Align BadH (characterized)
to candidate AO353_04045 AO353_04045 3-ketoacyl-ACP reductase
Query= metacyc::MONOMER-893 (255 letters) >FitnessBrowser__pseudo3_N2E3:AO353_04045 Length = 252 Score = 140 bits (353), Expect = 3e-38 Identities = 91/260 (35%), Positives = 139/260 (53%), Gaps = 22/260 (8%) Query: 3 RLQNKTAVITGGGGGIGGATCRRFAQEGAKIAVFDLNLDAAEKVAGAIRDAGGTAEAVRC 62 +L +K +ITGG G+G + FA +GAK+A+ DLN + ++ A + AG A A C Sbjct: 2 KLTDKVIIITGGCQGLGRSMAEYFAAKGAKLALVDLNQEKLDQAVAACKAAGVEARAYLC 61 Query: 63 DIADRTSVDAAIATTTTTLGPVDILVNNAGWDIFK----------PFTKTEPGEWERLIA 112 ++A+ V +A G + L+NNAG I + TK +W+ +I Sbjct: 62 NVANEEQVTHMVAQVAEDFGAIHGLINNAG--ILRDGLLIKVKDGEMTKMSLAQWQAVID 119 Query: 113 INLTGALHMHHAVLPGMVE-RRHGRIVNIASDAARVGSSGEAVYAACKGGLVAFSKTLAR 171 +NLTG V M+E + G IVNI+S +R G+ G+ Y+A K G+ A + T A+ Sbjct: 120 VNLTGVFLCTREVAAKMIELKTGGAIVNISS-ISRAGNVGQTNYSAAKAGVAAATVTWAK 178 Query: 172 EHARHGITVNVVCPGPTDTALLADVTSGAANPEKLIEAFTKAIPLGRLGKPDDLAGAIAF 231 E ARHGI V + PG +T + + PE L E T IPL R+GKP+++A + A+ Sbjct: 179 ELARHGIRVAGIAPGFIETEMTLSM-----KPEAL-EKMTSGIPLKRMGKPEEIAHSAAY 232 Query: 232 FGSDDAGFITGQVLSVSGGL 251 +D + TG++L + GGL Sbjct: 233 IFEND--YYTGRILEMDGGL 250 Lambda K H 0.318 0.135 0.398 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: 160 Number of extensions: 8 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: 255 Length of database: 252 Length adjustment: 24 Effective length of query: 231 Effective length of database: 228 Effective search space: 52668 Effective search space used: 52668 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: 47 (22.7 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