Align [amino group carrier protein]-gamma-(L-lysyl)-L-glutamate aminotransferase (EC 2.6.1.118) (characterized)
to candidate CA265_RS18530 CA265_RS18530 aspartate aminotransferase family protein
Query= BRENDA::Q93R93 (395 letters) >FitnessBrowser__Pedo557:CA265_RS18530 Length = 382 Score = 217 bits (553), Expect = 4e-61 Identities = 131/372 (35%), Positives = 206/372 (55%), Gaps = 12/372 (3%) Query: 23 VYNKHDLLIVRGQGARVWDAEGNEYIDCVGGYGVANLGHGNPEVVEAVKRQAETLMAMPQ 82 VY +D+ I + G+ VWDA +Y+D GG+ V ++GH NP V + Q + Sbjct: 6 VYPLNDIEITKAAGSNVWDANDQQYLDLYGGHAVISIGHTNPHYVNRLTDQLNKVGFYSN 65 Query: 83 TLPTPMRGEFYRTLTAILPPELNRVFPVNSGTEANEAALKFARAHTGRKKFVAAMRGFSG 142 ++ P++ + L + + ++F NSG EANE ALK A + GRKK +A F G Sbjct: 66 SVKIPLQVQLAEKLGEVSGKKDFQLFLCNSGAEANENALKLASFYNGRKKVIAFTGAFHG 125 Query: 143 RTMGSLSVTWEPKYREPFLPLVEPVEFIPYNDVEALK---RAVDEETAAVILEPVQGEGG 199 RT +++VT PK P + E V F+P+N+ AL+ +A E +AVI+E +QG GG Sbjct: 126 RTSLAVAVTDNPKIVAP-VNQTENVIFLPFNNEIALEETFKAQGNEISAVIIEGIQGVGG 184 Query: 200 VRPATPEFLRAAREITQEKGALLILDEIQTGMGRTGKRFAFEHFGIVPDILTLAKALGGG 259 ++ A+ FL+ R + E A+ I D +Q G GRTG ++ ++ G+ D+ T+AK +G G Sbjct: 185 IKEASKSFLQKIRSLCDEYNAVYIADSVQCGYGRTGSFYSHDYSGVEADVYTMAKGMGNG 244 Query: 260 VPL-GVAVMREEVARSMPKGGH-GTTFGGNPLAMAAGVAAIRYLERTRLWERAAELGPWF 317 P+ G+++ ++ P G GTTFGGN LA AA +A + +E+ L + A E+G + Sbjct: 245 FPVAGISI----ASKFKPWHGELGTTFGGNHLACAAALAVLEVMEKDNLIKNAEEVGNYL 300 Query: 318 MEKLRAIPSPKIREVRGMGLMVGLELKEKAAPYIARLEKEHRVLALQAGPTVIRFLPPLV 377 + +L+ ++ EVRG GLM+G+EL + A L H + +A P VIR LP L Sbjct: 301 IAELKKF--EQVVEVRGRGLMIGIELPAELAHVKKELLFTHHIFTGEAKPNVIRLLPALN 358 Query: 378 IEKEDLERVVEA 389 + K + + A Sbjct: 359 LTKAHADEFLAA 370 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: 327 Number of extensions: 10 Number of successful extensions: 4 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: 382 Length adjustment: 30 Effective length of query: 365 Effective length of database: 352 Effective search space: 128480 Effective search space used: 128480 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