Align [amino group carrier protein]-gamma-(L-lysyl)-L-glutamate aminotransferase (EC 2.6.1.118) (characterized)
to candidate WP_010936947.1 DET_RS06460 acetylornithine transaminase
Query= BRENDA::Q93R93 (395 letters) >NCBI__GCF_000011905.1:WP_010936947.1 Length = 398 Score = 283 bits (723), Expect = 8e-81 Identities = 163/396 (41%), Positives = 234/396 (59%), Gaps = 13/396 (3%) Query: 6 LEDWRALLEAEKTLDSGVYNKHDLLIVRGQGARVWDAEGNEYIDCVGGYGVANLGHGNPE 65 +++W+ E E + + + IV+GQGA+VWD +G EY+D V G+ V +LGH +P Sbjct: 1 MDNWQ---ELEHKYYMQTFYRAPITIVKGQGAKVWDDKGKEYLDFVAGWAVNSLGHCHPA 57 Query: 66 VVEAVKRQAETLMAMPQTLPTPMRGEFYRTLTAILPPELNRVFPVNSGTEANEAALKFAR 125 VV+AV QA TL+ T + + + L + L+R+F NSGTEA E A+K AR Sbjct: 58 VVKAVSEQAGTLIQTSNNFYTIPQLKLAKLL--VDNSVLDRIFFCNSGTEATEGAVKLAR 115 Query: 126 AH-----TGRKKFVAAMRGFSGRTMGSLSVTWEPKYREPFLPLVEPVEFIPYNDVEALKR 180 + G + + A F GRT+ +S + + KY+EP+ PL + YN+ +A+K Sbjct: 116 RYGKLKLKGAYEVITATGSFHGRTLAMVSASGQSKYQEPYTPLPTGFINVEYNNPQAIKT 175 Query: 181 AVDEETAAVILEPVQGEGGVRPATPEFLRAAREITQEKGALLILDEIQTGMGRTGKRFAF 240 A+ ++T AV+LEP+QGE GV +L+A R+I E G LLILDEIQTG+GRTGK FA+ Sbjct: 176 AITDKTCAVMLEPIQGESGVNVPDKGYLKAVRQICDEAGILLILDEIQTGIGRTGKLFAY 235 Query: 241 EHFGIVPDILTLAKALGGGVPLGVAVMREEVARSMPKGGHGTTFGGNPLAMAAGVAAIRY 300 EH GI PDI+TLAK L GG+P+G A M +E A KG HG+TFGGNPLA AAG AA+++ Sbjct: 236 EHSGIEPDIITLAKGLAGGIPIG-AFMAKESASVFAKGEHGSTFGGNPLACAAGYAAMKF 294 Query: 301 LERTRLWERAAELGPWFMEKLR--AIPSPKIREVRGMGLMVGLELKEKAAPYIARLEKEH 358 + + E A +G + E L I I+ RG GL++ L+ K A I E Sbjct: 295 ILDNHISENAGSMGSYLAEGLEKLKIKHSLIQGCRGCGLLMALDFKTNIAKEIVESCLEE 354 Query: 359 RVLALQAGPTVIRFLPPLVIEKEDLERVVEAVRAVL 394 +L P +RF+PPL I + D++ + + +VL Sbjct: 355 GLLLNAVKPNALRFMPPLNITQADIDAAIAKLDSVL 390 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: 359 Number of extensions: 14 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: 398 Length adjustment: 31 Effective length of query: 364 Effective length of database: 367 Effective search space: 133588 Effective search space used: 133588 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