V+G+ VWDA+GN YIDCV G V N+GH NP+V EA+ Sbjct: 6 IIEMDSKYVMQTYGRHKIALVKGKDTTVWDADGNSYIDCVAGIAVNNVGHSNPKVGEAIC 65 Query: 72 RQAETLMAMPQTLPTPMRGEFYRTLTAILPPELNRVFPVNSGTEANEAALKFARAHTGRK 131 Q + L+ T + + L + P + + F NSG EANE A+K AR H+G+ Sbjct: 66 NQVKKLIHTSNLYYTEEQVTLAKLLVDVSPHQ--KAFFCNSGAEANEGAIKLARKHSGKG 123 Query: 132 KFVAAMRGFSGRTMGSLSVTWEPKYREPFLPLVEPVEFIPYNDVEALKRAVDEETAAVIL 191 + + + F GRT+ +++ T +PKY++ F PL ++ PY D+EA+K + TAAV++ Sbjct: 124 EIITMINSFHGRTITTITATGQPKYQKGFEPLTPGFKYAPYGDIEAVKEMISPSTAAVLV 183 Query: 192 EPVQGEGGVRPATPEFLRAAREITQEKGALLILDEIQTGMGRTGKRFAFEHFGIVPDILT 251 EPVQGE GV +L+ +E+ ++ LLI DE+QTG GRTG+ FA + FG+ PDI + Sbjct: 184 EPVQGESGVIVPPEGYLKQLKEVCEDSNVLLIFDEVQTGFGRTGEMFASQTFGVTPDITS 243 Query: 252 LAKALGGGVPLGVAVMREEVARSMPKGGHGTTFGGNPLAMAAGVAAIRYLERTRLWERAA 311 LAKA+ GG P+G + +VA S G H TFGGNPL AA A+I ++ +L +++ Sbjct: 244 LAKAIAGGFPMGAVLANNDVAESFVPGDHAATFGGNPLGCAAAKASINFILEEKLLDKSK 303 Query: 312 ELGPWFMEKLRAIPSPK--IREVRGMGLMVGLELKEKAAPYIARLEKEHRVLALQAGPTV 369 E G +F+EKL + + I EVRG GLMVG+E+K + L KE ++ AG V Sbjct: 304 ENGSYFVEKLLKLQNQHELINEVRGKGLMVGVEMKTDCGCMVDELFKEGIIVNCAAG-NV 362 Query: 370 IRFLPPLVIEKEDLERVVEAVRAVLA 395 +RF+PPL I KE ++ V A+ VL+ Sbjct: 363 LRFVPPLTITKEQIDTVTAALNNVLS 388 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: 381 Number of extensions: 18 Number of successful extensions: 4 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: 390 Length adjustment: 31 Effective length of query: 364 Effective length of database: 359 Effective search space: 130676 Effective search space used: 130676 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 10 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