Align putrescine-2-oxoglutarate transaminase (EC 2.6.1.82) (characterized)
to candidate 199805 SO0617 acetylornithine aminotransferase (NCBI ptt file)
Query= BRENDA::P42588 (459 letters) >FitnessBrowser__MR1:199805 Length = 405 Score = 190 bits (483), Expect = 6e-53 Identities = 130/362 (35%), Positives = 193/362 (53%), Gaps = 21/362 (5%) Query: 78 DTQGQEFIDCLGGFGIFNVGHRNPVVVSAVQNQLAKQPLHSQELLDPLRAMLAKTLAALT 137 D +G EFID GG + +GH +P +V+A++ Q K S + + LA L T Sbjct: 37 DQEGNEFIDFAGGIAVNCLGHCHPALVNALKTQGEKLWHLSNVMTNEPALELATKLVNST 96 Query: 138 PGKLKYSFFCNSGTESVEAALKLAKAYQSPRG---KFTFIATSGAFHGKSLGALSATAKS 194 + Y F NSG E+ EAALKLA+ Y + K IA AFHG++ +S ++ Sbjct: 97 FAERVY--FANSGAEANEAALKLARRYALEKHGVEKDEIIAFDKAFHGRTFFTVSVGGQA 154 Query: 195 TFRKPFMPLLPGFRHVPFGNIEAMRTALNECKKTGDDVAAVILEPIQGEGGVILPPPGYL 254 + F P H+PF ++ A+ A++ D A++LEP+QGEGG+I P +L Sbjct: 155 AYSDGFGPKPQSITHLPFNDVAALEAAVS------DKTCAIMLEPLQGEGGIIDADPAFL 208 Query: 255 TAVRKLCDEFGALMILDEVQTGMGRTGKMFACEHENVQPDILCLAKALGGGVMPIGATIA 314 AVR+L ++ AL+I DEVQTG+GRTG+++A ++ PDIL AKALGGG PI A + Sbjct: 209 KAVRELANKHNALVIFDEVQTGVGRTGELYAYMGTDIVPDILTTAKALGGG-FPIAAMLT 267 Query: 315 TEEVFSVLFDNPFLHTTTFGGNPLACAAALATINVLLEQNLPAQAEQKGDMLLDGFRQLA 374 T E+ L H +T+GGNPLACA A ++V+ + + + +L DG ++ Sbjct: 268 TTEIAEHL--KVGTHGSTYGGNPLACAIGNAVLDVVNTPEVLNGVKHREQLLRDGLNKIN 325 Query: 375 REYPDLVQEARGKGMLMAIEFVDNEIGYNFASEMFRQRVLVAGTLN---NAKTIRIEPPL 431 +Y + E RGKG+L+ V NE Y S F + G ++ A +R P L Sbjct: 326 EKY-HVFSEVRGKGLLLGA--VLNE-QYQGRSRDFLVASVAEGLMSLMAGANVVRFAPSL 381 Query: 432 TL 433 + Sbjct: 382 VI 383 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: 362 Number of extensions: 15 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: 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