Align putrescine-2-oxoglutarate transaminase (EC 2.6.1.82) (characterized)
to candidate WP_041097708.1 SUTH_RS05530 aspartate aminotransferase family protein
Query= BRENDA::P42588 (459 letters) >NCBI__GCF_000828635.1:WP_041097708.1 Length = 390 Score = 217 bits (552), Expect = 6e-61 Identities = 145/372 (38%), Positives = 205/372 (55%), Gaps = 23/372 (6%) Query: 76 LVDTQGQEFIDCLGGFGIFNVGHRNPVVVSAVQNQLAKQPLHSQELLDPLRAMLAKTLAA 135 L D QG+ ++D L G + +GH +P +V A+ NQ+A+ +H+ L A A A Sbjct: 23 LFDEQGKSYLDALAGIAVNTLGHNHPRLVKALSNQVARL-IHTSNLYRISEAEAASDRLA 81 Query: 136 LTPGKLKYSFFCNSGTESVEAALKLAKAYQSPRG--KFTFIATSGAFHGKSLGALSATAK 193 G + FFCNSG E+ EAA+KLA+ Y +G + I AFHG++L LSAT Sbjct: 82 ALSG-MDEVFFCNSGCEANEAAIKLARMYGHQQGVEQPAIIVMEHAFHGRTLATLSATGN 140 Query: 194 STFRKPFMPLLPGFRHVPFGNIEAMRTALNECKKTGDDVAAVILEPIQGEGGVILPPPGY 253 + F PL+ GF VPF ++ A+ + + +V AV+ EPIQGEGG+ L + Sbjct: 141 RKVQAGFEPLVSGFVRVPFDDL----AAIEQLAERNPNVVAVLFEPIQGEGGINLAHNDF 196 Query: 254 LTAVRKLCDEFGALMILDEVQTGMGRTGKMFACEHENVQPDILCLAKALGGGVMPIGATI 313 + A+RK+CD L ++DEVQ G+GRTG FA +H + PD++ LAK LG GV PIGA + Sbjct: 197 MRALRKICDRKNWLFMVDEVQCGIGRTGVWFAHQHAGILPDVMTLAKGLGSGV-PIGACL 255 Query: 314 ATEEVFSVLFDNPFLHTTTFGGNPLACAAALATINVLLEQNLPAQAEQKGDMLLDGFRQL 373 A V P H +TFGGNPLAC AAL T++V+ L A+A G+ + G R Sbjct: 256 AAGRAAGVF--KPGNHGSTFGGNPLACVAALTTLDVVEADGLMARATMLGETIRGGLRSG 313 Query: 374 AREYPDLVQEARGKGMLMAIEFVDNEIGYNFASEMFRQRVLVAGTLNNA---KTIRIEPP 430 V E RG G+++ IE +D G ++ R R L +G L N K +R+ P Sbjct: 314 LAGTSGFV-EVRGDGLMIGIE-LDRPCG-----DLVR-RGLESGLLINVTADKVVRLLPA 365 Query: 431 LTLT-IEQCELV 441 L ++ E ELV Sbjct: 366 LVMSDAEGAELV 377 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: 410 Number of extensions: 21 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: 390 Length adjustment: 32 Effective length of query: 427 Effective length of database: 358 Effective search space: 152866 Effective search space used: 152866 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: 50 (23.9 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