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 7023380 Shewana3_0610 bifunctional N-succinyldiaminopimelate-aminotransferase/acetylornithine transaminase protein (RefSeq)
Query= metacyc::MONOMER-18314 (387 letters) >FitnessBrowser__ANA3:7023380 Length = 405 Score = 237 bits (604), Expect = 5e-67 Identities = 147/395 (37%), Positives = 215/395 (54%), Gaps = 20/395 (5%) Query: 3 LIQLYGDRGLTIVKGEAQYVWDIEGRRYLDFHTGIGVAFLGHRNPIILEYLKNQLENISI 62 ++ Y + V+GE VWD EG ++DF GI V LGH +P ++ LK Q E + Sbjct: 16 MVPNYAPAAVIPVRGEGSRVWDQEGNEFIDFAGGIAVNCLGHCHPALVNALKTQGEKLWH 75 Query: 63 LSTSFSTPIKDEMLQALDKVKPDKMDNAMLLNSGTEAVEAALKTARKITGRK------KI 116 LS + E+ L V + NSG EA EAALK AR+ K +I Sbjct: 76 LSNVMTNEPALELATKL--VNSTFAERVYFANSGAEANEAALKLARRYALEKFGVEKDEI 133 Query: 117 IAFKNAFHGRTAGSLSVTWNKKYREPFEPLVGPVEFLTFNNIEDL-SKIDNETAAVIVEP 175 IAF AFHGRT ++SV Y + F P + L +N++ L + + ++T A+++EP Sbjct: 134 IAFDKAFHGRTFFTVSVGGQAAYSDGFGPKPQSITHLPYNDVAALEAAVSDKTCAIMLEP 193 Query: 176 IQGESGVIPANIEFMKALKEKTENTGSLLIFDEIQTGFGRTGKLWAYKHYNIVPDILTAG 235 +QGE G+I A+ F+KA++E +L+IFDE+QTG GRTG+L+AY +IVPDILT Sbjct: 194 LQGEGGIIDADPAFLKAVRELANKHNALVIFDEVQTGVGRTGELYAYMGTDIVPDILTTA 253 Query: 236 KAIGGGFPVSVVFLPDHIANKLEEGDHGSTYGGNPMAMAAVTAACKVIEKENVVEQANQK 295 KA+GGGFP++ + IA L+ G HGSTYGGNP+A A A V+ V+ + Sbjct: 254 KALGGGFPIAAMLTTAEIAEHLKVGTHGSTYGGNPLACAIGNAVLDVVNTPEVLNGVKHR 313 Query: 296 GQQFSNILVKNLADLKVVREVRGKGLMIGIDIRFQ-PGQVLKYL---QEKGILAVKAGST 351 Q + L K V E+RGKGL++G + Q G+ +L +G++++ AG+ Sbjct: 314 EQLLRDGLNKINEKYHVFSEIRGKGLLLGAVLNEQYQGRSRDFLVASVAEGLMSLMAGAN 373 Query: 352 VIRFLPSYLITYENMEEASNVLREGLLKIENKAVS 386 V+RF PS +I + + EGL + E S Sbjct: 374 VVRFAPSLVIPEAD-------IAEGLARFERAVAS 401 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: 372 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: 387 Length of database: 405 Length adjustment: 31 Effective length of query: 356 Effective length of database: 374 Effective search space: 133144 Effective search space used: 133144 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