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 BWI76_RS26000 BWI76_RS26000 aspartate aminotransferase family protein
Query= metacyc::MONOMER-18314 (387 letters) >FitnessBrowser__Koxy:BWI76_RS26000 Length = 406 Score = 247 bits (630), Expect = 5e-70 Identities = 145/377 (38%), Positives = 212/377 (56%), Gaps = 13/377 (3%) Query: 3 LIQLYGDRGLTIVKGEAQYVWDIEGRRYLDFHTGIGVAFLGHRNPIILEYLKNQLENISI 62 ++ +Y VKG+ VWD +G+ Y+DF GI V LGH +P ++ L Q E + Sbjct: 17 ILPIYAPAEFIPVKGKGSRVWDQQGKEYVDFAGGIAVTALGHCHPALVAALHEQGEKLWH 76 Query: 63 LSTSFSTPIKDEMLQALDKVKPDKMDNAMLLNSGTEAVEAALKTARKITGRK------KI 116 S F+ + + L V D + +NSGTEA E A K AR T + KI Sbjct: 77 TSNVFTNEPALRLGRKL--VDATFADRVVFMNSGTEANETAFKLARHYTVTRHSPYKTKI 134 Query: 117 IAFKNAFHGRTAGSLSVTWNKKYREPFEPLVGPVEFLTFNNIEDLSKI-DNETAAVIVEP 175 IAF NAFHGR+ ++SV KY + F P + + FN++ + + D+ T AV+VEP Sbjct: 135 IAFHNAFHGRSLFTVSVGGQPKYSDGFGPKPADIVHVPFNDLHAVKAVMDDHTCAVVVEP 194 Query: 176 IQGESGVIPANIEFMKALKEKTENTGSLLIFDEIQTGFGRTGKLWAYKHYNIVPDILTAG 235 IQGE GV A EF++ L++ + +LL+FDE+Q G GRTG L+AY HY + PDILT+ Sbjct: 195 IQGEGGVTAATPEFLQGLRDLCDQHQALLVFDEVQCGMGRTGSLFAYMHYGVTPDILTSA 254 Query: 236 KAIGGGFPVSVVFLPDHIANKLEEGDHGSTYGGNPMAMAAVTAACKVIEKENVVEQANQK 295 KA+GGGFP+S + IA+ G HGSTYGGNP+A A AA +I V++ K Sbjct: 255 KALGGGFPISAMLTTHDIASAFHAGSHGSTYGGNPLACAVGGAAFDLINTPEVLDGVTAK 314 Query: 296 GQQFSNILVKNLADLKVVREVRGKGLMIGIDIRFQ-PGQVLKYL---QEKGILAVKAGST 351 + F L + A + ++RG GL+IG +++ Q G+ +L E G++ + AG Sbjct: 315 RELFVQHLQQIDARFDLFSDIRGMGLLIGAELKPQYHGKARDFLYAAAEAGVMVLNAGPD 374 Query: 352 VIRFLPSYLITYENMEE 368 V+RF+PS +I ++ E Sbjct: 375 VMRFVPSLVIDDSDIAE 391 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: 394 Number of extensions: 11 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