Align beta-alanine-pyruvate transaminase (EC 2.6.1.18); alanine-glyoxylate transaminase (EC 2.6.1.44) (characterized)
to candidate N515DRAFT_3308 N515DRAFT_3308 acetylornithine/N-succinyldiaminopimelate aminotransferase
Query= BRENDA::Q9SR86 (481 letters) >FitnessBrowser__Dyella79:N515DRAFT_3308 Length = 411 Score = 182 bits (462), Expect = 2e-50 Identities = 129/384 (33%), Positives = 190/384 (49%), Gaps = 37/384 (9%) Query: 94 VFDENGRRYLDAFGGIATVSCGHCHPEVVNSVVKQLKLINHSTILYLNHTISDFAEALVS 153 V+D GR Y+D GIA + GH P++V+++V Q + + HS+ ++ AE LV Sbjct: 37 VWDTEGRDYVDLGAGIAVNALGHQDPDLVDALVTQARKLWHSSNVFYTEPPLHLAEELVQ 96 Query: 154 TLPGDLKVVFFTNSGTEANELAMMMARLYTGCND-------IVSLRNSYHGNAAATMGAT 206 G + VF NSGTEANE A+ + R + I++ R S+HG A + AT Sbjct: 97 A-SGFAERVFLCNSGTEANEAAIKLVRKWAASKGRAPEQRVILTFRGSFHGRTLAAVTAT 155 Query: 207 AQSNWKFNVVQSGVHHAINPDPYRGIFGSDGEKYA--SDVHDLIQFGTSGQVAGFIGESI 264 AQ ++ N +P G G +Y +DV L G VA + E + Sbjct: 156 AQPKYQENY-----------EPLPG-----GFRYLDFNDVAGLEAAFAQGDVAAVMLEPV 199 Query: 265 QGVGGIVELAPGYLPAAYDIVRKAGGVCIADEVQSGFARTGTHFWGFQSHGVIPDIVTMA 324 QG GG++ +P ++ A ++ + + DE+Q G RTGT F Q GV PDIVT+A Sbjct: 200 QGEGGVLPASPAFIRRARELCDTHEALLVLDEIQCGMGRTGTLFAHAQD-GVTPDIVTLA 258 Query: 325 KGIGNGIPLGAVVTTPEIAGVLSRRSYFNTFGGNPMCTAAGHAVLRVLHEEKLQENANLV 384 K +G G P+GA++ P++A V+ ++ TFGGNPM A LR L +L N Sbjct: 259 KALGCGFPIGAMLAGPKVAEVMQYGAHGTTFGGNPMAAAVARVALRKLASAELMANVAKQ 318 Query: 385 GSHLKRRLTLLKNKYELIGDVRGRGLMLGVEFVKDRDLKTPAKAETLHLMDQMKEMGVLV 444 L+ L + + +L +VRGRGLMLG L K ++D G+LV Sbjct: 319 AQALRDGLAAIDGELKLFAEVRGRGLMLGAV------LAEAYKGRAGEVLDHAAAHGLLV 372 Query: 445 GKGGFYGNVFRITPPLCFTLSDAD 468 + G +V R PPL ++DAD Sbjct: 373 LQAG--PDVLRFVPPL--NITDAD 392 Lambda K H 0.320 0.136 0.406 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: 471 Number of extensions: 27 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: 481 Length of database: 411 Length adjustment: 32 Effective length of query: 449 Effective length of database: 379 Effective search space: 170171 Effective search space used: 170171 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 (21.8 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