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 6938908 Sama_3011 bifunctional N-succinyldiaminopimelate-aminotransferase/acetylornithine transaminase protein (RefSeq)
Query= metacyc::MONOMER-18314 (387 letters) >FitnessBrowser__SB2B:6938908 Length = 404 Score = 240 bits (612), Expect = 6e-68 Identities = 144/389 (37%), Positives = 214/389 (55%), Gaps = 13/389 (3%) Query: 3 LIQLYGDRGLTIVKGEAQYVWDIEGRRYLDFHTGIGVAFLGHRNPIILEYLKNQLENISI 62 ++ Y + V+GE VWD +G Y+DF GI V LGH +P ++ LK Q E + Sbjct: 16 MVPNYAPAAVIPVRGEGSRVWDQQGTEYVDFAGGIAVNCLGHCHPALVGALKEQGEKLWH 75 Query: 63 LSTSFSTPIKDEMLQALDKVKPDKMDNAMLLNSGTEAVEAALKTARKITGRK------KI 116 LS + + + + A V+ D NSG EA EAALK AR+ K ++ Sbjct: 76 LSNTMTN--EPALALATKLVEATFADRVYFANSGAEANEAALKLARRYAIEKFGEHKVEV 133 Query: 117 IAFKNAFHGRTAGSLSVTWNKKYREPFEPLVGPVEFLTFNNIEDL-SKIDNETAAVIVEP 175 IAF AFHGRT ++SV Y + F P + L FN+I L + + + T A+++EP Sbjct: 134 IAFDKAFHGRTFFTVSVGGQAAYSDGFGPKPAAITHLPFNDIAALEAAVSDNTCAIMLEP 193 Query: 176 IQGESGVIPANIEFMKALKEKTENTGSLLIFDEIQTGFGRTGKLWAYKHYNIVPDILTAG 235 +QGE G+I + EF++A++ + +L+IFDE+QTG GRTG L+AY IVPDILT Sbjct: 194 LQGEGGIINGDPEFLRAVRRLADKHNALVIFDEVQTGVGRTGDLYAYMGTEIVPDILTTA 253 Query: 236 KAIGGGFPVSVVFLPDHIANKLEEGDHGSTYGGNPMAMAAVTAACKVIEKENVVEQANQK 295 KA+GGGFP++ + IA+ L+ G HGSTYGGNP+A A A V+ V++ + Sbjct: 254 KALGGGFPIAAMLTTADIASHLKVGTHGSTYGGNPLACAIGNAVMDVVNTPEVLDGVKHR 313 Query: 296 GQQFSNILVKNLADLKVVREVRGKGLMIGIDIRFQ-PGQVLKYLQ---EKGILAVKAGST 351 Q F + L + V E+RGKGL++G + Q G+ +L +G+L + AG+ Sbjct: 314 EQLFRDGLAQINEKYHVFSEIRGKGLLLGAVLNEQFAGRSRDFLNASVAEGLLTLMAGAN 373 Query: 352 VIRFLPSYLITYENMEEASNVLREGLLKI 380 V+RF PS +I ++ E + K+ Sbjct: 374 VVRFTPSLVIPEADIVEGLARFERAVAKV 402 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: 374 Number of extensions: 13 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: 404 Length adjustment: 31 Effective length of query: 356 Effective length of database: 373 Effective search space: 132788 Effective search space used: 132788 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