Align putrescine-2-oxoglutarate transaminase (EC 2.6.1.82) (characterized)
to candidate WP_128083232.1 CAter10_RS21330 4-aminobutyrate--2-oxoglutarate transaminase
Query= BRENDA::P42588 (459 letters) >NCBI__GCF_001584165.1:WP_128083232.1 Length = 420 Score = 211 bits (536), Expect = 5e-59 Identities = 147/398 (36%), Positives = 212/398 (53%), Gaps = 32/398 (8%) Query: 78 DTQGQEFIDCLGGFGIFNVGHRNPVVVSAVQNQLAKQPLHSQELLDPLRAM--LAKTLAA 135 D +G+ FID G + N GHR+P +V+A+Q QL K H+ + P + LA+ + A Sbjct: 31 DVEGRRFIDFAAGIAVLNTGHRHPKLVAAIQEQLGKFT-HTAYQIVPYGSYVELAERINA 89 Query: 136 LTPGK-LKYSFFCNSGTESVEAALKLAKAYQSPRGKFTFIATSGAFHGKSLGALSATAKS 194 +TPG K + F ++G E+VE A+K+A+A G+ IA SGAFHG+++ ++ T K Sbjct: 90 VTPGDHAKKTTFFSTGAEAVENAVKIARA---ATGRSAVIAFSGAFHGRTMMGMALTGKV 146 Query: 195 T-FRKPFMPLLPGFRHVPFG------NIEAMRTALNECKKTGDD---VAAVILEPIQGEG 244 ++ F P HVPF +IE AL K D VAA+ILEP+QGEG Sbjct: 147 VPYKVGFGPFPAEVYHVPFPVELHGVSIENSLAALQSLFKADVDPKRVAAIILEPVQGEG 206 Query: 245 GVILPPPGYLTAVRKLCDEFGALMILDEVQTGMGRTGKMFACEHENVQPDILCLAKALGG 304 G PP ++ A+RKLCDE G L+++DEVQTG RTGK+FA EH V PD++ +AK+L G Sbjct: 207 GFYAAPPAFMQALRKLCDEHGILLVVDEVQTGFARTGKLFAVEHSGVIPDLMTMAKSLAG 266 Query: 305 GVMPIGATIATEEVFSVLFDNPFLHTTTFGGNPLACAAALATINVLLEQNLPAQAEQKGD 364 G MP+ A E+ P T+ GNPLA A+ALA ++V+ E+ L +A G Sbjct: 267 G-MPLSAVCGRAEIMDAA--APGGLGGTYAGNPLAVASALAVLDVIEEEKLVERANVLGG 323 Query: 365 MLLDGFRQLAREYPDLVQEARGKGMLMAIEFV-------DNEIGYNFASEMFRQRVLVAG 417 L L + P + + RG G ++A+EF D + +E + +L+ Sbjct: 324 RLKQVLEGLRADVPQ-IADIRGLGAMVAVEFTQPGSKQPDADFTKKVQAEALKNGLLLLS 382 Query: 418 TLNNAKTIRIEPPLT----LTIEQCELVIKAARKALAA 451 + IR PLT L E ++ KA R AA Sbjct: 383 CGVYSNAIRFLFPLTIEDALMDEALAILSKAMRTVAAA 420 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: 435 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: 420 Length adjustment: 32 Effective length of query: 427 Effective length of database: 388 Effective search space: 165676 Effective search space used: 165676 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