Align putrescine-2-oxoglutarate transaminase (EC 2.6.1.82) (characterized)
to candidate Synpcc7942_0031 Synpcc7942_0031 aminotransferase
Query= BRENDA::P42588 (459 letters) >FitnessBrowser__SynE:Synpcc7942_0031 Length = 424 Score = 177 bits (449), Expect = 6e-49 Identities = 131/388 (33%), Positives = 193/388 (49%), Gaps = 33/388 (8%) Query: 71 GSLNTLVDTQGQEFIDCLGGFGIFNVGHRNPVVVSAVQNQLA--KQPLHSQELLDPLRAM 128 G+ TL D G+E IDC+ + + GH + +V A+ Q A + + + +P Sbjct: 28 GARLTLAD--GRELIDCISSWWVNLHGHAHLRIVEAIAQQAATLEHVIFAGFSHEPAER- 84 Query: 129 LAKTLAALTPGKLKYSFFCNSGTESVEAALKLAKAY----QSPRGKFTFIATSGAFHGKS 184 LA L + P KL FF ++G+ +VE ALK+A Y PR + +A GA+HG + Sbjct: 85 LAMELCKILPEKLTRVFFSDNGSTAVEVALKMALQYWHNLDQPRSRI--LAFDGAYHGDT 142 Query: 185 LGALSATAKSTFRKPFMPLLPGFRHVPFGNI----------EAMRTALNECKKTGDDVAA 234 GA+S +S F PF LL +P+ EA A E DVAA Sbjct: 143 FGAMSVGERSLFNAPFEKLLFSVEFLPYPETWWGDETVEAKEAAAIAAVEQALAAGDVAA 202 Query: 235 VILEP-IQGEGGVILPPPGYLTAVRKLCDEFGALMILDEVQTGMGRTGKMFACEHENVQP 293 VI+EP +QG GG+ + P +L + G+L+I DEV TG GRTG FAC+ +QP Sbjct: 203 VIIEPLVQGAGGMRMARPQFLQQLAARVQAAGSLLIADEVMTGFGRTGAWFACQRAGIQP 262 Query: 294 DILCLAKALGGGVMPIGATIATEEVFSVLF----DNPFLHTTTFGGNPLACAAALATINV 349 D++CL+K L GG +P+ T+ATE ++ D+ F H ++ NPL CAAA+A++ + Sbjct: 263 DLICLSKGLTGGFLPLSITVATEVIYDTFCSGNPDHTFYHGHSYTANPLGCAAAIASLEL 322 Query: 350 LLEQNLPAQAEQKGDMLLDGFRQLAREYPDLVQEARGKGMLMAIEFVDNEIGY-NFASEM 408 LL+ Q + D L G LA ++P V R G + A + V + GY + Sbjct: 323 LLDSEAIVQGLE--DAHLPGLELLA-QHPK-VTRPRLTGGIAACDLVSDRGGYLDPIGLR 378 Query: 409 FRQRVLVAGTLNN--AKTIRIEPPLTLT 434 RQ + G L + + PP LT Sbjct: 379 VRQAAIARGLLLRPLGNVLYLLPPYCLT 406 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: 470 Number of extensions: 36 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: 459 Length of database: 424 Length adjustment: 32 Effective length of query: 427 Effective length of database: 392 Effective search space: 167384 Effective search space used: 167384 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