Align putrescine-2-oxoglutarate transaminase (EC 2.6.1.82) (characterized)
to candidate WP_164924158.1 NGR_RS12135 aspartate aminotransferase family protein
Query= BRENDA::P42588 (459 letters) >NCBI__GCF_000018545.1:WP_164924158.1 Length = 399 Score = 219 bits (559), Expect = 1e-61 Identities = 133/384 (34%), Positives = 212/384 (55%), Gaps = 20/384 (5%) Query: 76 LVDTQGQEFIDCLGGFGIFNVGHRNPVVVSAVQNQLAKQPLHSQELLD-PLRAMLAKTLA 134 L+ G ++D G + ++GH +P +V A++ Q A++ H L D P + LA+ L Sbjct: 26 LIAEDGTRYLDFAAGVAVNSLGHAHPHLVEALKAQ-AEKLWHVSNLYDVPGQESLARRLT 84 Query: 135 ALTPGKLKYSFFCNSGTESVEAALKLAKAYQSPRG---KFTFIATSGAFHGKSLGALSAT 191 A+T FF NSG E++E A+K A+ Y +G +F I GAFHG+++ ++A Sbjct: 85 AVTFADRV--FFTNSGAEALECAIKTARRYHFAKGHPERFHVITFEGAFHGRTIATIAAG 142 Query: 192 AKSTFRKPFMPLLPGFRHVPFGNIEAMRTALNECKKTGDDVAAVILEPIQGEGGVILPPP 251 + + + F P PGF VPFG+I A++ A+N D+ AA+++EPIQGEGG+ L Sbjct: 143 GQQKYIEGFGPKAPGFYQVPFGDIAAVKNAIN------DETAAILIEPIQGEGGIRLASK 196 Query: 252 GYLTAVRKLCDEFGALMILDEVQTGMGRTGKMFACEHENVQPDILCLAKALGGGVMPIGA 311 ++ +R LCDE+G L+ILDEVQ G+GRTGK+FA E + PDI+ +AK +GGG P+GA Sbjct: 197 EFMQELRALCDEYGLLLILDEVQCGVGRTGKLFAHEWSGITPDIMAVAKGIGGG-FPLGA 255 Query: 312 TIATEEVFSVLFDNPFLHTTTFGGNPLACAAALATINVLLEQNLPAQAEQKGDMLLDGFR 371 +ATE + + H +T+GGNPLA A A ++V+L + + G Sbjct: 256 CLATEAAAAGMVAG--THGSTYGGNPLAMAVGNAVLDVVLAEGFLENVRDVALVFRQGLA 313 Query: 372 QLAREYPDLVQEARGKGMLMAIEFVDNEIGYNFASEMFRQRVLVAGTLNNAKTIRIEPPL 431 L +PD+++E RG G+++ I+ ++ + R L+A +R+ PPL Sbjct: 314 SLKDRFPDVIEEIRGDGLMLGIK---AKVPCADVLKAIRAEKLLAVPAGE-NVLRLLPPL 369 Query: 432 TLTIEQCELVIKAARKALAAMRVS 455 T + + +A A+R + Sbjct: 370 ITTAAEAREGLARLERAAEAVRAA 393 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: 400 Number of extensions: 20 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: 399 Length adjustment: 32 Effective length of query: 427 Effective length of database: 367 Effective search space: 156709 Effective search space used: 156709 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