Align [amino group carrier protein]-gamma-(L-lysyl)-L-glutamate aminotransferase (EC 2.6.1.118) (characterized)
to candidate BWI76_RS26000 BWI76_RS26000 aspartate aminotransferase family protein
Query= BRENDA::Q93R93 (395 letters) >FitnessBrowser__Koxy:BWI76_RS26000 Length = 406 Score = 271 bits (693), Expect = 2e-77 Identities = 154/389 (39%), Positives = 223/389 (57%), Gaps = 19/389 (4%) Query: 23 VYNKHDLLIVRGQGARVWDAEGNEYIDCVGGYGVANLGHGNPEVVEAVKRQAETLMAMPQ 82 +Y + + V+G+G+RVWD +G EY+D GG V LGH +P +V A+ Q E L Sbjct: 20 IYAPAEFIPVKGKGSRVWDQQGKEYVDFAGGIAVTALGHCHPALVAALHEQGEKLWHTSN 79 Query: 83 TLPTPMRGEFYRTLTAILPPELNRVFPVNSGTEANEAALKFARAHTGRK------KFVAA 136 R L + +RV +NSGTEANE A K AR +T + K +A Sbjct: 80 VFTNEPALRLGRKL--VDATFADRVVFMNSGTEANETAFKLARHYTVTRHSPYKTKIIAF 137 Query: 137 MRGFSGRTMGSLSVTWEPKYREPFLPLVEPVEFIPYNDVEALKRAVDEETAAVILEPVQG 196 F GR++ ++SV +PKY + F P + +P+ND+ A+K +D+ T AV++EP+QG Sbjct: 138 HNAFHGRSLFTVSVGGQPKYSDGFGPKPADIVHVPFNDLHAVKAVMDDHTCAVVVEPIQG 197 Query: 197 EGGVRPATPEFLRAAREITQEKGALLILDEIQTGMGRTGKRFAFEHFGIVPDILTLAKAL 256 EGGV ATPEFL+ R++ + ALL+ DE+Q GMGRTG FA+ H+G+ PDILT AKAL Sbjct: 198 EGGVTAATPEFLQGLRDLCDQHQALLVFDEVQCGMGRTGSLFAYMHYGVTPDILTSAKAL 257 Query: 257 GGGVPLGVAVMREEVARSMPKGGHGTTFGGNPLAMAAGVAAIRYLERTRLWERAAELGPW 316 GGG P+ + ++A + G HG+T+GGNPLA A G AA + + + Sbjct: 258 GGGFPISAMLTTHDIASAFHAGSHGSTYGGNPLACAVGGAAFDLINTPEVLDGVTAKREL 317 Query: 317 FMEKLRAIPS--PKIREVRGMGLMVGLELKE----KAAPYIARLEKEHRVLALQAGPTVI 370 F++ L+ I + ++RGMGL++G ELK KA ++ E V+ L AGP V+ Sbjct: 318 FVQHLQQIDARFDLFSDIRGMGLLIGAELKPQYHGKARDFL-YAAAEAGVMVLNAGPDVM 376 Query: 371 RFLPPLVIEKED----LERVVEAVRAVLA 395 RF+P LVI+ D + R +AV VL+ Sbjct: 377 RFVPSLVIDDSDIAEGMARFAQAVERVLS 405 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: 375 Number of extensions: 19 Number of successful extensions: 6 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 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