Align putrescine-2-oxoglutarate transaminase (EC 2.6.1.82) (characterized)
to candidate CCNA_02326 CCNA_02326 acetylornithine aminotransferase/succinyldiaminopimelate aminotransferase
Query= BRENDA::P42588 (459 letters) >FitnessBrowser__Caulo:CCNA_02326 Length = 405 Score = 225 bits (573), Expect = 2e-63 Identities = 139/382 (36%), Positives = 206/382 (53%), Gaps = 18/382 (4%) Query: 76 LVDTQGQEFIDCLGGFGIFNVGHRNPVVVSAVQNQLAKQPLHSQELLDPLRAMLAKTLAA 135 L+ T+G+E++DC+ G +GH +P +V ++ Q K S P + LA L A Sbjct: 33 LISTEGEEYLDCVAGIATNGLGHAHPALVEVLKAQAEKLWHVSNIYRIPEQEELADALCA 92 Query: 136 LTPGKLKYSFFCNSGTESVEAALKLAKAYQSPRG---KFTFIATSGAFHGKSLGALSATA 192 + + FF NSGTE+VE ALK A+ Y S G + G+FHG++ A++A+ Sbjct: 93 NSFADVV--FFTNSGTEAVECALKTARKYHSANGQPERIDIYGFDGSFHGRTYAAVNASG 150 Query: 193 KSTFRKPFMPLLPGFRHVPFGNIEAMRTALNECKKTGDDVAAVILEPIQGEGGVILPPPG 252 ++ F P LPG+ + FG+ +A++ A+ AA+I+EP+QGEGG P Sbjct: 151 NPSYVDGFGPRLPGYSQLTFGDHDAIKAAI-----ASPTTAAIIVEPVQGEGGARSIPTQ 205 Query: 253 YLTAVRKLCDEFGALMILDEVQTGMGRTGKMFACE-HENVQPDILCLAKALGGGVMPIGA 311 L +R+LCDE G L+I DEVQ GMGRTGK+FA E E +P I+ +AKALGGG PIGA Sbjct: 206 CLVGLRQLCDEHGVLLIYDEVQCGMGRTGKLFAYEWAEGGEPHIMAVAKALGGG-FPIGA 264 Query: 312 TIATEEVFSVLFDNPFLHTTTFGGNPLACAAALATINVLLEQNLPAQAEQKGDMLLDGFR 371 +AT E + H +TFGGNPLA A A + ++ + Sbjct: 265 CLATTEAAKGM--TVAAHGSTFGGNPLAMAVGKAALEIIKSPETLDNVKTVSGFFTQQLN 322 Query: 372 QLAREYPDLVQEARGKGMLMAIEFVDNEIGYNFASEMFRQRVLVAGTLNNAKTIRIEPPL 431 L +PD++ + RGKGML+ ++ + N + + +++L+AG +N +R+ PPL Sbjct: 323 GLKDRFPDVIVDVRGKGMLIGVKLIPNNRDFMVLAR--DEKLLIAGGGDNC--VRLLPPL 378 Query: 432 TLTIEQCELVIKAARKALAAMR 453 LTIE+ I KA A R Sbjct: 379 NLTIEEASEAIAKLEKACEAAR 400 Lambda K H 0.320 0.135 0.393 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: 430 Number of extensions: 23 Number of successful extensions: 9 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: 459 Length of database: 405 Length adjustment: 32 Effective length of query: 427 Effective length of database: 373 Effective search space: 159271 Effective search space used: 159271 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 Sep 17 2021. The underlying query database was built on Sep 17 2021.
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