Align putrescine-2-oxoglutarate transaminase (EC 2.6.1.82) (characterized)
to candidate WP_092481894.1 BM299_RS02515 putrescine aminotransferase
Query= BRENDA::P42588 (459 letters) >NCBI__GCF_900115975.1:WP_092481894.1 Length = 453 Score = 541 bits (1394), Expect = e-158 Identities = 270/440 (61%), Positives = 342/440 (77%), Gaps = 6/440 (1%) Query: 11 LACSAHALNLIEKRTLDHEEMKALNREVIEYFKEHVNPGFLEYRKSVTAGGDYGAVEWQA 70 +A S L +I + L EE + + +EV+E F+E+VNPGFLEYRKSV+ DY +VEW+ Sbjct: 9 IARSQRYLEIISQSELTQEEKEWVVKEVVEGFRENVNPGFLEYRKSVST--DYTSVEWK- 65 Query: 71 GSLNTLVDTQGQEFIDCLGGFGIFNVGHRNPVVVSAVQNQLAKQPLHSQELLDPLRAMLA 130 S +T D G+EFIDCLGG+GI+NVGHR+P V+ AV +QL +Q LHSQELLDPLRA LA Sbjct: 66 DSGSTFTDIWGKEFIDCLGGYGIYNVGHRHPKVLKAVMDQLQRQALHSQELLDPLRAFLA 125 Query: 131 KTLAALTPGKLKYSFFCNSGTESVEAALKLAKAYQSPRGKFTFIATSGAFHGKSLGALSA 190 K L ++TPG L+Y+FF NSGTESVEA +K AK Y G+ +FI+T+ AFHGKSLG+LSA Sbjct: 126 KLLGSITPGDLQYAFFVNSGTESVEAGIKFAKMYT---GRRSFISTTRAFHGKSLGSLSA 182 Query: 191 TAKSTFRKPFMPLLPGFRHVPFGNIEAMRTALNECKKTGDDVAAVILEPIQGEGGVILPP 250 TAK FRKPF+PL+PGF HVP+GN EA+ L C G+DVAAVI+EP+QGEGGVI+PP Sbjct: 183 TAKGVFRKPFLPLIPGFHHVPYGNAEAVEMMLESCAFVGEDVAAVIVEPVQGEGGVIIPP 242 Query: 251 PGYLTAVRKLCDEFGALMILDEVQTGMGRTGKMFACEHENVQPDILCLAKALGGGVMPIG 310 YL +R+LCD++GAL+ILDEVQTGMGRTGKMFACEH NV PDILCLAKA GGG+MPIG Sbjct: 243 EDYLPKLRELCDKYGALLILDEVQTGMGRTGKMFACEHSNVVPDILCLAKAFGGGIMPIG 302 Query: 311 ATIATEEVFSVLFDNPFLHTTTFGGNPLACAAALATINVLLEQNLPAQAEQKGDMLLDGF 370 AT+A + ++ L +NPFLHTTTFGGNP+ CAAA+A INVLLE+NLP ++ + G +L Sbjct: 303 ATVARKPMWEKLVENPFLHTTTFGGNPVCCAAAIANINVLLEENLPQRSAESGVYMLGKL 362 Query: 371 RQLAREYPDLVQEARGKGMLMAIEFVDNEIGYNFASEMFRQRVLVAGTLNNAKTIRIEPP 430 R+LA +YP +VQE RGKG+++ IEF ++E+GY A +F + VLVAGTL NAK+IRIEPP Sbjct: 363 RELAEKYPAVVQEVRGKGLMIGIEFFNDELGYEVAKGLFARGVLVAGTLINAKSIRIEPP 422 Query: 431 LTLTIEQCELVIKAARKALA 450 LT++ EQ + VI+ LA Sbjct: 423 LTISREQQDQVIERLDNTLA 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: 595 Number of extensions: 23 Number of successful extensions: 3 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: 453 Length adjustment: 33 Effective length of query: 426 Effective length of database: 420 Effective search space: 178920 Effective search space used: 178920 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