Align [amino group carrier protein]-gamma-(L-lysyl)-L-glutamate aminotransferase (EC 2.6.1.118) (characterized)
to candidate WP_072909607.1 BUB13_RS15120 aspartate aminotransferase family protein
Query= BRENDA::Q93R93 (395 letters) >NCBI__GCF_900142125.1:WP_072909607.1 Length = 401 Score = 252 bits (644), Expect = 1e-71 Identities = 141/383 (36%), Positives = 219/383 (57%), Gaps = 11/383 (2%) Query: 21 SGVYNKHDLLIVRGQGARVWDAEGNEYIDCVGGYGVANLGHGNPEVVEAVKRQAETLMAM 80 + Y ++ L+ G G + D +G Y+D + G V NLGH +P+VV+A++ QA L+ Sbjct: 16 AATYGRYPLVADCGDGCWLLDVDGKRYLDFLAGVAVNNLGHCHPKVVKAIQEQAGKLLHC 75 Query: 81 PQTLPTPMRGEFYRTLTAILPPELNRVFPVNSGTEANEAALKFARAHT------GRKKFV 134 P + E L + RVF NSG EANEAA+K AR ++ R + + Sbjct: 76 SNFYHIPQQIELAELLCTHSFGD--RVFFCNSGVEANEAAIKLARKYSYENHGKERNEVI 133 Query: 135 AAMRGFSGRTMGSLSVTWEPKYREPFLPLVEPVEFIPYNDVEALKRAVDEETAAVILEPV 194 A+ F GRT+ +S T + K +E F P++ + +P+ D EA++ AV T A++LEPV Sbjct: 134 TAVASFHGRTLAGISATGQDKVKEGFAPMLPGFKHVPFGDFEAMRAAVGPNTCAIMLEPV 193 Query: 195 QGEGGVRPATPEFLRAAREITQEKGALLILDEIQTGMGRTGKRFAFEHFGIVPDILTLAK 254 QGEGGV +L++ RE+ E LLI DE+Q G GRTG FA++ G+ PDI+TLAK Sbjct: 194 QGEGGVNIPPAGYLQSIRELCDENNLLLIFDEVQVGCGRTGSLFAYQQEGVEPDIMTLAK 253 Query: 255 ALGGGVPLGVAVMREEVARSMPKGGHGTTFGGNPLAMAAGVAAIRYLERTRLWERAAELG 314 AL GG P+G + RE+ A ++ G HG+TFGGNPL +A +AA++ + E + G Sbjct: 254 ALAGGPPIGAMISREKHAGALGPGTHGSTFGGNPLLASAALAAMKVYLEDGVLENCRKTG 313 Query: 315 PWFMEKLRAIPSPK--IREVRGMGLMVGLELKEKAAPYIARLEKEHRVLALQAGPTVIRF 372 + KL + + EVRG GL++G+EL A + + E +L V+RF Sbjct: 314 DYLRAKLEELQEKYDFVVEVRGRGLIIGMEL-NIAGGEMVKTALERGLLINCTVDKVLRF 372 Query: 373 LPPLVIEKEDLERVVEAVRAVLA 395 +PPL+I+ +++++++E + + A Sbjct: 373 VPPLIIDTDEIDQMIEILEGIFA 395 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: 373 Number of extensions: 19 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: 395 Length of database: 401 Length adjustment: 31 Effective length of query: 364 Effective length of database: 370 Effective search space: 134680 Effective search space used: 134680 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 10 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