Align putrescine-2-oxoglutarate transaminase (EC 2.6.1.82) (characterized)
to candidate WP_041100608.1 SUTH_RS15840 adenosylmethionine--8-amino-7-oxononanoate transaminase
Query= BRENDA::P42588 (459 letters) >NCBI__GCF_000828635.1:WP_041100608.1 Length = 426 Score = 152 bits (384), Expect = 2e-41 Identities = 125/389 (32%), Positives = 187/389 (48%), Gaps = 30/389 (7%) Query: 81 GQEFIDCLGGFGIFNVGHRNPVVVSAVQNQLAKQP-LHSQELLDPLRAMLAKTLAALTPG 139 G+E ID + + G+ +P + +A++ QLA P + L+ A LA+ LAAL PG Sbjct: 41 GRELIDGISSWWTACHGYNHPHIRAAIERQLASLPHVMFAGLVHEPAARLAQRLAALLPG 100 Query: 140 KLKYSFFCNSGTESVEAALKLAKAYQSPRG---KFTFIATSGAFHGKSLGALS-ATAKST 195 L+ FF SG+ +VE ALK+A Y +G K + +HG + ++ + Sbjct: 101 DLERVFFTESGSVAVEVALKMAIQYWRNKGQAEKQRIVYFRHGYHGDTFATMALCDPEEG 160 Query: 196 FRKPFMPLLPGFRHVPFGNIEAMRTALNECKKT-GDDVAAVILEP-IQGEGGVILPPPGY 253 F +P + E MR A +T G+ +AAVI+EP +QG GG+ + Sbjct: 161 MHSLFAGAMPDQIMAELPSDETMRRAFELLLETHGERLAAVIIEPLVQGAGGMQMHDAAT 220 Query: 254 LTAVRKLCDEFGALMILDEVQTGMGRTGKMFACEH----ENVQPDILCLAKALGGGVMPI 309 L + C L+I DE+ TG GRTG+MFACE + PDI+CL+KAL GG +P+ Sbjct: 221 LAFIAAACARHKLLLIADEIMTGFGRTGRMFACEEADELTSTIPDIVCLSKALTGGTLPL 280 Query: 310 GATIATEEVF-SVLFDNP---FLHTTTFGGNPLACAAALATINVLLEQNLPAQA---EQK 362 AT+A VF + L D+P +H T+ N LACAAA A++++ + AQ E + Sbjct: 281 AATVARRHVFEAFLADDPAAALMHGPTYMANALACAAANASLDLFESEPRLAQVAAIEAQ 340 Query: 363 GDMLLDGFRQLAREYPDLVQEARGKGMLMAIEFVDNEIGYNFASEMFRQRVLVAGTLNN- 421 L R LA V E R KG + A+ E+ + R+R G Sbjct: 341 LAAELGPCRDLAG-----VAEVRVKGAIGAV-----ELAGRIELDALRRRFAELGVWVRP 390 Query: 422 -AKTIRIEPPLTLTIEQCELVIKAARKAL 449 K + + PP + E + A R+ L Sbjct: 391 FGKVVYLMPPFVIAAEDLTTLTAAVRQVL 419 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: 406 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: 426 Length adjustment: 32 Effective length of query: 427 Effective length of database: 394 Effective search space: 168238 Effective search space used: 168238 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 Apr 09 2024. 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