Align [amino group carrier protein]-gamma-(L-lysyl)-L-glutamate aminotransferase (EC 2.6.1.118) (characterized)
to candidate CCNA_02326 CCNA_02326 acetylornithine aminotransferase/succinyldiaminopimelate aminotransferase
Query= BRENDA::Q93R93 (395 letters) >FitnessBrowser__Caulo:CCNA_02326 Length = 405 Score = 234 bits (597), Expect = 3e-66 Identities = 148/392 (37%), Positives = 209/392 (53%), Gaps = 21/392 (5%) Query: 22 GVYNKHDLLIVRGQGARVWDAEGNEYIDCVGGYGVANLGHGNPEVVEAVKRQAETLMAMP 81 GVYN+ L RG+GAR+ EG EY+DCV G LGH +P +VE +K QAE L + Sbjct: 16 GVYNRAPLAFERGRGARLISTEGEEYLDCVAGIATNGLGHAHPALVEVLKAQAEKLWHVS 75 Query: 82 QTLPTPMRGEFYRTLTAILPPELNRVFPVNSGTEANEAALKFARAHTG------RKKFVA 135 P + E L A ++ VF NSGTEA E ALK AR + R Sbjct: 76 NIYRIPEQEELADALCANSFADV--VFFTNSGTEAVECALKTARKYHSANGQPERIDIYG 133 Query: 136 AMRGFSGRTMGSLSVTWEPKYREPFLPLVEPVEFIPYNDVEALKRAV-DEETAAVILEPV 194 F GRT +++ + P Y + F P + + + D +A+K A+ TAA+I+EPV Sbjct: 134 FDGSFHGRTYAAVNASGNPSYVDGFGPRLPGYSQLTFGDHDAIKAAIASPTTAAIIVEPV 193 Query: 195 QGEGGVRPATPEFLRAAREITQEKGALLILDEIQTGMGRTGKRFAFEHF-GIVPDILTLA 253 QGEGG R + L R++ E G LLI DE+Q GMGRTGK FA+E G P I+ +A Sbjct: 194 QGEGGARSIPTQCLVGLRQLCDEHGVLLIYDEVQCGMGRTGKLFAYEWAEGGEPHIMAVA 253 Query: 254 KALGGGVPLGVAVMREEVARSMPKGGHGTTFGGNPLAMAAGVAAIRYLERTRLWERAAEL 313 KALGGG P+G + E A+ M HG+TFGGNPLAMA G AA+ ++ + + Sbjct: 254 KALGGGFPIGACLATTEAAKGMTVAAHGSTFGGNPLAMAVGKAALEIIKSPETLDNVKTV 313 Query: 314 GPWFMEKLRAIPS---PKIREVRGMGLMVGLELKEKAAPYIARLEKEHRVLALQAGPTVI 370 +F ++L + I +VRG G+++G++L ++ L ++ ++L G + Sbjct: 314 SGFFTQQLNGLKDRFPDVIVDVRGKGMLIGVKLIPNNRDFMV-LARDEKLLIAGGGDNCV 372 Query: 371 RFLPPLVIEKED-------LERVVEAVRAVLA 395 R LPPL + E+ LE+ EA RA A Sbjct: 373 RLLPPLNLTIEEASEAIAKLEKACEAARAKAA 404 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: 378 Number of extensions: 23 Number of successful extensions: 6 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: 405 Length adjustment: 31 Effective length of query: 364 Effective length of database: 374 Effective search space: 136136 Effective search space used: 136136 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 09 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