Align putrescine-2-oxoglutarate transaminase (EC 2.6.1.82) (characterized)
to candidate 8502443 DvMF_3149 acetylornithine aminotransferase (RefSeq)
Query= BRENDA::P42588 (459 letters) >FitnessBrowser__Miya:8502443 Length = 402 Score = 201 bits (510), Expect = 5e-56 Identities = 127/387 (32%), Positives = 199/387 (51%), Gaps = 24/387 (6%) Query: 71 GSLNTLVDTQGQEFIDCLGGFGIFNVGHRNPVVVSAVQNQLAKQPLHSQELLDPLRAMLA 130 G + L D G+E++D L G + ++GH + + Q K S + LA Sbjct: 30 GQGSRLWDVDGREYVDLLSGIAVTSLGHCHEELAEVAAAQARKLVHVSNLFYQEEQLDLA 89 Query: 131 KTLAALTPGKLKYSFFCNSGTESVEAALKLAKAYQSP---RGKFTFIATSGAFHGKSLGA 187 + L L+ +FFCNSG E+ EAA+KLA+ Y R + I +GAFHG++L Sbjct: 90 ERL--LSTSHCTKAFFCNSGAEANEAAIKLARRYMQRVQGREAYEIITLTGAFHGRTLAT 147 Query: 188 LSATAKSTFRKPFMPLLPGFRHVPFGNIEAMRTALNECKKTGDDVAAVILEPIQGEGGVI 247 ++AT ++ F+ F P+ GFR VP G+IEA+R A+ G A V++E +QGEGGV Sbjct: 148 VAATGQAKFQDGFYPMPEGFRQVPSGDIEALRAAI------GPQTAGVLVEVVQGEGGVC 201 Query: 248 LPPPGYLTAVRKLCDEFGALMILDEVQTGMGRTGKMFACEHENVQPDILCLAKALGGGVM 307 P Y AV+ LC E G L + DE+Q GM RTG+ ++ ++ ++PDI+ AKAL G + Sbjct: 202 PLDPDYARAVQALCREKGVLFMTDEIQAGMCRTGRFWSFQNYGLEPDIVSCAKALANG-L 260 Query: 308 PIGATIATEEVFSVLFDNPFLHTTTFGGNPLACAAALATINVLLEQNLPAQAEQKGDMLL 367 P+GA + T+EV H TTFG L A A T+ ++L +L +A +G ++ Sbjct: 261 PMGAMMTTDEVARGFVAGS--HATTFGAGALVSAVASRTVEIMLRDDLAGRAATEGARIM 318 Query: 368 DGFRQLAREYPDLVQEARGKGMLMAIEFVDNEIGYNFASEMFRQRVLVAGTLNNAK---T 424 D FR + ++ P + RG G+++ + F + Q ++ G + N Sbjct: 319 DRFRAMGQKLPGTIDHVRGLGLMIGVVLA-------FPGKEVWQALIDRGFICNLTQDCV 371 Query: 425 IRIEPPLTLTIEQCELVIKAARKALAA 451 +R+ P LT+ + A L+A Sbjct: 372 LRLLPALTIPRADLDAFADALEDILSA 398 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: 387 Number of extensions: 20 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: 402 Length adjustment: 32 Effective length of query: 427 Effective length of database: 370 Effective search space: 157990 Effective search space used: 157990 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