Align Putrescine aminotransferase; PAT; PATase; EC 2.6.1.82; Cadaverine transaminase; EC 2.6.1.-; Putrescine transaminase; Putrescine--2-oxoglutaric acid transaminase (uncharacterized)
to candidate WP_010960134.1 MCA_RS04000 aspartate aminotransferase family protein
Query= curated2:B7LZM2 (459 letters) >NCBI__GCF_000008325.1:WP_010960134.1 Length = 462 Score = 244 bits (622), Expect = 6e-69 Identities = 145/369 (39%), Positives = 215/369 (58%), Gaps = 19/369 (5%) Query: 31 MKALNREVIEYFKEHVNPGFLEYRKSVTAGGDYGAVEWQAGGLNTLVDTQGQEFIDCLGG 90 +K E + ++H+N + K++ Y V +A G L D Q +E++D L G Sbjct: 9 LKNRRGENFDLHEKHLNTQMVRVLKTI----GYDRVYVRAQG-PYLYDDQDREYLDLLSG 63 Query: 91 FGIFNVGHRNPVVVSAVQNQL-AKQPLHSQELLDPLRAMLAKTVAALTPGKLKYSFFCNS 149 FG+F +G +P VV A+++ L A+ P Q + L +L++ + PG L F+CNS Sbjct: 64 FGVFALGRNHPQVVGALKDVLDAQLPDLVQMDVSLLSGLLSEKILQRCPGDLSRMFYCNS 123 Query: 150 GTESVEAALKLAKAYQSPRGKFTFIATSGAFHGKSLGALSATAKSTFRKPFMPLLPGFRH 209 G E+VEAA+K A+ Y + R K + FHG +LGALS + FR F PLLP + Sbjct: 124 GAEAVEAAIKFAR-YTTKREKIVYC--EHGFHGLTLGALSLNGEQVFRDGFGPLLPACKA 180 Query: 210 VPFGNIEAMRTALNECKKTGDDVAAVILEPIQGEGGVILPPPGYLTAVRKLCDEFGALMI 269 VPF ++ A+ AL +DVAA I+EPIQG+G V LP GYL +LC + GAL + Sbjct: 181 VPFNDLGALEAALRH-----NDVAAFIVEPIQGKG-VNLPDEGYLAEAARLCRKHGALFV 234 Query: 270 LDEVQTGMGRTGKMFACEHENVQPDILCLAKALGGGVMPIGATIATEEVFSVLF---DNP 326 DE+QTG+GRTGK +A EH V+PD++ +AKAL GG +P+GA + + +F D Sbjct: 235 ADEIQTGIGRTGKFWAIEHWGVEPDMILMAKALSGGFIPVGAVAMKKHIMEAVFNRMDRA 294 Query: 327 FLHTTTFGGNPLACAAALATINVLLEQNLPAQAEQKGDMLLDGFRQLAREYPDLVQEARG 386 +H +TF N +A AA +AT+ VL E+ L A + G+ ++ G R + Y +L+ RG Sbjct: 295 VVHGSTFSKNNMAMAAGIATLEVLAEERLVENAAKLGEQIISGIRAMTDRY-ELLHAVRG 353 Query: 387 KGMLMAIEF 395 KGM++A+EF Sbjct: 354 KGMMIAVEF 362 Lambda K H 0.320 0.136 0.395 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: 464 Number of extensions: 22 Number of successful extensions: 7 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: 462 Length adjustment: 33 Effective length of query: 426 Effective length of database: 429 Effective search space: 182754 Effective search space used: 182754 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