Align [amino group carrier protein]-gamma-(L-lysyl)-L-glutamate aminotransferase (EC 2.6.1.118) (characterized)
to candidate AO353_15640 AO353_15640 acetylornithine aminotransferase
Query= BRENDA::Q93R93 (395 letters) >FitnessBrowser__pseudo3_N2E3:AO353_15640 Length = 391 Score = 259 bits (663), Expect = 7e-74 Identities = 152/381 (39%), Positives = 207/381 (54%), Gaps = 12/381 (3%) Query: 24 YNKHDLLIVRGQGARVWDAEGNEYIDCVGGYGVANLGHGNPEVVEAVKRQAETLMAMPQT 83 Y L RG G R+WD G EY+D V G V N+GH +P+VV A+ QA L+ Sbjct: 10 YQPLALSFTRGLGTRLWDQAGREYLDAVAGVAVTNVGHSHPKVVSAISEQAGLLLHTSNL 69 Query: 84 LPTPMRGEFYRTLTAILPPELNRVFPVNSGTEANEAALKFARAHTGRKKF-----VAAMR 138 + LT + L+RVF NSG EANE ALK AR + K V Sbjct: 70 YSIDWQQRLAHKLTQL--SGLDRVFFNNSGAEANETALKLARLYGWHKGVEQPLVVVMEN 127 Query: 139 GFSGRTMGSLSVTWEPKYREPFLPLVEPVEFIPYNDVEALKRAVD---EETAAVILEPVQ 195 F GRT+G+LS + P R F L +P+ D+ AL +A + AV++EP+Q Sbjct: 128 AFHGRTLGTLSASDGPAVRLGFQELPGDFIKVPFGDLAALDKAHQTHGQRIVAVLMEPIQ 187 Query: 196 GEGGVRPATPEFLRAAREITQEKGALLILDEIQTGMGRTGKRFAFEHFGIVPDILTLAKA 255 GE GV+ A P +L+A RE+ + LL+LDEIQTG+GRTG+ FAF+H GIVPD++TLAK Sbjct: 188 GESGVQLALPGYLKALRELCNRRNWLLMLDEIQTGIGRTGQWFAFQHEGIVPDVMTLAKG 247 Query: 256 LGGGVPLGVAVMREEVARSMPKGGHGTTFGGNPLAMAAGVAAIRYLERTRLWERAAELGP 315 LG GVP+G + R + A G HG+TFGGNPLA G + +E L E A G Sbjct: 248 LGNGVPIGACLARGKAAELFTPGSHGSTFGGNPLACRVGCTVLEIIEEQGLLENAKRQGE 307 Query: 316 WFMEKLRA--IPSPKIREVRGMGLMVGLELKEKAAPYIARLEKEHRVLALQAGPTVIRFL 373 + +L A SP++ +RG GLM+G+EL ++H +L IR L Sbjct: 308 RLLARLHAELDGSPQVLAIRGQGLMIGIELARPIRDLTLIAARDHGLLINVTRGKTIRLL 367 Query: 374 PPLVIEKEDLERVVEAVRAVL 394 PPL I++ ++E +V V V+ Sbjct: 368 PPLTIDEREVEMIVRGVGRVV 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: 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: 391 Length adjustment: 31 Effective length of query: 364 Effective length of database: 360 Effective search space: 131040 Effective search space used: 131040 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