Align L-2-keto-3-deoxyrhamnonate 4-dehydrogenase subunit (EC 1.1.1.401) (characterized)
to candidate WP_050462861.1 AKL27_RS10995 hypothetical protein
Query= metacyc::MONOMER-16233 (285 letters) >NCBI__GCF_001189915.1:WP_050462861.1 Length = 337 Score = 147 bits (370), Expect = 4e-40 Identities = 83/186 (44%), Positives = 107/186 (57%), Gaps = 8/186 (4%) Query: 90 PMMFMKALSSLNGPNDEVVLPKNSTHGDWEVELGVVIGETCRFVSEDEALSKVAGYVLVN 149 P F K +SSL P ++ +P ++ DWE+ELGVVI + V EA + VAGY +VN Sbjct: 147 PYAFPKLISSLADPFSQITIPSDAKQFDWELELGVVISKPAWRVPRSEAFNYVAGYTIVN 206 Query: 150 DVSER---FNQKQRG--TQWSKGKGHDTFCPVGPWLVTPDEVGDPQDLDMHLNVNGTRMQ 204 D+S R + RG T W + K F P GP+LV V DPQDL + L VNG MQ Sbjct: 207 DLSRRELIYRDDMRGIGTDWLRAKSGPGFMPCGPFLVPQRFVADPQDLKLRLTVNGKTMQ 266 Query: 205 TGNTKTMIFNVAQLISYVSEYITLYPGDLMITGTPPGVGEGKKPQAIYLKAGDVMELGIE 264 +T MIF++A I YV+ Y L PGDL+ TG+P G G ++L+AGDVM IE Sbjct: 267 NESTADMIFDIATQIEYVTSYARLLPGDLLATGSPAGNG---MHHGVFLQAGDVMTGAIE 323 Query: 265 KLGTQR 270 LG QR Sbjct: 324 GLGMQR 329 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: 294 Number of extensions: 11 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: 285 Length of database: 337 Length adjustment: 27 Effective length of query: 258 Effective length of database: 310 Effective search space: 79980 Effective search space used: 79980 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: 48 (23.1 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