Align L-fuconate dehydratase; L-rhamnonate dehydratase (EC 4.2.1.68; EC 4.2.1.90) (characterized)
to candidate WP_011840277.1 RSPH17029_RS01345 altronate dehydratase family protein
Query= reanno::BFirm:BPHYT_RS34230 (431 letters) >NCBI__GCF_000015985.1:WP_011840277.1 Length = 500 Score = 189 bits (479), Expect = 2e-52 Identities = 139/413 (33%), Positives = 201/413 (48%), Gaps = 35/413 (8%) Query: 4 AAQQPTLEGYLRGDGRKGIRNVVAVAYLVECAHHVAREIVTQFREPLDAFDDPSAEREPP 63 A + T EGYLR DGR G RN + + V C+ V I DA + R P Sbjct: 100 APARQTFEGYLRPDGRVGTRNYIGIMASVNCSSTVCNAIA-------DAANRTLLPRFPG 152 Query: 64 VH----LIGFPGCYPNGYAE------KMLERLTTHPNVGAVLFVSLGCESMNKHYLVDVV 113 + ++ GC E ++L+ HPN G VL V LGCE +N+ L Sbjct: 153 IDGFAPIVHDQGCGMASAGEGFDALVRVLKGYRDHPNFGGVLIVGLGCE-VNQLTLYKRT 211 Query: 114 RASGRPVEVLTIQEKGGTRSTIQYGVDWIRGAREQLAAQQKVPMALSELVIGTICGGSDG 173 + + + IQ+ GG+ S ++ ++ + ++ +S+LV+G CGGSDG Sbjct: 212 DWTEERIGIFNIQDVGGSASAVRRALELLEPICAAANEDRRSAQPVSKLVLGMQCGGSDG 271 Query: 174 TSGITANPAVGRAFDHLIDAGATCIFEETGELVGCEFHMKTRAARPALGDEIVACVAKAA 233 SGITANPA+G A D L+ AG T I ET E+ G E H+ A G +I + Sbjct: 272 FSGITANPALGVASDMLVAAGGTSILSETPEIYGAE-HLLIARADAETGRKIEGMIDWWR 330 Query: 234 RYYSILG---HGSFAVGNADGGLTTQEEKSLGAYAKSGASPIVGIIKPGDIPPTGGLYLL 290 Y + G + + GN GGLTT EKSLGA AK G SP+ G + G + Sbjct: 331 DYAAKNGASLDNNPSPGNKRGGLTTILEKSLGAVAKGGLSPLSGAFAYAEPIRIPGFVYM 390 Query: 291 DVVPDGEPRFGFPNISDNAEIGELIACGAHVILFTTGRGSVVGSAISPVIKVCANPATYR 350 D P A G+ +A GA++I FTTGRGS G+ +P IK+ +N R Sbjct: 391 D----------SPGYDPVAATGQ-VASGANLIAFTTGRGSCFGAKPAPSIKLTSNSDLAR 439 Query: 351 NLSGDMDVDAGRILEGRGTLDEVGREVFEQTVAVSRGAASKSETLGH--QEFI 401 + DMD+D G ++E +L+E+GR +++ + + G SKSE G+ EF+ Sbjct: 440 RMPEDMDIDCGVVIEEGVSLEEMGRRIYDLLLDTASGKKSKSEEFGYGDNEFV 492 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: 584 Number of extensions: 28 Number of successful extensions: 5 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: 500 Length adjustment: 33 Effective length of query: 398 Effective length of database: 467 Effective search space: 185866 Effective search space used: 185866 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 Apr 10 2024. 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