Align L-talarate dehydratase (EC 4.2.1.156); galactarate dehydratase (EC 4.2.1.42) (characterized)
to candidate SMa1351 SMa1351 enolase
Query= BRENDA::Q8ZL58 (398 letters) >FitnessBrowser__Smeli:SMa1351 Length = 402 Score = 142 bits (358), Expect = 2e-38 Identities = 110/356 (30%), Positives = 176/356 (49%), Gaps = 32/356 (8%) Query: 57 LTEVAIIIAEIRSRDGFEG--VGFSYSKRAGGQGIYAHAK--EIADNLLGEDPNDIDKIY 112 LT I I + DG G G + + AG G H E+ L+G D DI ++ Sbjct: 41 LTTFDAAILRIETDDGIVGWGEGKNAAGSAGSYGTLVHMLNYEVGPRLVGRDAADISAVW 100 Query: 113 TKLLWAGA-------------SVGRSGMAVQAISPIDIALWDMKAKRAGLPLAKLLGAHR 159 ++L+ G + R G+++ AIS +DIALWD+ K G+P+ KLLG + Sbjct: 101 -EMLYNGVRHERAAMSGHAMPELSRRGLSIAAISAVDIALWDILGKSLGVPVWKLLGGRK 159 Query: 160 -DSVQCYNTSGGFLHTPLDQVLKNVVISRENGIGGIKLKVGQPNCAEDIR--RLTAVREA 216 D + Y + G + L++ + S G +K++VG + A + R+ A R+A Sbjct: 160 ADRLPAYASGGWESAEKIGGQLQSYLAS--GGFKAVKMRVGAMDGAPYVSAARVRAARKA 217 Query: 217 LGDEFPLMVDANQQWDRETAIRMGRKMEQFNLIWIEEPLDAYDIEGHAQLAAALDTPIAT 276 LG +MVDA+ + A R + + +L W EEP+ A D G A++ AA + PIAT Sbjct: 218 LGPSVDIMVDAHGTYTVADAKRFIQLVRDCDLAWFEEPVIADDKAGMAEVRAAGNVPIAT 277 Query: 277 GEMLTSFREHEQLILGNASDFVQPDAPRVGGISPFLKIMDLAAKHGRKLAPHF-----AM 331 GE + L + ++D QPD GGI+ ++I +A+ +LAPH Sbjct: 278 GESEATRFAFRDLAVLRSADIFQPDPAFCGGITEAMRIGAIASAFNLRLAPHLWAGAPCF 337 Query: 332 EVHLHLSAAYPLEPWLEHFEWLNPLFNEQLE----LRDGRMWISDRHGLGFTLSEQ 383 LH+ AA P +E+ NP+ ++ +E ++DG + I D+ GLGFT++E+ Sbjct: 338 FSGLHICAASPASFVVEYSVGANPMIHDLVEETVAVKDGMLEIPDKPGLGFTINER 393 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: 400 Number of extensions: 21 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: 398 Length of database: 402 Length adjustment: 31 Effective length of query: 367 Effective length of database: 371 Effective search space: 136157 Effective search space used: 136157 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