Align [amino group carrier protein]-gamma-(L-lysyl)-L-glutamate aminotransferase (EC 2.6.1.118) (characterized)
to candidate WP_041304058.1 BTUS_RS09720 ornithine--oxo-acid transaminase
Query= BRENDA::Q93R93 (395 letters) >NCBI__GCF_000092905.1:WP_041304058.1 Length = 394 Score = 275 bits (704), Expect = 1e-78 Identities = 152/391 (38%), Positives = 217/391 (55%), Gaps = 12/391 (3%) Query: 12 LLEAEKTLDSGVYNKHDLLIVRGQGARVWDAEGNEYIDCVGGYGVANLGHGNPEVVEAVK 71 ++E E + Y+ +++ +G+G V D EG Y+D + Y N GH +P +++A+K Sbjct: 1 MIEREDRYGARNYDPLPVVLTKGEGVWVEDVEGRRYLDMLSAYSALNQGHRHPRIIQALK 60 Query: 72 RQAETLMAMPQTLPTPMRGEFYRTLTAILPPELNRVFPVNSGTEANEAALKFARAHTGRK 131 QA+ + + G FY L + + + P+N+GTEA E A+K R R Sbjct: 61 AQADRITLTSRAFYNDKLGFFYERLAQLTHKDT--ILPMNTGTEAVETAIKAMRRWAYRV 118 Query: 132 K--------FVAAMRGFSGRTMGSLSVTWEPKYREPFLPLVEPVEFIPYNDVEALKRAVD 183 + + A F GRT +S + EP+YRE F PL +PY D+EAL+RA Sbjct: 119 RGVPEDQAEIIVATGNFHGRTTTVISFSSEPEYREGFGPLTPGFRVVPYGDIEALRRAAG 178 Query: 184 EETAAVILEPVQGEGGVRPATPEFLRAAREITQEKGALLILDEIQTGMGRTGKRFAFEHF 243 TA V+LEP+QGE G+ +LR R I E G + DEIQTG+GRTG+ FA + Sbjct: 179 PHTAGVLLEPIQGEAGIVLPPDGYLREVRRICTENGIVFAADEIQTGLGRTGQWFACDWE 238 Query: 244 GIVPDILTLAKALGGGV-PLGVAVMREEVARSMPKGGHGTTFGGNPLAMAAGVAAIRYLE 302 + PD+ L KALGGGV P+ ++ G HG+TFGGNPLA A V A++ +E Sbjct: 239 NVTPDLYILGKALGGGVYPVSAVAANRDILGVFEPGSHGSTFGGNPLAAAVAVTALQVIE 298 Query: 303 RTRLWERAAELGPWFMEKLRAIPSPKIREVRGMGLMVGLELKEKAAPYIARLEKEHRVLA 362 +L +R+ ELG +F+ +LR + P IREVRG GL +GLEL A PY +L K +L Sbjct: 299 DEKLVDRSRELGAYFLVRLRTLRHPAIREVRGRGLFIGLELTSPARPYCEKL-KNRGLLC 357 Query: 363 LQAGPTVIRFLPPLVIEKEDLERVVEAVRAV 393 + T IRF PPLVI+KE+L+ E + V Sbjct: 358 KETHETTIRFAPPLVIQKEELDWAFEQIAEV 388 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: 420 Number of extensions: 22 Number of successful extensions: 5 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: 394 Length adjustment: 31 Effective length of query: 364 Effective length of database: 363 Effective search space: 132132 Effective search space used: 132132 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 10 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