Align putrescine-2-oxoglutarate transaminase (EC 2.6.1.82) (characterized)
to candidate WP_015739397.1 ADEG_RS07165 aspartate aminotransferase family protein
Query= BRENDA::P42588 (459 letters) >NCBI__GCF_000024605.1:WP_015739397.1 Length = 460 Score = 342 bits (877), Expect = 2e-98 Identities = 188/448 (41%), Positives = 272/448 (60%), Gaps = 37/448 (8%) Query: 29 EEMKALNREVIEYFKEHVNPGFLEYRKSVTAGGDYGAVEWQAGSLNTLVDTQGQEFIDCL 88 E ++ +V E +E++N G + + + + E L D +G+ + D L Sbjct: 9 EALELSREKVRELHREYLNAGLCQLLRLLDFDKRFVKAEGAK-----LWDEEGKMYWDFL 63 Query: 89 GGFGIFNVGHRNPVVVSAVQNQLAKQPLHSQELLDPLRAMLAKTLAALTPGKLKYSFFCN 148 G FG N+GH +P V++A+ + + P Q L PL LA+ L L PG +K +FFCN Sbjct: 64 GSFGAMNIGHNHPKVLAAL-DLVRGFPTMVQTTLSPLAGALARNLCRLAPGGMKRAFFCN 122 Query: 149 SGTESVEAALKLAKAYQSPRGKFTFIATSGAFHGKSLGALSATAKSTFRKPFMPLLPGFR 208 SG E+VE ALKLA+A G+ FI +FHGK+ GALS T + +++PF+PLLP + Sbjct: 123 SGAEAVEGALKLARA---ATGRPGFIYCHNSFHGKTFGALSVTGRKKYQEPFLPLLPNCQ 179 Query: 209 HVPFGNIEAMRTALNECKKTGDDVAAVILEPIQGEGGVILPPPGYLTAVRKLCDEFGALM 268 +P+ ++ A+ AL++ + AA I+EPIQGEGG+I+P PGYL ++LC +G L+ Sbjct: 180 AIPYDDLAALEEALHK-----KEAAAFIVEPIQGEGGIIVPSPGYLREAKRLCSRYGTLL 234 Query: 269 ILDEVQTGMGRTGKMFACEHENVQPDILCLAKALGGGVMPIGATIATEEVFSVLFDNP-- 326 I+DE+QTG+GRTGK+FACEH+ V+PDI+CLAK+LGGGV+PIGA + T+ +++ + +P Sbjct: 235 IVDEIQTGLGRTGKLFACEHDGVEPDIICLAKSLGGGVIPIGAFLTTDAIWNKAYGSPDR 294 Query: 327 -FLHTTTFGGNPLACAAALATINVLLEQNLPAQAEQKGDMLLDGFRQLAREYPDLVQEAR 385 LHT+TFGGN ACAAALAT+ V+LE++LP QA +KG+ L R+L YP L++E R Sbjct: 295 AQLHTSTFGGNAWACAAALATLEVILEEDLPRQAARKGEFFLARLRELQARYPHLIKEVR 354 Query: 386 GKGMLMAIEFVDNEIGY----------NFASEMF----------RQRVLVAGTLNNAKTI 425 GKG+L+ +EF + + G A E R R+L A TLNN I Sbjct: 355 GKGLLVGVEFAEKQKGVLSRLTFGWVDRLAEEFLGSLVAGQLLNRFRILTAYTLNNPNVI 414 Query: 426 RIEPPLTLTIEQCELVIKAARKALAAMR 453 R+EPPL + E V +A K L R Sbjct: 415 RLEPPLVVEEEGLLQVAEALEKILKENR 442 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: 527 Number of extensions: 29 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: 460 Length adjustment: 33 Effective length of query: 426 Effective length of database: 427 Effective search space: 181902 Effective search space used: 181902 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 24 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