Align [amino group carrier protein]-gamma-(L-lysyl)-L-glutamate aminotransferase (EC 2.6.1.118) (characterized)
to candidate RR42_RS21370 RR42_RS21370 4-aminobutyrate aminotransferase
Query= BRENDA::Q93R93 (395 letters) >FitnessBrowser__Cup4G11:RR42_RS21370 Length = 420 Score = 220 bits (560), Expect = 7e-62 Identities = 145/391 (37%), Positives = 201/391 (51%), Gaps = 29/391 (7%) Query: 33 RGQGARVWDAEGNEYIDCVGGYGVANLGHGNPEVVEAVKRQAETLMAMP-QTLPTPMRGE 91 R + + +WD EG YID G V N GH +P +VEA++RQ E Q +P E Sbjct: 28 RAENSEIWDVEGKRYIDFAAGIAVLNTGHRHPRLVEAMQRQLERFTHTAYQIVPYASYIE 87 Query: 92 FYRTLTAILPPE-LNRVFPVNSGTEANEAALKFARAHTGRKKFVAAMRGFSGRTMGSLSV 150 + P + +G EA E A+K ARA TGR +A GF GRTM +++ Sbjct: 88 LAERINQRAPGRGAKKTAFFTTGAEAVENAIKIARAATGRPGVIAFSGGFHGRTMMGMAL 147 Query: 151 TWEP-KYREPFLPLVEPVEFIPYN------DVEALKRAVD---------EETAAVILEPV 194 T + Y+ F P V PY VE +A++ + AA+I EPV Sbjct: 148 TGKVVPYKVGFGPFPGEVFHAPYPCALHGVSVEDALKAMEHLFKADVDPKRVAAIIFEPV 207 Query: 195 QGEGGVRPATPEFLRAAREITQEKGALLILDEIQTGMGRTGKRFAFEHFGIVPDILTLAK 254 QGEGG A P F++A R I E G LL+ DE+QTG GRTGK FA EH+ + PD+ T+AK Sbjct: 208 QGEGGFNVAPPAFVKALRAICDEHGILLVADEVQTGFGRTGKLFAMEHYDVAPDLTTMAK 267 Query: 255 ALGGGVPLGVAVMREEVARSMPKGGHGTTFGGNPLAMAAGVAAIRYLERTRLWERAAELG 314 +L GG+PL R EV + GG G T+ GNPLA+A+ +A + LE +L R A LG Sbjct: 268 SLAGGMPLSAVCGRAEVMDAPAPGGLGGTYAGNPLAVASALAVLDVLEGEQLIPRGAALG 327 Query: 315 PWFMEKLRAIPS--PKIREVRGMGLMVGLELKEKAAPYIARLEKEHRVLALQAG------ 366 + +L A+ + P+I E+RG+G MV +E + A +E + AL+ G Sbjct: 328 QRLVARLEALKARVPQIAEIRGLGAMVAVEFRRADGAPDAEFTREVQNRALEQGLLLLSC 387 Query: 367 ---PTVIRFLPPLVIEKEDLERVVEAVRAVL 394 VIRFL PL I + ++ + VL Sbjct: 388 GVYGNVIRFLFPLTISDAVMNEGLDILADVL 418 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: 415 Number of extensions: 16 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: 420 Length adjustment: 31 Effective length of query: 364 Effective length of database: 389 Effective search space: 141596 Effective search space used: 141596 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