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 17422 b3359 bifunctional acetylornithine aminotransferase/ succinyldiaminopimelate aminotransferase (NCBI)
Query= metacyc::MONOMER-18314 (387 letters) >FitnessBrowser__Keio:17422 Length = 406 Score = 256 bits (653), Expect = 1e-72 Identities = 146/389 (37%), Positives = 218/389 (56%), Gaps = 13/389 (3%) Query: 3 LIQLYGDRGLTIVKGEAQYVWDIEGRRYLDFHTGIGVAFLGHRNPIILEYLKNQLENISI 62 ++ +Y VKG+ +WD +G+ Y+DF GI V LGH +P ++ LK Q E + Sbjct: 17 ILPIYAPAEFIPVKGQGSRIWDQQGKEYVDFAGGIAVTALGHCHPALVNALKTQGETLWH 76 Query: 63 LSTSFSTPIKDEMLQALDKVKPDKMDNAMLLNSGTEAVEAALKTARKITG------RKKI 116 +S F+ + + L ++ + + +NSGTEA E A K AR + KI Sbjct: 77 ISNVFTNEPALRLGRKL--IEATFAERVVFMNSGTEANETAFKLARHYACVRHSPFKTKI 134 Query: 117 IAFKNAFHGRTAGSLSVTWNKKYREPFEPLVGPVEFLTFNNIEDLSKI-DNETAAVIVEP 175 IAF NAFHGR+ ++SV KY + F P + + FN++ + + D+ T AV+VEP Sbjct: 135 IAFHNAFHGRSLFTVSVGGQPKYSDGFGPKPADIIHVPFNDLHAVKAVMDDHTCAVVVEP 194 Query: 176 IQGESGVIPANIEFMKALKEKTENTGSLLIFDEIQTGFGRTGKLWAYKHYNIVPDILTAG 235 IQGE GV A EF++ L+E + +LL+FDE+Q G GRTG L+AY HY + PDILT+ Sbjct: 195 IQGEGGVTAATPEFLQGLRELCDQHQALLVFDEVQCGMGRTGDLFAYMHYGVTPDILTSA 254 Query: 236 KAIGGGFPVSVVFLPDHIANKLEEGDHGSTYGGNPMAMAAVTAACKVIEKENVVEQANQK 295 KA+GGGFP+S + IA+ G HGSTYGGNP+A A AA +I V+E K Sbjct: 255 KALGGGFPISAMLTTAEIASAFHPGSHGSTYGGNPLACAVAGAAFDIINTPEVLEGIQAK 314 Query: 296 GQQFSNILVKNLADLKVVREVRGKGLMIGIDIRFQ-PGQVLKYL---QEKGILAVKAGST 351 Q+F + L K V ++RG GL+IG +++ Q G+ +L E G++ + AG Sbjct: 315 RQRFVDHLQKIDQQYDVFSDIRGMGLLIGAELKPQYKGRARDFLYAGAEAGVMVLNAGPD 374 Query: 352 VIRFLPSYLITYENMEEASNVLREGLLKI 380 V+RF PS ++ +++E + K+ Sbjct: 375 VMRFAPSLVVEDADIDEGMQRFAHAVAKV 403 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: 427 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: 387 Length of database: 406 Length adjustment: 31 Effective length of query: 356 Effective length of database: 375 Effective search space: 133500 Effective search space used: 133500 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