Align putrescine-2-oxoglutarate transaminase (EC 2.6.1.82) (characterized)
to candidate WP_027489558.1 LRK54_RS06590 acetylornithine/succinylornithine family transaminase
Query= BRENDA::P42588 (459 letters) >NCBI__GCF_021560695.1:WP_027489558.1 Length = 408 Score = 214 bits (546), Expect = 3e-60 Identities = 137/370 (37%), Positives = 211/370 (57%), Gaps = 26/370 (7%) Query: 78 DTQGQEFIDCLGGFGIFNVGHRNPVVVSAVQNQLAKQPLHSQELL---DPLRAMLAKTLA 134 DT+G++++D G + +GH++P +++A+ Q A + HS + PLR LA+ L Sbjct: 37 DTEGRDYVDFGAGIAVNALGHQDPDLLAALAAQ-AHKLWHSSNVFYTEPPLR--LAEELV 93 Query: 135 ALTPGKLKYSFFCNSGTESVEAALKLAKAYQSPRGKF----TFIATSGAFHGKSLGALSA 190 + G + F CNSG E+ EAA+KL + + + +G+ + +G+FHG++L ++A Sbjct: 94 HAS-GFAERVFLCNSGAEANEAAIKLVRKWAAAQGRAPERRVIVTFNGSFHGRTLATVTA 152 Query: 191 TAKSTFRKPFMPLLPGFRHVPFGNIEAMRTALNECKKTGDDVAAVILEPIQGEGGVILPP 250 TA++ +++ + PL GFR++ F + EA+ E DVAAV+LEP+QGEGGV+ Sbjct: 153 TAQAKYQQGYEPLPEGFRYLDFNDAEAL-----EATFAAGDVAAVMLEPVQGEGGVLPAA 207 Query: 251 PGYLTAVRKLCDEFGALMILDEVQTGMGRTGKMFACEHENVQPDILCLAKALGGGVMPIG 310 PG+L VR+LCD+ AL++LDE+Q GMGRTG +FA H++V PDI+ LAKALGGG PIG Sbjct: 208 PGFLKRVRELCDQHDALLVLDEIQCGMGRTGTLFAHVHDHVVPDIVTLAKALGGG-FPIG 266 Query: 311 ATIATEEVFSVLFDNPFLHTTTFGGNPLACAAALATINVLLEQNLPAQAEQKGDMLLDGF 370 A +A +V V+ H TTFGGNP+A A A + L + E++ + L G Sbjct: 267 AMLAGPKVAEVM--QYGAHGTTFGGNPMAAAVARVALAKLSSPAVLMNVERQANDLRAGL 324 Query: 371 RQLAREYPDLVQEARGKGMLMAIEFVDNEIGYNFASEMFRQRVLVAGTL---NNAKTIRI 427 ++ E L E RG+G+++ D Y + G L +R Sbjct: 325 ARINHEL-QLFAEVRGRGLMIGAVLAD---AYKGKAGAVLDHAATRGLLLLQAGPDVLRF 380 Query: 428 EPPLTLTIEQ 437 PPLT+T E+ Sbjct: 381 VPPLTITDEE 390 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: 461 Number of extensions: 18 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: 408 Length adjustment: 32 Effective length of query: 427 Effective length of database: 376 Effective search space: 160552 Effective search space used: 160552 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