Align L-talarate dehydratase (EC 4.2.1.156); galactarate dehydratase (EC 4.2.1.42) (characterized)
to candidate CA265_RS12250 CA265_RS12250 enolase
Query= BRENDA::Q8ZL58 (398 letters) >FitnessBrowser__Pedo557:CA265_RS12250 Length = 388 Score = 139 bits (351), Expect = 1e-37 Identities = 118/370 (31%), Positives = 177/370 (47%), Gaps = 35/370 (9%) Query: 40 LATPVSDAKVLTGRQKPLTEVAIIIAEIRSRDGFEGVGFSYSKRAGGQGIYAHAKEIADN 99 L P+ +AK LT + + I + G +G G + + G GI A +N Sbjct: 11 LRCPIPEAKQHVSDYGLLTSFDMTLVVITTDSGLQGFGEAKAA-VGSCGICASIVNCIEN 69 Query: 100 -----LLGEDPNDIDKIYTKL---------LWAGAS---VGRSGMAVQAISPIDIALWDM 142 LLG+ +I +++ ++ L G +GR G+ + A+S ID ALWD+ Sbjct: 70 ELKPMLLGKSVKNITRLWEEMYNGTRDHYALSRGRKFPILGRRGLTISAMSGIDTALWDL 129 Query: 143 KAKRAGLPLAKLLG-AHRDSVQCYNTSGGFLHTPLDQVLKNVVISRENGIGGIKLKVG-- 199 K K +P+A LLG A R + Y + G + + L V G G+K++VG Sbjct: 130 KGKMLNVPVADLLGGACRTKMPAYASGGWADEQNIGEQLMGYV---NKGFKGVKMRVGVM 186 Query: 200 QPNCAEDIRRLTAVREALGDEFPLMVDANQQWDRETAIRMGRKMEQFNLIWIEEPLDAYD 259 + I R+ A R ALG + LMVDA+ + A + R +E N+ W EEP+ + Sbjct: 187 DDTVQKSINRVKAARAALGPDIKLMVDAHGTFSVPEAKQFCRGVEDCNVYWFEEPISPDN 246 Query: 260 IEGHAQLAAALDTPIATGEM-LTSFREHEQLILGNASDFVQPDAPRVGGISPFLKIMDLA 318 +G A++ AA D PIA GE TSF H+ L + A D VQPDA +GGIS +++ LA Sbjct: 247 RKGTAEVRAATDIPIAAGESEFTSFDIHDLLQI-RAIDVVQPDAAIIGGISEAMRVSHLA 305 Query: 319 AKHGRKLAPH-----FAMEVHLHLSAAYPLEPWLEHFEWLNP----LFNEQLELRDGRMW 369 + H +LAPH F+ L ++ A +E NP L NEQ+ + +G + Sbjct: 306 SVHQVELAPHCWGSAFSFMAGLTVAFASASATIIEFSLGGNPMMYDLVNEQIAVVNGEIS 365 Query: 370 ISDRHGLGFT 379 GLG T Sbjct: 366 APTAPGLGLT 375 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: 356 Number of extensions: 22 Number of successful extensions: 2 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: 398 Length of database: 388 Length adjustment: 31 Effective length of query: 367 Effective length of database: 357 Effective search space: 131019 Effective search space used: 131019 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