Align L-talarate dehydratase (EC 4.2.1.156); galactarate dehydratase (EC 4.2.1.42) (characterized)
to candidate HSERO_RS05235 HSERO_RS05235 fuconate dehydratase
Query= BRENDA::Q8ZL58 (398 letters) >FitnessBrowser__HerbieS:HSERO_RS05235 Length = 425 Score = 107 bits (268), Expect = 5e-28 Identities = 69/194 (35%), Positives = 108/194 (55%), Gaps = 3/194 (1%) Query: 136 DIALWDMKAKRAGLPLAKLLGAHRDSVQCYNTSGGFLHTPLDQVLKNVVISRENGIGGIK 195 D AL ++ K AG +L ++ CY TS G+L ++ + + + G +K Sbjct: 159 DEALALLREKEAG-KAERLRVLEQEGYPCYTTSAGWLGYEDAKLRRLCQEAIDQGFNHVK 217 Query: 196 LKVGQPNCAEDIRRLTAVREALGDEFPLMVDANQQWDRETAIRMGRKMEQFNLIWIEEPL 255 LKVG+ + A+D RR+T RE LG E LM+DANQ W+ AI ++ +IEEP Sbjct: 218 LKVGR-DLADDKRRVTIAREVLGPERKLMIDANQVWEVHQAIDWVNQLAFAQPWFIEEPT 276 Query: 256 DAYDIEGHAQLAAALD-TPIATGEMLTSFREHEQLILGNASDFVQPDAPRVGGISPFLKI 314 D+EGH ++ + +ATGEM + +Q I+ +A D VQ D+ R+GG++ L + Sbjct: 277 SPDDVEGHRKIREGIGAVKVATGEMCQNRVLFKQFIMRDAIDVVQIDSCRLGGVNEILAV 336 Query: 315 MDLAAKHGRKLAPH 328 M +AAK+G+ + PH Sbjct: 337 MLMAAKYGKVVCPH 350 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: 419 Number of extensions: 30 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: 425 Length adjustment: 31 Effective length of query: 367 Effective length of database: 394 Effective search space: 144598 Effective search space used: 144598 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