Align L-fuconate dehydratase; L-rhamnonate dehydratase (EC 4.2.1.68; EC 4.2.1.90) (characterized)
to candidate WP_013721830.1 ALIDE2_RS08545 altronate dehydratase
Query= reanno::BFirm:BPHYT_RS34230 (431 letters) >NCBI__GCF_000204645.1:WP_013721830.1 Length = 507 Score = 197 bits (501), Expect = 6e-55 Identities = 136/407 (33%), Positives = 197/407 (48%), Gaps = 36/407 (8%) Query: 6 QQPTLEGYLRGDGRKGIRNVVAVAYLVECAHHVAREIVTQFR-EPLDAFDDPSAEREPPV 64 ++ T +G++R DGR G RN + + V C+ R I F E L A+ V Sbjct: 106 RRATFKGFVRADGRVGTRNFIGILSSVNCSATAIRHIAAHFTPERLAAYPHVDGV----V 161 Query: 65 HLIGFPGCYPNGYAE------KMLERLTTHPNVGAVLFVSLGCESMNKHYLVDVVRAS-G 117 GC + +E + L HPN+ L V LGCE LV G Sbjct: 162 AFAQTSGCGMSSPSEHFDVLRRTLAGYARHPNLAGALIVGLGCERNQVDALVQSQGLQPG 221 Query: 118 RPVEVLTIQEKGGTRSTIQYGVDWIRGAREQLAAQQKVPMALSELVIGTICGGSDGTSGI 177 + + +Q+ GGTR+TI G+ I ++ ++ S L IG CGGSDG SGI Sbjct: 222 QLLRTFVMQDMGGTRATIAAGIAAIEEMLPIANQARRQTVSASHLKIGLECGGSDGFSGI 281 Query: 178 TANPAVGRAFDHLIDAGATCIFEETGELVGCEFHMKTRAARPALGDEIVACVA------- 230 TANPA+G A D L+ G T I ET E+ G EF + RA P +G +++ +A Sbjct: 282 TANPALGAAMDILVRHGGTAILSETPEIHGVEFMLTRRAVSPEVGQKLLDRLAWWEKYAA 341 Query: 231 -KAARYYSILGHGSFAVGNADGGLTTQEEKSLGAYAKSGASPIVGIIKPGDIPPTGGLYL 289 + A++ ++GH GN GGL EKSLG+ K G +P+ + + + G Sbjct: 342 GQNAQFNGVVGH-----GNQAGGLANIFEKSLGSAMKGGTTPLQAVYEYAEPITQNGFVF 396 Query: 290 LDVVPDGEPRFGFPNISDNAEIGELIACGAHVILFTTGRGSVVGSAISPVIKVCANPATY 349 +D P A G+ IA GA++I FTTGRGS+ GS +P +K+ N Y Sbjct: 397 MD----------SPGYDPVAATGQ-IASGANMICFTTGRGSMFGSKPAPTVKLATNTPMY 445 Query: 350 RNLSGDMDVDAGRILEGRGTLDEVGREVFEQTVAVSRGAASKSETLG 396 L DMD++ G I++G T+ E+G +F Q + + G +KSE LG Sbjct: 446 LRLQEDMDINCGLIVDGECTVPEMGERIFAQILRHASGEPTKSELLG 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: 564 Number of extensions: 31 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: 507 Length adjustment: 33 Effective length of query: 398 Effective length of database: 474 Effective search space: 188652 Effective search space used: 188652 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