Align L-fuconate dehydratase; L-rhamnonate dehydratase (EC 4.2.1.68; EC 4.2.1.90) (characterized)
to candidate WP_012403588.1 BPHY_RS21620 hydrolase
Query= reanno::BFirm:BPHYT_RS34230 (431 letters) >NCBI__GCF_000020045.1:WP_012403588.1 Length = 435 Score = 768 bits (1982), Expect = 0.0 Identities = 377/426 (88%), Positives = 399/426 (93%) Query: 3 VAAQQPTLEGYLRGDGRKGIRNVVAVAYLVECAHHVAREIVTQFREPLDAFDDPSAEREP 62 V QP L+GYLRGDGRKGIRNVVAVAYLVECAHHVAREIV QFR LDAFDD SAER+ Sbjct: 7 VNGTQPELQGYLRGDGRKGIRNVVAVAYLVECAHHVAREIVAQFRPSLDAFDDASAERDA 66 Query: 63 PVHLIGFPGCYPNGYAEKMLERLTTHPNVGAVLFVSLGCESMNKHYLVDVVRASGRPVEV 122 PVHLIGFPGCYPN YAEKM+E+L THPNVGAVLFVSLGCESMNKHYLVDVVRASGRPV V Sbjct: 67 PVHLIGFPGCYPNSYAEKMMEQLATHPNVGAVLFVSLGCESMNKHYLVDVVRASGRPVHV 126 Query: 123 LTIQEKGGTRSTIQYGVDWIRGAREQLAAQQKVPMALSELVIGTICGGSDGTSGITANPA 182 LTIQEKGGTRSTIQYGVDW+R AR +LA Q+K+PMALSELVIGTICGGSDGTSGITANPA Sbjct: 127 LTIQEKGGTRSTIQYGVDWVREARSELAKQKKMPMALSELVIGTICGGSDGTSGITANPA 186 Query: 183 VGRAFDHLIDAGATCIFEETGELVGCEFHMKTRAARPALGDEIVACVAKAARYYSILGHG 242 VGRAFDH I+ ATCIFEETGELVGCEFHMK+RAAR LGDEIVACVAKAARYY+ILGHG Sbjct: 187 VGRAFDHFIEHDATCIFEETGELVGCEFHMKSRAARDDLGDEIVACVAKAARYYTILGHG 246 Query: 243 SFAVGNADGGLTTQEEKSLGAYAKSGASPIVGIIKPGDIPPTGGLYLLDVVPDGEPRFGF 302 SFA GNADGGLTTQEEKSLGAYAKSGASPIVGI+KPGD+PPTGGLYLLDVVPDGEPRFGF Sbjct: 247 SFAPGNADGGLTTQEEKSLGAYAKSGASPIVGIVKPGDVPPTGGLYLLDVVPDGEPRFGF 306 Query: 303 PNISDNAEIGELIACGAHVILFTTGRGSVVGSAISPVIKVCANPATYRNLSGDMDVDAGR 362 PNISDNAEI ELIACGAHVILFTTGRGSVVGSAISPVIKVCANP TYRNLSGDMDVDAGR Sbjct: 307 PNISDNAEIAELIACGAHVILFTTGRGSVVGSAISPVIKVCANPDTYRNLSGDMDVDAGR 366 Query: 363 ILEGRGTLDEVGREVFEQTVAVSRGAASKSETLGHQEFILTYKTFEPVGPACLPSSAAAQ 422 ILEGR TLDEVGREVF+ T+AV++GAASKSE+LGHQEFILTYKTFEPVGPACLPS+AA Sbjct: 367 ILEGRATLDEVGREVFDLTLAVAQGAASKSESLGHQEFILTYKTFEPVGPACLPSNAALP 426 Query: 423 HRVVAI 428 HR+V++ Sbjct: 427 HRIVSV 432 Lambda K H 0.318 0.137 0.408 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: 816 Number of extensions: 26 Number of successful extensions: 1 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: 431 Length of database: 435 Length adjustment: 32 Effective length of query: 399 Effective length of database: 403 Effective search space: 160797 Effective search space used: 160797 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: 51 (24.3 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