Align L-talarate dehydratase (EC 4.2.1.156); galactarate dehydratase (EC 4.2.1.42) (characterized)
to candidate N515DRAFT_1251 N515DRAFT_1251 L-fuconate dehydratase
Query= BRENDA::Q8ZL58 (398 letters) >FitnessBrowser__Dyella79:N515DRAFT_1251 Length = 442 Score = 121 bits (304), Expect = 3e-32 Identities = 93/307 (30%), Positives = 145/307 (47%), Gaps = 57/307 (18%) Query: 113 TKLLWAGASVGRSGMAVQAISPIDIALWDMKAKRAGLPL--------------------- 151 ++L W G G MA+ A+ A WD+ A+RAG PL Sbjct: 101 SQLRWLGPEKGVMHMAIGAVIN---AGWDLAARRAGKPLWRYIAELTPEQLVATIDFRYL 157 Query: 152 ---------------------AKLLGAHRDSVQCYNTSGGFLHTPLDQVLKNVVISRENG 190 A++ + Y TS G+L +++L+ + +G Sbjct: 158 SDAITPDEALQMLRAAEPAKSARIEQLLAEGYPAYTTSPGWLGYTDEKMLRLAREAVADG 217 Query: 191 IGGIKLKVGQPNCAEDIRRLTAVREALGDEFPLMVDANQQWDRETAIRMGRKMEQFNLIW 250 IKLKVG + +D+RR + VR+ +G + + VDANQ+WD AI R++E F+L W Sbjct: 218 FRTIKLKVGL-SVEDDVRRCSLVRQTVGPDVAIAVDANQRWDVHAAIDWLRRLEGFDLAW 276 Query: 251 IEEPLDAYDIEGHAQLAAALDTPIATGEMLTSFREHEQLILGNASDFVQPDAPRVGGISP 310 IEEP D+ GHA + A+ P++TGE + +QL A D VQ DA RVGG++ Sbjct: 277 IEEPTSPDDVLGHAAIRRAVSVPVSTGEHTQNRVIFKQLFQAGAVDLVQIDAARVGGVNE 336 Query: 311 FLKIMDLAAKHGRKLAPHFA----MEVHLHLSAAYPL-------EPWLEHFEWLNPLFNE 359 L I+ +AAK G ++ PH E+ HL+ A + + +E + L+ F++ Sbjct: 337 NLAILLMAAKFGVRVFPHAGGVGLCELVQHLAMADFVAITGRKDDRAIEFVDHLHEHFDD 396 Query: 360 QLELRDG 366 + +RDG Sbjct: 397 PVTIRDG 403 Lambda K H 0.319 0.136 0.410 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: 467 Number of extensions: 23 Number of successful extensions: 3 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 398 Length of database: 442 Length adjustment: 32 Effective length of query: 366 Effective length of database: 410 Effective search space: 150060 Effective search space used: 150060 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 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