Align beta-alanine-pyruvate transaminase (EC 2.6.1.18); alanine-glyoxylate transaminase (EC 2.6.1.44) (characterized)
to candidate CCNA_02326 CCNA_02326 acetylornithine aminotransferase/succinyldiaminopimelate aminotransferase
Query= BRENDA::Q9SR86 (481 letters) >FitnessBrowser__Caulo:CCNA_02326 Length = 405 Score = 164 bits (415), Expect = 5e-45 Identities = 129/411 (31%), Positives = 189/411 (45%), Gaps = 46/411 (11%) Query: 80 YN-TPLNIVEAKMQYVFDENGRRYLDAFGGIATVSCGHCHPEVVNSVVKQLKLINHSTIL 138 YN PL + + G YLD GIAT GH HP +V + Q + + H + + Sbjct: 18 YNRAPLAFERGRGARLISTEGEEYLDCVAGIATNGLGHAHPALVEVLKAQAEKLWHVSNI 77 Query: 139 YLNHTISDFAEALVSTLPGDLKVVFFTNSGTEANELAMMMARLYTGCN------DIVSLR 192 Y + A+AL + D VVFFTNSGTEA E A+ AR Y N DI Sbjct: 78 YRIPEQEELADALCANSFAD--VVFFTNSGTEAVECALKTARKYHSANGQPERIDIYGFD 135 Query: 193 NSYHGNAAATMGATAQSNWKFNVVQSGVHHAINPDPYRGIFGSDGEKYASDV---HDLIQ 249 S+HG A + A+ NP G FG Y+ HD I+ Sbjct: 136 GSFHGRTYAAVNASG-----------------NPSYVDG-FGPRLPGYSQLTFGDHDAIK 177 Query: 250 FG-TSGQVAGFIGESIQGVGGIVELAPGYLPAAYDIVRKAGGVCIADEVQSGFARTGTHF 308 S A I E +QG GG + L + + G + I DEVQ G RTG F Sbjct: 178 AAIASPTTAAIIVEPVQGEGGARSIPTQCLVGLRQLCDEHGVLLIYDEVQCGMGRTGKLF 237 Query: 309 WGFQSHGVIPDIVTMAKGIGNGIPLGAVVTTPEIAGVLSRRSYFNTFGGNPMCTAAGHAV 368 + G P I+ +AK +G G P+GA + T E A ++ ++ +TFGGNP+ A G A Sbjct: 238 AYEWAEGGEPHIMAVAKALGGGFPIGACLATTEAAKGMTVAAHGSTFGGNPLAMAVGKAA 297 Query: 369 LRVLHEEKLQENANLVGSHLKRRLTLLKNKY-ELIGDVRGRGLMLGVEFV-KDRDLKTPA 426 L ++ + +N V ++L LK+++ ++I DVRG+G+++GV+ + +RD A Sbjct: 298 LEIIKSPETLDNVKTVSGFFTQQLNGLKDRFPDVIVDVRGKGMLIGVKLIPNNRDFMVLA 357 Query: 427 KAETLHLMDQMKEMGVLVGKGGFYGNVFRITPPLCFTLSDADFLVDVMDHA 477 + E L L+ GG N R+ PPL T+ +A + ++ A Sbjct: 358 RDEKL-----------LIAGGG--DNCVRLLPPLNLTIEEASEAIAKLEKA 395 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: 452 Number of extensions: 21 Number of successful extensions: 4 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 1 Length of query: 481 Length of database: 405 Length adjustment: 32 Effective length of query: 449 Effective length of database: 373 Effective search space: 167477 Effective search space used: 167477 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