Align acetylornithine transaminase (EC 2.6.1.11); 4-aminobutyrate-2-oxoglutarate transaminase (EC 2.6.1.19) (characterized)
to candidate WP_013135213.1 ARNIT_RS07040 glutamate-1-semialdehyde-2,1-aminomutase
Query= BRENDA::P73133 (429 letters) >NCBI__GCF_000092245.1:WP_013135213.1 Length = 426 Score = 131 bits (329), Expect = 5e-35 Identities = 111/346 (32%), Positives = 165/346 (47%), Gaps = 45/346 (13%) Query: 30 DFDTYVMNTYGRFPIAIARGQGSTLWDTEGKSYLDFVAGIATCTLGHA----HPALVRAV 85 D N+ G P IARG+G+ L D +G YLDF+ GH A++R V Sbjct: 21 DSPVRAFNSVGGTPPFIARGEGAYLIDIDGNKYLDFIQSWGPLIFGHCDKDIEEAVIRTV 80 Query: 86 SDQIQKLHHVSNLYYIPE--QGELAKWIVE-HSCADRVFFCNSGAEANEAAIKLVRKYAH 142 D + + P + ELA+ IVE + D+V F +SG EA +AI+L R Sbjct: 81 MDGLS--------FGAPSVLETELAREIVEMYDNLDKVRFVSSGTEATMSAIRLARGVTG 132 Query: 143 TVLDFLEQPVILTAKASFHGRTLATITATGQPKYQQYFDPLVPGFD--------YVPYND 194 + IL + +HG + + + G + P PG YN+ Sbjct: 133 -------KNDILKFEGCYHGHSDSLLVQAGSGM-ATFGTPSSPGVPADLTKHTLLCEYNN 184 Query: 195 IRSLENKVADLDEGNSRVAAIFLEPLQGEGGVRPGDLAYFKRVREICDQNDILLVFDEVQ 254 I +L+ E +S +A I +EP+ G G P D+ + K REICD+N+ LL++DEV Sbjct: 185 IENLKKCF----EQSSDIACIIIEPIAGNMGFIPADIEFLKACREICDENNTLLIYDEVM 240 Query: 255 VGVGRTGKLWGYEHLGVEP--DIFTSAKGLAGGVPIGAMMC-KKFCDVFEPGN---HAST 308 G RT L G + VEP DI T K + G+P+GA K+ P A T Sbjct: 241 TGF-RT-SLKGTSGI-VEPQADIITFGKVIGAGMPVGAFASNKEIMAHLSPDGAVYQAGT 297 Query: 309 FGGNPLACAAGLAVLKTIEGD-RLLDNVQARGEQLRSGLAEIKNQY 353 GNP+A AAGL L+ ++ + + D++ A+ +L +GL E+ N+Y Sbjct: 298 LSGNPVAMAAGLTSLRKLKANPAIYDDLNAKAVRLTTGLKEVANKY 343 Lambda K H 0.320 0.137 0.405 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: 445 Number of extensions: 27 Number of successful extensions: 6 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: 429 Length of database: 426 Length adjustment: 32 Effective length of query: 397 Effective length of database: 394 Effective search space: 156418 Effective search space used: 156418 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 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