Align 4-aminobutyrate-2-oxoglutarate transaminase (EC 2.6.1.19) (characterized)
to candidate WP_041100608.1 SUTH_RS15840 adenosylmethionine--8-amino-7-oxononanoate transaminase
Query= BRENDA::Q0K2K2 (423 letters) >NCBI__GCF_000828635.1:WP_041100608.1 Length = 426 Score = 140 bits (354), Expect = 6e-38 Identities = 126/403 (31%), Positives = 190/403 (47%), Gaps = 40/403 (9%) Query: 40 EGRAYTDFAAGIAVLNTGHRHPRVMQAIAAQLERFTHTAYQIVPYQGYVTLAERINALVP 99 +GR D + G+ HP + AI QL H + + ++ LA+R+ AL+P Sbjct: 40 DGRELIDGISSWWTACHGYNHPHIRAAIERQLASLPHVMFAGLVHEPAARLAQRLAALLP 99 Query: 100 IQGLNKTALFTTGAEAVENAIKIARAHTGRPG------VIAFSGAFHGRTLLGMALTG-K 152 L + +G+ AVE A+K+A + G ++ F +HG T MAL + Sbjct: 100 -GDLERVFFTESGSVAVEVALKMAIQYWRNKGQAEKQRIVYFRHGYHGDTFATMALCDPE 158 Query: 153 VAPYKIGFGPFPSDIYHAPFPSALHGVSTERALQALEGLFKTDIDPARVAAIIVEP-VQG 211 + + G P I A PS E +A E L +T + R+AA+I+EP VQG Sbjct: 159 EGMHSLFAGAMPDQIM-AELPS------DETMRRAFELLLETHGE--RLAAVIIEPLVQG 209 Query: 212 EGGFQAAPADFMRGLRAVCDQHGIVLIADEVQTGFGRTGKMFAMSHHD----VEPDLITM 267 GG Q A + + A C +H ++LIADE+ TGFGRTG+MFA D PD++ + Sbjct: 210 AGGMQMHDAATLAFIAAACARHKLLLIADEIMTGFGRTGRMFACEEADELTSTIPDIVCL 269 Query: 268 AKSLAGG-MPLSAVSGRAAIMDAPL---PGGL---GGTYAGNPLAVAAAHAVIDVIEEEK 320 +K+L GG +PL+A R + +A L P G TY N LA AAA+A +D+ E E Sbjct: 270 SKALTGGTLPLAATVARRHVFEAFLADDPAAALMHGPTYMANALACAAANASLDLFESEP 329 Query: 321 LCERSASLGQQLREHLLAQRKHCPAMAEVRGLGSMVAAEFCDPATGQPSAEHAKRVQTRA 380 + A++ QL L + +AEVR G++ A E G+ + +R R Sbjct: 330 RLAQVAAIEAQLAAE-LGPCRDLAGVAEVRVKGAIGAVEL----AGRIELDALRR---RF 381 Query: 381 LEAGLVLLTCGTYGNVIRFLYPLTIPQAQFDAALAVLTQALAE 423 E G+ + +G V+ + P I A + Q L E Sbjct: 382 AELGVWV---RPFGKVVYLMPPFVIAAEDLTTLTAAVRQVLTE 421 Lambda K H 0.321 0.136 0.400 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: 3 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: 423 Length of database: 426 Length adjustment: 32 Effective length of query: 391 Effective length of database: 394 Effective search space: 154054 Effective search space used: 154054 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 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