Align putrescine-2-oxoglutarate transaminase (EC 2.6.1.82) (characterized)
to candidate Dsui_0023 Dsui_0023 acetylornithine/succinylornithine aminotransferase
Query= BRENDA::P42588 (459 letters) >FitnessBrowser__PS:Dsui_0023 Length = 396 Score = 188 bits (477), Expect = 3e-52 Identities = 130/386 (33%), Positives = 204/386 (52%), Gaps = 32/386 (8%) Query: 76 LVDTQGQEFIDCLGGFGIFNVGHRNPVVVSAVQNQLAKQPLHSQELLDPLRAMLAKTLAA 135 LVD QG+ ++D + G+ + +GH +P +V A+ +Q K L++P A + Sbjct: 33 LVDQQGKRYLDFVQGWAVNCLGHGHPAIVEALASQAGK-------LINPSPAFYNEPSLK 85 Query: 136 LTPGKLKYS-----FFCNSGTESVEAALKLAKAYQSPR--GKFTFIATSGAFHGKSLGAL 188 L G +S FF ++G E+ E A+KLA+ + G I +G FHG++L + Sbjct: 86 LAAGLAAHSCFDRVFFASTGAEANEGAIKLARKWGQKHKGGAHEIITFAGGFHGRTLATM 145 Query: 189 SATAKSTFRKPFMPLLPGFRHVPFGNIEAMRTALNECKKTGDDVAAVILEPIQGEGGVIL 248 SA+ K + F P +PGF +++++ +NE A++LEPIQGEGGV+ Sbjct: 146 SASGKPGWDTLFAPQVPGFPKAQLNDLDSVAALINE------RTVAIMLEPIQGEGGVVP 199 Query: 249 PPPGYLTAVRKLCDEFGALMILDEVQTGMGRTGKMFACEHENVQPDILCLAKALGGGVMP 308 +L +R++CD+ G L+I+DEVQTGMGRTGK+FA +H ++PDI+ L K +GGGV P Sbjct: 200 ASAEFLQLLRQICDDRGLLLIVDEVQTGMGRTGKLFAHQHAGIEPDIMTLGKGIGGGV-P 258 Query: 309 IGATIATEEVFSVLFDNPFLHTTTFGGNPLACAAALATINVLLEQNLPAQAEQKGDMLLD 368 + A +A E V + T+ GNPL A A + VL A+ KG+ L Sbjct: 259 LSALLAKESVCCFEAGD---QGGTYNGNPLMTAVGAAVLEVLTAPGFLAEVAAKGEYLGA 315 Query: 369 GFRQLAREYPDLVQEARGKGMLMAIEFVDNEIGYNFASEMFRQRVLVAGTLNNA---KTI 425 G ++L+ ++ RG+G+L A+ D E G E R+R G L NA + Sbjct: 316 GLQRLSDRLG--LRGERGQGLLRALLLAD-ERGPAIV-EAARERG-PEGLLLNAPRPHLL 370 Query: 426 RIEPPLTLTIEQCELVIKAARKALAA 451 R P LT++ E+ + ++ + L A Sbjct: 371 RFMPSLTVSREEIDQMLAWLEELLRA 396 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: 400 Number of extensions: 16 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: 459 Length of database: 396 Length adjustment: 32 Effective length of query: 427 Effective length of database: 364 Effective search space: 155428 Effective search space used: 155428 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