Align 4-aminobutyrate-2-oxoglutarate transaminase (EC 2.6.1.19) (characterized)
to candidate CA265_RS14455 CA265_RS14455 L-lysine 6-transaminase
Query= BRENDA::P80404 (500 letters) >FitnessBrowser__Pedo557:CA265_RS14455 Length = 443 Score = 206 bits (525), Expect = 1e-57 Identities = 143/466 (30%), Positives = 222/466 (47%), Gaps = 50/466 (10%) Query: 50 VPGPRSQELMKQLNIIQNAEAVHFFCNYEESRGNYLVDVDGNR-MLDLYSQISSVPIGYS 108 VP R E + + + + + + E+S G Y+ D NR +LD ++ +SVP+GY+ Sbjct: 6 VPADRVNESLSKHILADGFDLTY---DMEKSHGAYIYDAKHNRTLLDFFTCFASVPLGYN 62 Query: 109 HPAL-----------LKLIQQPQNASMFVNRPALGILPPENFVEKLRQSLLSVAPKGMSQ 157 HP + L + P N+ ++ + A FVE + + P + Sbjct: 63 HPKMINDEAFKKNLFLAALANPSNSDVYTQQYA-------QFVETFSKVGI---PDYLPH 112 Query: 158 LITMACGSCSNENALKTIFMWYRSKERGQRGFSQEELETCMINQAPGCPDYSILSFMGAF 217 +A G + ENA+K W + ++ +G+++E+ + +L F AF Sbjct: 113 AFFIAGGGLAVENAIKVAMDW-KVQKNFAKGYTEEK-------------GFKVLHFERAF 158 Query: 218 HGRTMGCLATTHSKAIHKIDIPSFDWPIAPFPRLKYPLE-EFVKENQQEEARCLEEVEDL 276 HGRT L+ T++ FDWP P +K+PL + Q E L +++ Sbjct: 159 HGRTGYTLSLTNTLPDKTKWFAKFDWPRVAVPEVKFPLSGNNLSHAIQTEETSLAQIKKA 218 Query: 277 IVKYRKKKKTVAGIIVEPIQSEGGDNHASDDFFRKLRDIARKHGCAFLVDEVQTGGGCTG 336 I K + IIVEPIQSEGGDNH ++F +++ +A ++ + DEVQTG G TG Sbjct: 219 IAD---NKDDICAIIVEPIQSEGGDNHLREEFLIQIKALADENDAFLIYDEVQTGVGLTG 275 Query: 337 KFWAHEHWGLDDPADVMTFSKKMMTGGFF--HK-EEFRPN---APYRIFNTWLGDPSKNL 390 KFW H+H+ D++ F KKM G HK ++ N P RI +TW G+ + Sbjct: 276 KFWCHQHFSEKARPDILAFGKKMQVCGILVGHKVDQVETNVFKVPSRINSTWGGNLVDMV 335 Query: 391 LLAEVINIIKREDLLNNAAHAGKALLTGLLDLQARYPQFISRVRGRGTFCSFDTPDDSIR 450 +++ I++ + L NA G L L +L R+ Q ++ VRGRG CSFD P +R Sbjct: 336 RSTQILQIVEEDQLCENATKVGLYLKDQLENLSHRFDQ-MTNVRGRGLLCSFDFPTKEMR 394 Query: 451 NKLILIARNKGVVLGGCGDKSIRFRPTLVFRDHHAHLFLNIFSDIL 496 N I V+ GCG+K+IRFRP L H L + IL Sbjct: 395 NTFIAKGLENNVMFLGCGEKTIRFRPALCIEQKHIDEGLTVMDKIL 440 Lambda K H 0.323 0.138 0.423 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: 495 Number of extensions: 23 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: 500 Length of database: 443 Length adjustment: 33 Effective length of query: 467 Effective length of database: 410 Effective search space: 191470 Effective search space used: 191470 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 (21.9 bits) S2: 51 (24.3 bits)
This GapMind analysis is from Sep 17 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