Align L-2-keto-3-deoxyrhamnonate 4-dehydrogenase subunit (EC 1.1.1.401) (characterized)
to candidate WP_011840244.1 RSPH17029_RS01090 FAA hydrolase family protein
Query= metacyc::MONOMER-16233 (285 letters) >NCBI__GCF_000015985.1:WP_011840244.1 Length = 228 Score = 115 bits (287), Expect = 1e-30 Identities = 80/230 (34%), Positives = 116/230 (50%), Gaps = 19/230 (8%) Query: 48 SLPLVEGEPRYGVPVKGIGKIVAIGLNYEDHAIESNLPIPTEPMMFMKALSSLNGPNDEV 107 SLP+ E + + PV+ ++ IG NY HA+E EP F + P+ Sbjct: 13 SLPVAESQTLF--PVR---RVYCIGRNYAAHAVEMGGDPDREPPFFFQKNPDNLDPSGRF 67 Query: 108 VLPKNSTHGDWEVELGVVIGETCRFVSEDEALSKVAGYVLVNDVSERFNQ---KQRGTQW 164 P S+ EVEL V++G + +EA++ V GY L D++ R Q K+ G W Sbjct: 68 PYPPESSDVHHEVELAVMLGSGGTDIPVEEAMAHVWGYALALDMTRRDLQGEAKKAGRPW 127 Query: 165 SKGKGHDTFCPVGPWLVTPD-EVGDPQDLDMHLNVNGTRMQTGNTKTMIFNVAQLISYVS 223 GK + PVGP V P +G P+ + L VNG Q G+ MI+ V ++IS +S Sbjct: 128 EVGKAFERSAPVGP--VHPAARIGHPEAGRIELRVNGALRQEGDLNQMIWKVPEMISVLS 185 Query: 224 EYITLYPGDLMITGTPPGVGEGKKPQAIYLKAGDVMELGIEKLGTQRQQV 273 + L GD+++TGTP GVG ++ GDVME I+ LGT R +V Sbjct: 186 RHFALAAGDVILTGTPSGVGA--------VQRGDVMEASIDGLGTLRVEV 227 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: 187 Number of extensions: 14 Number of successful extensions: 4 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: 228 Length adjustment: 24 Effective length of query: 261 Effective length of database: 204 Effective search space: 53244 Effective search space used: 53244 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: 47 (22.7 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