Align [amino group carrier protein]-gamma-(L-lysyl)-L-glutamate aminotransferase (EC 2.6.1.118) (characterized)
to candidate BPHYT_RS22435 BPHYT_RS22435 4-aminobutyrate aminotransferase
Query= BRENDA::Q93R93 (395 letters) >FitnessBrowser__BFirm:BPHYT_RS22435 Length = 427 Score = 211 bits (537), Expect = 3e-59 Identities = 146/399 (36%), Positives = 208/399 (52%), Gaps = 34/399 (8%) Query: 28 DLLIVRGQGARVWDAEGNEYIDCVGGYGVANLGHGNPEVVEAVKRQAETLMAMP-QTLPT 86 D R + A +WD EG +ID G V N GH +P+++ A++ Q + Q +P Sbjct: 23 DFYAERAENAELWDVEGRRFIDFAAGIAVCNTGHRHPKILAAIRDQLDHFTHTAYQIVPY 82 Query: 87 PMRGEFYRTLTAILP---PELNRVFPVNSGTEANEAALKFARAHTGRKKFVAAMRGFSGR 143 E L P P+ F +G EA E A+K ARA TGR +A GF GR Sbjct: 83 ASYVELAEKLNERAPGDHPKKTAFF--TTGAEAVENAIKIARAATGRPGVIAFTGGFHGR 140 Query: 144 TMGSLSVTWE-PKYREPFLPLVEPVEFIPYND-------------VEALKRA-VD-EETA 187 T+ +++T + Y+ F P V P+ + +E L +A +D + A Sbjct: 141 TLMGMALTGKVAPYKIGFGPFPSDVFHAPFPNPLHGVTTADSLKAIEFLFKADIDPKRVA 200 Query: 188 AVILEPVQGEGGVRPATPEFLRAAREITQEKGALLILDEIQTGMGRTGKRFAFEHFGIVP 247 A+I EPVQGEGG PA EF+RA R++ E G LLI DE+QTG RTGK FA H+ +VP Sbjct: 201 AIIFEPVQGEGGFYPAPAEFVRALRKLCNEHGILLIADEVQTGFARTGKLFAMHHYDVVP 260 Query: 248 DILTLAKALGGGVPLGVAVMREEVARSMPKGGHGTTFGGNPLAMAAGVAAIRYLERTRLW 307 D++T+AK+L GG+PL + R +V + GG G T+ GNPLA+AA A + ++ +L Sbjct: 261 DLMTVAKSLAGGMPLSGVIGRADVMDAAAPGGLGGTYAGNPLAVAAAHAVLDIIDEEKLC 320 Query: 308 ERAAELGPWFMEKLRAIPS--PKIREVRGMGLMVGLEL-----KEKAAPYIARLEK---E 357 ERA LG KL A+ S P+I +VRG G MV +E E A + R++ E Sbjct: 321 ERATLLGDRVKAKLIALQSDVPQIADVRGPGGMVAVEFCKAGGTEPDAEFTKRVQTRALE 380 Query: 358 HRVLALQAG--PTVIRFLPPLVIEKEDLERVVEAVRAVL 394 +L L G V+RFL PL I+ + + + V+ Sbjct: 381 RGLLLLVCGVYSNVVRFLFPLTIQDAVFDEAMAILEDVI 419 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: 433 Number of extensions: 24 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: 427 Length adjustment: 31 Effective length of query: 364 Effective length of database: 396 Effective search space: 144144 Effective search space used: 144144 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