Align [amino group carrier protein]-gamma-(L-lysyl)-L-glutamate aminotransferase (EC 2.6.1.118) (characterized)
to candidate WP_011033352.1 MM_RS07280 aspartate aminotransferase family protein
Query= BRENDA::Q93R93 (395 letters) >NCBI__GCF_000007065.1:WP_011033352.1 Length = 395 Score = 323 bits (828), Expect = 5e-93 Identities = 171/368 (46%), Positives = 239/368 (64%), Gaps = 6/368 (1%) Query: 24 YNKHDLLIVRGQGARVWDAEGNEYIDCVGGYGVANLGHGNPEVVEAVKRQAETLMAMPQT 83 Y + L++ +G+GA V D G EYIDCV G V N+GH +P VV+A++ QAE L+ + Sbjct: 30 YGRQPLVLSKGKGAVVQDIYGKEYIDCVAGIAVNNVGHCHPTVVKAIQAQAEKLIHVSNL 89 Query: 84 LPTPMRGEFYRTLTAILPPELNRVFPVNSGTEANEAALKFARAHTGRKKFVAAMRGFSGR 143 T ++ EF TL +I E VF NSG EA EAA+K AR TG+ FVAA F GR Sbjct: 90 YYTEIQAEFAETLASITGMEC--VFFCNSGAEAVEAAMKLARVATGKSAFVAAEHSFHGR 147 Query: 144 TMGSLSVTWEPKYREPFLPLVEP-VEFIPYNDVEALKRAVDEETAAVILEPVQGEGGVRP 202 T+G+LSVT + YR+PF+P V F+PY+D +A+++A+ E+TAAV+LEP+QGEGGV Sbjct: 148 TIGALSVTHKSMYRDPFMPPVSSKTSFVPYSDADAIRKAISEDTAAVVLEPIQGEGGVNV 207 Query: 203 ATPEFLRAAREITQEKGALLILDEIQTGMGRTGKRFAFEHFGIVPDILTLAKALGGGVPL 262 P +L+ REI E G LLI DE+QTG GRTG F E FG+ PDI+++AKA+GGG P+ Sbjct: 208 PDPGYLKEVREICDETGTLLIFDEVQTGFGRTGTWFCKEQFGVEPDIMSMAKAIGGGFPM 267 Query: 263 GVAVMREEVARSMPKGGHGTTFGGNPLAMAAGVAAIRYLERTRLWERAAELGPWFMEKLR 322 G R + S +G H +TFGG PLA AA +A+I+ ++ +L ER+ E+G +F +KL Sbjct: 268 GAIAARSGL--SFGRGQHASTFGGGPLACAAALASIQAIKEEKLLERSKEMGAYFTKKLS 325 Query: 323 AIPSPKIREVRGMGLMVGLELKEKAAPYIARLEKEHRVLALQAGPTVIRFLPPLVIEKED 382 + I EVRG GLM+G+E+K ++ +EH VL +V+R +PPLVI KE Sbjct: 326 GMARDDIVEVRGKGLMIGVEIKYPCGKFV-DFAREHGVLVNCTSDSVLRLVPPLVITKEQ 384 Query: 383 LERVVEAV 390 ++ VV+ + Sbjct: 385 IDSVVDVL 392 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: 404 Number of extensions: 24 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: 395 Length adjustment: 31 Effective length of query: 364 Effective length of database: 364 Effective search space: 132496 Effective search space used: 132496 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