Align L-fuconate dehydratase; L-rhamnonate dehydratase (EC 4.2.1.68; EC 4.2.1.90) (characterized)
to candidate 8501270 DvMF_2003 Altronate dehydratase (RefSeq)
Query= reanno::BFirm:BPHYT_RS34230 (431 letters) >FitnessBrowser__Miya:8501270 Length = 387 Score = 175 bits (443), Expect = 2e-48 Identities = 131/403 (32%), Positives = 198/403 (49%), Gaps = 34/403 (8%) Query: 9 TLEGYLRGDGRKGIRNVVAVAYLVECAHHVAREIVTQFREPLDAFDDPSAEREPPVHL-I 67 T GY R +GR G+RN V + L + ++ + + + + A P + L + Sbjct: 5 TFLGYRRENGRVGVRNHVVILPLDDLSNAASEAVANNVKGTM-ALPHPYGRLQFGEDLEL 63 Query: 68 GFPGCYPNGYAEKMLERLTTHPNVGAVLFVSLGCESMNKHYLVDVVRASGRPVEVLTIQE 127 F + L + ++PNV AV V +G E + +V+ + +G+PV +I E Sbjct: 64 HF----------RTLIGVGSNPNVAAV--VVIGIEPQWTNRIVEGIAKTGKPVAGFSI-E 110 Query: 128 KGGTRSTIQYGVDWIRGAREQLAAQQKVPMALSELVIGTICGGSDGTSGITANPAVGRAF 187 + G +TI + Q+V +S+L + T CG SD TSGI +NP VG AF Sbjct: 111 QNGDHNTICNASRKAKEFMHWATELQRVECPVSDLWVSTKCGESDTTSGIASNPTVGNAF 170 Query: 188 DHLIDAGATCIFEETGELVGCEFHMKTRAARPALGDEIVACVAKAARYY-----SILGHG 242 D L + G T +F ET EL G E + R A + + + A+ S L Sbjct: 171 DKLYEQGCTLLFGETTELTGGEHLVLERCANDEVRKQFQFFFDRYAKLVDDHKTSDLSDS 230 Query: 243 SFAVGNADGGLTTQEEKSLGAYAKSGA-SPIVGIIKPGDIPPTGGLYLLDVVPDGEPRFG 301 GN +GGLTT EEK+LG K G +P+VG + + P GL+ +D Sbjct: 231 QPTKGNIEGGLTTIEEKALGNIQKIGRKAPVVGCLDKAEAPTGPGLWFMD---------- 280 Query: 302 FPNISDNAEIGELIACGAHVI-LFTTGRGSVVGSAISPVIKVCANPATYRNLSGDMDVDA 360 + S AE+ L A V+ LF TG+G+V+G+ I PV+K+CANP T R +S +DVD Sbjct: 281 --SSSAAAEMVTLCAAAGFVVHLFPTGQGNVIGNPILPVVKLCANPRTVRTMSEHIDVDV 338 Query: 361 GRILEGRGTLDEVGREVFEQTVAVSRGAASKSETLGHQEFILT 403 IL T+D G ++ E + + G + +E LGH+EF+LT Sbjct: 339 SGILRKELTMDGAGDKLVEMAIRTANGRNTAAEVLGHREFVLT 381 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: 431 Number of extensions: 19 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: 387 Length adjustment: 31 Effective length of query: 400 Effective length of database: 356 Effective search space: 142400 Effective search space used: 142400 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: 50 (23.9 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