Align [amino group carrier protein]-gamma-(L-lysyl)-L-glutamate aminotransferase (EC 2.6.1.118) (characterized)
to candidate 16752 b2662 4-aminobutyrate aminotransferase (NCBI)
Query= BRENDA::Q93R93 (395 letters) >FitnessBrowser__Keio:16752 Length = 426 Score = 206 bits (525), Expect = 8e-58 Identities = 137/408 (33%), Positives = 209/408 (51%), Gaps = 37/408 (9%) Query: 17 KTLDSGVYNKHDLLIVRGQGARVWDAEGNEYIDCVGGYGVANLGHGNPEVVEAVKRQAET 76 + + GV H + R + RVWD EG EY+D GG V N GH +P+VV AV+ Q Sbjct: 13 QAIPRGVGQIHPIFADRAENCRVWDVEGREYLDFAGGIAVLNTGHLHPKVVAAVEAQ--- 69 Query: 77 LMAMPQTLPTPMRGEFYRTLTAILPPEL-----NRVFPVNSGTEANEAALKFARAHTGRK 131 L + T + E Y L I+ ++ + V +G+EA E A+K ARA T R Sbjct: 70 LKKLSHTCFQVLAYEPYLELCEIMNQKVPGDFAKKTLLVTTGSEAVENAVKIARAATKRS 129 Query: 132 KFVAAMRGFSGRTMGSLSVTWEPKYREPFLPLVE----------PVEFIPYND-VEALKR 180 +A + GRT +L++T + + L+ P+ I +D + ++ R Sbjct: 130 GTIAFSGAYHGRTHYTLALTGKVNPYSAGMGLMPGHVYRALYPCPLHGISEDDAIASIHR 189 Query: 181 -----AVDEETAAVILEPVQGEGGVRPATPEFLRAAREITQEKGALLILDEIQTGMGRTG 235 A E+ AA+++EPVQGEGG ++P F++ R + E G +LI DE+Q+G GRTG Sbjct: 190 IFKNDAAPEDIAAIVIEPVQGEGGFYASSPAFMQRLRALCDEHGIMLIADEVQSGAGRTG 249 Query: 236 KRFAFEHFGIVPDILTLAKALGGGVPLGVAVMREEVARSMPKGGHGTTFGGNPLAMAAGV 295 FA E G+ PD+ T AK++ GG PL R EV ++ GG G T+ GNP+A A + Sbjct: 250 TLFAMEQMGVAPDLTTFAKSIAGGFPLAGVTGRAEVMDAVAPGGLGGTYAGNPIACVAAL 309 Query: 296 AAIRYLERTRLWERAAELGPWFMEKLRAIPS--PKIREVRGMGLMVGLELKE-------- 345 ++ E+ L ++A +LG + L AI P+I +VRG+G M+ +EL E Sbjct: 310 EVLKVFEQENLLQKANDLGQKLKDGLLAIAEKHPEIGDVRGLGAMIAIELFEDGDHNKPD 369 Query: 346 -KAAPYIARLEKEHRVLALQAGP--TVIRFLPPLVIEKEDLERVVEAV 390 K I ++ ++ L GP V+R L PL IE + + +E + Sbjct: 370 AKLTAEIVARARDKGLILLSCGPYYNVLRILVPLTIEDAQIRQGLEII 417 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: 389 Number of extensions: 17 Number of successful extensions: 4 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: 395 Length of database: 426 Length adjustment: 31 Effective length of query: 364 Effective length of database: 395 Effective search space: 143780 Effective search space used: 143780 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