Align putrescine-2-oxoglutarate transaminase (EC 2.6.1.82) (characterized)
to candidate WP_013451594.1 CALNI_RS07435 glutamate-1-semialdehyde-2,1-aminomutase
Query= BRENDA::P42588 (459 letters) >NCBI__GCF_000183405.1:WP_013451594.1 Length = 422 Score = 139 bits (350), Expect = 2e-37 Identities = 111/351 (31%), Positives = 168/351 (47%), Gaps = 19/351 (5%) Query: 31 MKALNREVIEYFKEHVNPGFLEYRKSVTAGGDYGAVEWQAGSLNTLVDTQGQEFIDCLGG 90 MK L E Y VN R + GG+ ++ GS + D G+E+ID + Sbjct: 1 MKNLFEESKRYIPGGVNS---PVRAFGSVGGEPIFIDRGKGS--KIYDVDGKEYIDYVCS 55 Query: 91 FGIFNVGHRNPVVVSAVQNQLAKQPLHSQELLDPLRAMLAKTLAALTPGKLKYSFFCNSG 150 +G GH + +++ V+ L K + L LAK + + P ++ +SG Sbjct: 56 WGPLIHGHADDDIITEVERVLKKGTTFGAPTV--LELELAKKVVEMVPS-IEMVRMVSSG 112 Query: 151 TESVEAALKLAKAYQSPRGKFTFIATSGAFHGKSLGAL--SATAKSTFRKPFMPLLPG-- 206 TE+V +A++LA+ Y G+ I G +HG S L + + TF +P P +P Sbjct: 113 TEAVMSAIRLARGYT---GRDKIIKFEGCYHGHSDSLLVKAGSGALTFGQPSSPGVPADL 169 Query: 207 FRHVPFGNIEAMRTALNECKKTGDDVAAVILEPIQGEGGVILPPPGYLTAVRKLCDEFGA 266 +H + + + + +A VI+EP+ G GV+LP G+L+ +R LC GA Sbjct: 170 AKHTLIADYNDLNSVKQLFINNKNQIACVIVEPVAGNMGVVLPEEGFLSGLRDLCSNEGA 229 Query: 267 LMILDEVQTGMGRTGKMFACEHENVQPDILCLAKALGGGVMPIGATIATEEVFSVLFD-N 325 L+I DEV TG R A E+ NV PDI L K LGGG +P+GA +E+ + Sbjct: 230 LLIFDEVITGF-RLAPGGAQEYFNVMPDITTLGKILGGG-LPVGAYGGRKEIMEKISPLG 287 Query: 326 PFLHTTTFGGNPLACAAALATINVLLEQNLPAQAEQKGDMLLDGFRQLARE 376 P T GNPLA AA +A +N L +N + +K L +GF+ RE Sbjct: 288 PVYQAGTLSGNPLAMAAGIANLN-KLNENFYYELRKKSQYLWNGFKNNCRE 337 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: 442 Number of extensions: 19 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: 422 Length adjustment: 32 Effective length of query: 427 Effective length of database: 390 Effective search space: 166530 Effective search space used: 166530 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