Align [amino group carrier protein]-gamma-(L-lysyl)-L-glutamate aminotransferase (EC 2.6.1.118) (characterized)
to candidate WP_086510803.1 BZY95_RS15480 4-aminobutyrate--2-oxoglutarate transaminase
Query= BRENDA::Q93R93 (395 letters) >NCBI__GCF_002151265.1:WP_086510803.1 Length = 430 Score = 210 bits (534), Expect = 7e-59 Identities = 142/394 (36%), Positives = 205/394 (52%), Gaps = 33/394 (8%) Query: 33 RGQGARVWDAEGNEYIDCVGGYGVANLGHGNPEVVEAVKRQAETLMAMPQTLPTPMRG-- 90 R + A +WDA+GN ID GG GV N+GH +P+VVEAVK Q + +M QT+ P G Sbjct: 28 RAENALIWDADGNRIIDFAGGIGVLNIGHRHPKVVEAVKAQLDKVMHTCQTV-MPYEGYV 86 Query: 91 EFYRTLTAILPPELN-RVFPVNSGTEANEAALKFARAHTGRKKFVAAMRGFSGRTMGSLS 149 + L+ + P + +V NSG EA E A+K ARA TG+ + G+ GRT +++ Sbjct: 87 KVAEKLSQVTPVRGHAKVMLANSGAEALENAVKIARAATGKNNVICFDGGYHGRTFMTMA 146 Query: 150 VTWE-PKYREPFLPLVEPVEFIPY----------NDVEALKRAVD-----EETAAVILEP 193 + + Y F + V PY + LK A+ +TAA++LEP Sbjct: 147 MNGKVAPYASDFGTMPGNVFRAPYPVPYHGVSEDEAIRGLKMAIKTDANPRDTAAIVLEP 206 Query: 194 VQGEGGVRPATPEFLRAAREITQEKGALLILDEIQTGMGRTGKRFAFEHFGIVPDILTLA 253 V GEGG PA FL+A REI E G L+I+DE+Q+G GRTGK FA EH G+ PDI+T+A Sbjct: 207 VLGEGGFYPAPASFLKAIREICDEHGMLMIVDEVQSGFGRTGKLFAIEHSGVEPDIITMA 266 Query: 254 KALGGGVPLGVAVMREEVARSMPKGGHGTTFGGNPLAMAAGVAAIRYLERTRLWERAAEL 313 K++ G+P+ V ++V + G T+ GNPL+ AA +A + E + E++ L Sbjct: 267 KSMADGMPISAVVGTDKVMDASGPNSLGGTYTGNPLSCAATLAVLDVFEEENILEKSMAL 326 Query: 314 GPWFMEKLRAIPS--PKIREVRGMGLMVGLEL---KEKAAP------YIARLEKEHRVLA 362 G ++ + R MG M L+L K K P + + +E ++ Sbjct: 327 GDKLAKRFAQWQRDFDCVDNARNMGAMAALDLVTDKAKHTPDADLAAALCKKAREKGLIL 386 Query: 363 LQAG--PTVIRFLPPLVIEKEDLERVVEAVRAVL 394 L G IRFL P+ IE E LE ++ V A L Sbjct: 387 LSCGLYGNTIRFLMPVTIEDEILEEGLDIVEAAL 420 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: 417 Number of extensions: 24 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: 430 Length adjustment: 31 Effective length of query: 364 Effective length of database: 399 Effective search space: 145236 Effective search space used: 145236 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