Align [amino group carrier protein]-gamma-(L-lysyl)-L-glutamate aminotransferase (EC 2.6.1.118) (characterized)
to candidate WP_011612205.1 TERY_RS12675 aspartate aminotransferase family protein
Query= BRENDA::Q93R93 (395 letters) >NCBI__GCF_000014265.1:WP_011612205.1 Length = 423 Score = 260 bits (665), Expect = 5e-74 Identities = 148/390 (37%), Positives = 219/390 (56%), Gaps = 21/390 (5%) Query: 24 YNKHDLLIVRGQGARVWDAEGNEYIDCVGGYGVANLGHGNPEVVEAVKRQAETLMAMPQT 83 Y + + I RG+G RVWD EG EY+D V G LGH +P ++ V Q + L + Sbjct: 33 YGRFPIAIERGEGCRVWDTEGKEYLDFVAGIATCTLGHAHPVMMATVSEQIKRLHHVSNL 92 Query: 84 LPTPMRGEFYRTLTAILPPELNRVFPVNSGTEANEAALKFARAHTGRK------KFVAAM 137 P++GE + L I ++ F NSG EANE A+K AR + K + A Sbjct: 93 YYIPVQGELAQWL--IQHSCADKAFFCNSGAEANEGAIKLARKYAHEKLNIENPTILTAH 150 Query: 138 RGFSGRTMGSLSVTWEPKYREPFLPLVEPVEFIPYNDVEALKRAVDE------ETAAVIL 191 F GRT+ +++ T +PKY + F PL+ ++PYND+ A++ A++E + AA++L Sbjct: 151 ASFHGRTLATMTATGQPKYHKGFSPLMPGFYYVPYNDIAAIESAIEELDKDKRQVAAIML 210 Query: 192 EPVQGEGGVRPATPEFLRAAREITQEKGALLILDEIQTGMGRTGKRFAFEHFGIVPDILT 251 E +QGEGG+RP + + REI EKG LLILDE+Q GMGR+GK + +E+ GI PDI T Sbjct: 211 EALQGEGGIRPGDMTYFKRIREICNEKGILLILDEVQAGMGRSGKIWGYENLGIEPDIFT 270 Query: 252 LAKALGGGVPLGVAVMREEVARSMPKGGHGTTFGGNPLAMAAGVAAIRYLERTRLWERAA 311 AK LGGG+P+G + + P G H +TFGGNP A A +A LE+ L Sbjct: 271 SAKGLGGGIPIGAMLCKSHCDVFEP-GSHASTFGGNPFACAVALAVCHTLEQENLLANVQ 329 Query: 312 ELGPWFMEKLRAIPS--PKI-REVRGMGLMVGLELKEKA---APYIARLEKEHRVLALQA 365 + G +L+AI P + EVRG GL+ GLEL A + I + +L + A Sbjct: 330 QRGDELRIELKAIADKYPNLFSEVRGWGLINGLELNATATLTSIDIVKAAMNEGLLIVPA 389 Query: 366 GPTVIRFLPPLVIEKEDLERVVEAVRAVLA 395 GP V+RF+PPL++ + +++ ++ + +A Sbjct: 390 GPKVLRFVPPLIVTETEVKEAMDLLAKAIA 419 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: 387 Number of extensions: 16 Number of successful extensions: 7 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: 423 Length adjustment: 31 Effective length of query: 364 Effective length of database: 392 Effective search space: 142688 Effective search space used: 142688 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