Align [amino group carrier protein]-gamma-(L-lysyl)-L-glutamate aminotransferase (EC 2.6.1.118) (characterized)
to candidate WP_012977153.1 AZL_RS24705 4-aminobutyrate--2-oxoglutarate transaminase
Query= BRENDA::Q93R93 (395 letters) >NCBI__GCF_000010725.1:WP_012977153.1 Length = 429 Score = 207 bits (527), Expect = 5e-58 Identities = 143/394 (36%), Positives = 201/394 (51%), Gaps = 33/394 (8%) Query: 16 EKTLDSGVYNKHDLLIVRGQGARVWDAEGNEYIDCVGGYGVANLGHGNPEVVEAVKRQAE 75 E + G+ + I R + A +WD EG +ID GG V N GH +P+V+EAVK Q + Sbjct: 12 EAAVSRGISAGMPVYIDRAENAEMWDVEGKRFIDFAGGIAVLNTGHRHPKVMEAVKAQLD 71 Query: 76 TLM-AMPQTLPTPMRGEFYRTLTAILPP-ELNRVFPVNSGTEANEAALKFARAHTGRKKF 133 P E L A++P E + +G EA E A+K ARA TGR Sbjct: 72 RFTHTCAMVTPYDSFVELAEKLNALVPGREPKKTAFFTTGAEAVENAVKVARAATGRPGV 131 Query: 134 VAAMRGFSGRTMGSLSVTWEP-KYREPFLPLVEPVEFIPY-------NDVEALKRAVD-- 183 VA GF GRT+ ++ +T + Y+ F P + +P+ ++ E+LK + Sbjct: 132 VAFSGGFHGRTLLTMGLTGKVVPYKVGFGPFPAEIFHVPFPNAYRGISEAESLKALENLF 191 Query: 184 ------EETAAVILEPVQGEGGVRPATPEFLRAAREITQEKGALLILDEIQTGMGRTGKR 237 AA+I+EPVQGEGG A+P FL+A R + + G ++I+DEIQTG RTGK Sbjct: 192 KSDVDPARVAAIIIEPVQGEGGFNIASPSFLQALRAVCDKHGIVMIVDEIQTGFARTGKM 251 Query: 238 FAFEHFGIVPDILTLAKALGGGVPLGVAVMREEVARSMPKGGHGTTFGGNPLAMAAGVAA 297 FA EH GI PD++T+AK+L GG PL + + + GG G T+ G+PLA A +A Sbjct: 252 FAVEHAGIEPDLVTMAKSLAGGFPLSAVTGKAALMDAPIPGGLGGTYAGSPLATTAALAV 311 Query: 298 IRYLERTRLWERAAELGPWFMEKLRAIPSPK----IREVRGMGLMVGLEL------KEKA 347 I +E +L ER+ +LG + RA+ I +VR +G MV +EL KE A Sbjct: 312 INVIEEEKLVERSEKLGEHIAGRFRAMAQRNSLSVIGDVRNLGAMVAMELVTDRETKEPA 371 Query: 348 APYIARL-----EKEHRVLALQAGPTVIRFLPPL 376 A L EK +L+ VIR L PL Sbjct: 372 ADLTKALVAKAAEKGLVLLSCGTYANVIRILVPL 405 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: 18 Number of successful extensions: 3 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: 429 Length adjustment: 31 Effective length of query: 364 Effective length of database: 398 Effective search space: 144872 Effective search space used: 144872 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 Jul 25 2024. The underlying query database was built on Jul 25 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