Align [amino group carrier protein]-gamma-(L-lysyl)-L-glutamate aminotransferase (EC 2.6.1.118) (characterized)
to candidate WP_057509166.1 ABB28_RS13775 aspartate aminotransferase family protein
Query= BRENDA::Q93R93 (395 letters) >NCBI__GCF_001431535.1:WP_057509166.1 Length = 408 Score = 265 bits (676), Expect = 2e-75 Identities = 164/393 (41%), Positives = 219/393 (55%), Gaps = 28/393 (7%) Query: 23 VYNKHDLLIVRGQGARVWDAEGNEYIDCVGGYGVANLGHGNPEVVEAVKRQAETLMAMPQ 82 VY +++ RGQGARVWD++G EYID G V LGH +P++ A+ QA L Sbjct: 18 VYKPRQVVLERGQGARVWDSQGREYIDLAAGIAVCGLGHNDPDLTAALVEQAGKLWHTSN 77 Query: 83 TLPTPMRGEFYRTLTAILPPEL-------NRVFPVNSGTEANEAALKFAR---AHTGR-- 130 FY L EL RVF NSG EANE A+K R + GR Sbjct: 78 V--------FYSAPPLHLAEELVKASRFAERVFLCNSGAEANEVAIKMVRKWASSQGRPA 129 Query: 131 -KKFVAAMRG-FSGRTMGSLSVTWEPKYREPFLPLVEPVEFIPYNDVEALKRAVDE-ETA 187 ++ + RG F GRT+ +++ T +PKY+E + PL + ++ +ND L+ A+ + A Sbjct: 130 DRRVIVTFRGSFHGRTLAAVTATAQPKYQEGYEPLPQGFRYVDFNDEVQLETAMAAGDVA 189 Query: 188 AVILEPVQGEGGVRPATPEFLRAAREITQEKGALLILDEIQTGMGRTGKRFAFEHFGIVP 247 AV+LEPVQGEGGV PA P FL+ RE+ + GALL+LDEIQ GMGRTG FA G+VP Sbjct: 190 AVMLEPVQGEGGVMPARPGFLKRVRELCDQHGALLVLDEIQAGMGRTGTLFAHWQDGVVP 249 Query: 248 DILTLAKALGGGVPLGVAVMREEVARSMPKGGHGTTFGGNPLAMAAGVAAIRYLERTRLW 307 D++TLAKALGGG P+G + +VA +M G HGTTFGGNPLA A A+R L + Sbjct: 250 DMVTLAKALGGGFPIGAMLAGPKVAETMQFGAHGTTFGGNPLAAAVARVALRKLASDEIA 309 Query: 308 ERAAELGPWFMEKLRAIPSP--KIREVRGMGLMVGLELKEK---AAPYIARLEKEHRVLA 362 E I + +VRG GLM+G L + A I EH +L Sbjct: 310 ANVDRQSRALREGFERINAEFGVFGQVRGRGLMLGAVLSKDHLGQAGVILDHAAEHGLLT 369 Query: 363 LQAGPTVIRFLPPLVIEKEDLERVVEAVRAVLA 395 LQAGP V+RF+P L I E++ ++ +RA +A Sbjct: 370 LQAGPDVLRFVPSLNITDEEIAEGLKRLRAAVA 402 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: 438 Number of extensions: 22 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: 408 Length adjustment: 31 Effective length of query: 364 Effective length of database: 377 Effective search space: 137228 Effective search space used: 137228 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