Align SDR family oxidoreductase (characterized, see rationale)
to candidate WP_039103405.1 FPB0191_RS01165 3-oxoacyl-ACP reductase FabG
Query= uniprot:A0A4P7ABK7 (254 letters) >NCBI__GCF_000807275.1:WP_039103405.1 Length = 244 Score = 134 bits (337), Expect = 2e-36 Identities = 83/251 (33%), Positives = 132/251 (52%), Gaps = 18/251 (7%) Query: 7 RLAGKTVLITAAAQGIGRASTELFAREGARVIATDISKTHLEELASIAGV--ETHLLDVT 64 +LAGK L+T A++GIGRA E + GA VI T ++ E ++ G + LL+VT Sbjct: 2 KLAGKIALVTGASRGIGRAIAEKLVKNGATVIGTATTEKGAEAISQYLGANGKGFLLNVT 61 Query: 65 D----DDAIKALVAKVGTVDVLFNCAGYVAAGNILECDDKAWDFSFNLNAKAMFHTIRAV 120 D D I A+ ++ G +D+L N AG ++ + W + N ++F +A+ Sbjct: 62 DEKSIDSVIDAVKSQFGDIDILVNNAGITRDNLLMRMKENEWQDILDTNLTSVFRVSKAL 121 Query: 121 LPGMLAKKAGSIVNIASAASSVKGVANRFAYGASKAAVVGLTKSVAADFVSQGIRCNAIC 180 L M+ K+ G IV I S ++ G A + Y A+KA ++G +KS+A + S+GI N + Sbjct: 122 LRTMMKKRYGRIVTIGSVVGTM-GNAGQANYSAAKAGLIGFSKSLAREVASRGITVNVVA 180 Query: 181 PGTIESPSLNQRISTQAKETGKSEDEVRAAFVARQPMGRIGKAEEVAALALYLASDESNF 240 PG IE+ T DE R A +++ P R+G+ EE+A +L SD++ + Sbjct: 181 PGFIETDM-----------TRALSDEQRTAILSQVPANRLGEPEEIANAVAFLVSDDAAY 229 Query: 241 TTGSIHMIDGG 251 TG I+GG Sbjct: 230 ITGETLHINGG 240 Lambda K H 0.316 0.129 0.359 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: 141 Number of extensions: 5 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: 254 Length of database: 244 Length adjustment: 24 Effective length of query: 230 Effective length of database: 220 Effective search space: 50600 Effective search space used: 50600 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 46 (22.3 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