Align [amino group carrier protein]-gamma-(L-lysyl)-L-glutamate aminotransferase (EC 2.6.1.118) (characterized)
to candidate SM_b21186 SM_b21186 4-aminobutyrate aminotransferase
Query= BRENDA::Q93R93 (395 letters) >FitnessBrowser__Smeli:SM_b21186 Length = 422 Score = 223 bits (569), Expect = 6e-63 Identities = 146/390 (37%), Positives = 204/390 (52%), Gaps = 30/390 (7%) Query: 33 RGQGARVWDAEGNEYIDCVGGYGVANLGHGNPEVVEAVKRQAETLM-AMPQTLPTPMRGE 91 R + A +WD EGN YID G V N GH +P+V+ AVK Q + Q +P Sbjct: 26 RAENAEIWDKEGNRYIDFAAGIAVVNTGHRHPKVIAAVKAQLDRFTHTCHQVVPYENYVH 85 Query: 92 FYRTLTAILPPEL-NRVFPVNSGTEANEAALKFARAHTGRKKFVAAMRGFSGRTMGSLSV 150 L AI+P + + V +G EA E A+K ARA TGR+ VA GF GRT +++ Sbjct: 86 LAERLNAIVPGDFAKKTIFVTTGAEAVENAVKIARAATGRQAVVAFGGGFHGRTFMGMAL 145 Query: 151 TWEP-KYREPFLPLVEPVEFIPY----------NDVEALKR--AVDEE---TAAVILEPV 194 T + Y+ F + V P+ + ALK+ A D + AA+I+EPV Sbjct: 146 TGKVVPYKVGFGAMPADVFHAPFPIELHGVTVEQSLSALKKLFAADVDPARVAAIIIEPV 205 Query: 195 QGEGGVRPATPEFLRAAREITQEKGALLILDEIQTGMGRTGKRFAFEHFGIVPDILTLAK 254 QGEGG P F++A RE+ + G LLI DE+QTG RTGK FA EH G+ PD+ T+AK Sbjct: 206 QGEGGFYPVPTAFMKALREVCDQHGILLIADEVQTGFARTGKLFAMEHHGVAPDLTTMAK 265 Query: 255 ALGGGVPLGVAVMREEVARSMPKGGHGTTFGGNPLAMAAGVAAIRYLERTRLWERAAELG 314 +L GG PL R E+ + GG G T+GGNPL +AA A + + L ERA +LG Sbjct: 266 SLAGGFPLAAVTGRAEIMDAPGPGGLGGTYGGNPLGIAAAHAVLDVIAEENLCERANQLG 325 Query: 315 PWFMEKLRAI--PSPKIREVRGMGLMVGLELKE-KAAPYIARLEKEHRVLALQAG----- 366 ++L AI +P+I ++RG G M +E + + A + R+LAL+ G Sbjct: 326 NRLKQRLAAIREKAPEIVDIRGPGFMNAVEFNDVRTNLPSAEFANKVRLLALEKGLILLT 385 Query: 367 ----PTVIRFLPPLVIEKEDLERVVEAVRA 392 VIRFL P+ I+ E ++ + A Sbjct: 386 CGVHGNVIRFLAPITIQDEVFAEALDTIEA 415 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: 429 Number of extensions: 22 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: 422 Length adjustment: 31 Effective length of query: 364 Effective length of database: 391 Effective search space: 142324 Effective search space used: 142324 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