Align [amino group carrier protein]-gamma-(L-lysyl)-L-glutamate aminotransferase (EC 2.6.1.118) (characterized)
to candidate GFF3809 PS417_19505 2,4-diaminobutyrate 4-aminotransferase
Query= BRENDA::Q93R93 (395 letters) >FitnessBrowser__WCS417:GFF3809 Length = 464 Score = 233 bits (594), Expect = 9e-66 Identities = 157/416 (37%), Positives = 228/416 (54%), Gaps = 51/416 (12%) Query: 29 LLIVRGQGARVWDAEGNEYIDCVGGYGVANLGHGNPEVVEAVKR-QAETLMAMPQTLPTP 87 L + R +G V D EG +IDC+ G G LGH +P V+EA+++ A+ L L TP Sbjct: 45 LALKRAKGLYVEDVEGRRFIDCLAGAGTLALGHNHPVVIEAIQQVLADELPLHTLDLTTP 104 Query: 88 MRGEFYRTLTAILPPELNRVFPVN----SGTEANEAALKFARAHTGRKKFVAAMRGFSGR 143 ++ +F + L +LPP L R + +GT+A EAALK R TGR ++ G+ G Sbjct: 105 VKDQFVQDLFGLLPPALAREAKIQFCGPTGTDAVEAALKLVRTATGRSTVLSFQGGYHGM 164 Query: 144 TMGSLSVTWEPKYREPFLPLV-EPVEFIPYN-----------------DVEALKRAVDEE 185 + G+LS+ ++P L+ V+F+PY ++ L +++ Sbjct: 165 SQGALSLMGSLGPKKPLGALLGNGVQFLPYPYDYRCPFGLGGAEGVRVNLHYLDNLLNDP 224 Query: 186 ------TAAVILEPVQGEGGVRPATPEFLRAAREITQEKGALLILDEIQTGMGRTGKRFA 239 AAVI+E VQGEGGV PA ++LR R IT++ G LI+DEIQ+G GRTGK FA Sbjct: 225 EAGVLLPAAVIVEVVQGEGGVIPADLDWLRGLRRITEQAGVALIVDEIQSGFGRTGKLFA 284 Query: 240 FEHFGIVPDILTLAKALGGGVPLGVAVMREEVARSMPKGGHGTTFGGNPLAMAAGVAAIR 299 FEH GI+PD++ ++KA+GG +PL V V R+ + +P G H TF GN +AMAAG A +R Sbjct: 285 FEHAGIIPDVVVMSKAIGGSLPLAVVVYRDWLDTWLP-GAHAGTFRGNQMAMAAGSAVMR 343 Query: 300 YLERTRLWERAAELGPWFMEKLRAIPS--PKIREVRGMGLMVGLELKE------------ 345 YL+ L AA +G E LR + P + ++RG GLM+G+EL + Sbjct: 344 YLKDHDLAGHAAAMGERLGEHLRILQRDFPHLGDIRGRGLMLGVELVDPNGTLDVQGHPP 403 Query: 346 ---KAAPYIARLEKEHRVLALQAG---PTVIRFLPPLVIEKEDLERVVEAVRAVLA 395 + AP + R E R L L+ G +V+RFLPPLVI +++ V + LA Sbjct: 404 VHRQLAPLVQR-ECLKRGLILELGGRHGSVVRFLPPLVITAVEVDLVADIFGRALA 458 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: 502 Number of extensions: 20 Number of successful extensions: 7 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 1 Length of query: 395 Length of database: 464 Length adjustment: 32 Effective length of query: 363 Effective length of database: 432 Effective search space: 156816 Effective search space used: 156816 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: 51 (24.3 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