Align L-2-keto-3-deoxyrhamnonate 4-dehydrogenase subunit (EC 1.1.1.401) (characterized)
to candidate 200752 SO1585 fumarylacetoacetate hydrolase family protein (NCBI ptt file)
Query= metacyc::MONOMER-16233 (285 letters) >FitnessBrowser__MR1:200752 Length = 208 Score = 65.9 bits (159), Expect = 7e-16 Identities = 52/183 (28%), Positives = 81/183 (44%), Gaps = 26/183 (14%) Query: 67 KIVAIGLNYEDHAIESNLPIPTEPMMFMKALSSLNGPNDEVVLPKNSTHGDWEVELGVVI 126 KI+ IG NY DH E IP + ++F K PN + +S H + Sbjct: 15 KILCIGRNYVDHIHELGNEIPDDMVVFFK-------PNSAISAQLHSLH----------L 57 Query: 127 GETCRFVSEDEALSKVAGYVLVN---DVSERFNQ---KQRGTQWSKGKGHDTFCPVGPWL 180 GET + +E + + + V D+++R Q K +G W K K D P++ Sbjct: 58 GETLHYETELCFIYQQGRFSHVGVGLDLTKRELQSKLKAKGLPWEKAKAFDGAALFSPFV 117 Query: 181 VTPDEVGDPQDLDMHLNVNGTRMQTGNTKTMIFNVAQLISYVSEYITLYPGDLMITGTPP 240 D Q L ++G Q G+ MI+ ++S + + TL GD+++TGTP Sbjct: 118 AIDDASAQFQ---FSLCIDGVLTQEGHVDLMIYQPQTILSELQRFTTLEDGDIVMTGTPK 174 Query: 241 GVG 243 GVG Sbjct: 175 GVG 177 Lambda K H 0.316 0.137 0.411 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: 11 Number of successful extensions: 2 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: 285 Length of database: 208 Length adjustment: 23 Effective length of query: 262 Effective length of database: 185 Effective search space: 48470 Effective search space used: 48470 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: 42 (22.0 bits) S2: 46 (22.3 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