Align [amino group carrier protein]-gamma-(L-lysyl)-L-glutamate aminotransferase (EC 2.6.1.118) (characterized)
to candidate 15866 b1748 succinylornithine transaminase, PLP-dependent (NCBI)
Query= BRENDA::Q93R93 (395 letters) >FitnessBrowser__Keio:15866 Length = 406 Score = 261 bits (668), Expect = 2e-74 Identities = 151/373 (40%), Positives = 209/373 (56%), Gaps = 15/373 (4%) Query: 23 VYNKHDLLIVRGQGARVWDAEGNEYIDCVGGYGVANLGHGNPEVVEAVKRQAETLMAMPQ 82 VY + VRG+G+R+WD +G EYID GG V LGH +PE+ EA+ QA Sbjct: 17 VYAPAPFIPVRGEGSRLWDQQGKEYIDFAGGIAVNALGHAHPELREALNEQASKFWHTGN 76 Query: 83 TLPT-PMRGEFYRTLTAILPPELNRVFPVNSGTEANEAALKFAR--AH----TGRKKFVA 135 P+ + + A +RVF NSG EANEAALK AR AH + + VA Sbjct: 77 GYTNEPVLRLAKKLIDATFA---DRVFFCNSGAEANEAALKLARKFAHDRYGSHKSGIVA 133 Query: 136 AMRGFSGRTMGSLSVTWEPKYREPFLPLVEPVEFIPYNDVEALKRAVDEETAAVILEPVQ 195 F GRT+ ++S +P Y + F PL + YND+ + +D+ T AVI+EP+Q Sbjct: 134 FKNAFHGRTLFTVSAGGQPAYSQDFAPLPADIRHAAYNDINSASALIDDSTCAVIVEPIQ 193 Query: 196 GEGGVRPATPEFLRAAREITQEKGALLILDEIQTGMGRTGKRFAFEHFGIVPDILTLAKA 255 GEGGV PA+ FL+ RE+ ALLI DE+QTG+GRTG+ +A+ H+G+ PD+LT AKA Sbjct: 194 GEGGVVPASNAFLQGLRELCNRHNALLIFDEVQTGVGRTGELYAYMHYGVTPDLLTTAKA 253 Query: 256 LGGGVPLGVAVMREEVARSMPKGGHGTTFGGNPLAMAAGVAAIRYLERTRLWERAAELGP 315 LGGG P+G + EE AR M G HGTT+GGNPLA A + + + + Sbjct: 254 LGGGFPVGALLATEECARVMTVGTHGTTYGGNPLASAVAGKVLELINTPEMLNGVKQRHD 313 Query: 316 WFMEKLRAIPS--PKIREVRGMGLMVGLELKEKAAPYIARLEKEHR---VLALQAGPTVI 370 WF+E+L I EVRG+GL++G L A ++ +E V+ L AG V+ Sbjct: 314 WFVERLNTINHRYGLFSEVRGLGLLIGCVLNADYAGQAKQISQEAAKAGVMVLIAGGNVV 373 Query: 371 RFLPPLVIEKEDL 383 RF P L + +E++ Sbjct: 374 RFAPALNVSEEEV 386 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: 389 Number of extensions: 16 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: 406 Length adjustment: 31 Effective length of query: 364 Effective length of database: 375 Effective search space: 136500 Effective search space used: 136500 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