Align [amino group carrier protein]-gamma-(L-lysyl)-L-glutamate aminotransferase (EC 2.6.1.118) (characterized)
to candidate WP_041313637.1 HM1_RS08735 aspartate aminotransferase family protein
Query= BRENDA::Q93R93 (395 letters) >NCBI__GCF_000019165.1:WP_041313637.1 Length = 413 Score = 249 bits (635), Expect = 1e-70 Identities = 151/374 (40%), Positives = 210/374 (56%), Gaps = 11/374 (2%) Query: 32 VRGQGARVWDAEGNEYIDCVGGYGVANLGHGNPEVVEAVKRQAETLMAMPQTLPTPMRGE 91 VR +G V+D +G EYID +G +GV +LGH +P ++ ++ Q L + L Sbjct: 30 VRAEGCFVYDEQGREYIDFLGNFGVLSLGHRHPRIIASILEQLNGLAQTSRFLLDKATAS 89 Query: 92 FYRTLTAILPPELNRVFPVNSGTEANEAALKFARAHTGRKKFVAAMRGFSGRTMGSLSVT 151 L I P +L F NSG EA EAA+K AR TG+ F+A + GF G+T G+LSV+ Sbjct: 90 LAEALAGITPGDLQYCFFCNSGAEAVEAAIKIARLATGKSGFIATINGFHGKTFGALSVS 149 Query: 152 WEPKYREPFLPLVEPVEFIPYNDVEALKR--AVDEETAAVILEPVQGEGGVRPATPEFLR 209 +R PFLPL+ V +P+ D AL+ A D AA I+EPVQGEGGV +L+ Sbjct: 150 GREPFRAPFLPLLPRVIHVPFGDAAALEEVMARDRHIAAFIVEPVQGEGGVIVPPRGYLK 209 Query: 210 AAREITQEKGALLILDEIQTGMGRTGKRFAFEHFGIVPDILTLAKALGGGV-PLGVAVMR 268 + ++ G LLI DE+QTG+GRTG FA + G+VPD+L LAKALGGGV P+G V R Sbjct: 210 EVEALCRQAGVLLIADEVQTGLGRTGSLFACDEEGLVPDLLCLAKALGGGVMPIGAVVGR 269 Query: 269 EEVARSM--PKGGHGTTFGGNPLAMAAGVAAIRYLERTRLWERAAELGPWFMEKLRAIPS 326 + + H +TFGGNPLA AA +AAI L +A + G W + +L+ + S Sbjct: 270 PALWAPLFDHPWLHTSTFGGNPLACAAALAAIEVTIEEDLMGQARQKGDWLLSRLKELAS 329 Query: 327 ---PKIREVRGMGLMVGLEL-KEKAAPYIARLEKEHRVLA--LQAGPTVIRFLPPLVIEK 380 I +VRG GL++G+EL KE ++ E R++ P VIR PPL + Sbjct: 330 RHEQVIADVRGRGLLIGIELTKEGVGGFVIGRMMEERIIVGYTLNHPRVIRLEPPLNVPW 389 Query: 381 EDLERVVEAVRAVL 394 E L +V + V+ Sbjct: 390 EVLMQVYAVLEQVI 403 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: 376 Number of extensions: 18 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: 413 Length adjustment: 31 Effective length of query: 364 Effective length of database: 382 Effective search space: 139048 Effective search space used: 139048 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