Align L-talarate dehydratase (EC 4.2.1.156); galactarate dehydratase (EC 4.2.1.42) (characterized)
to candidate PP_2831 PP_2831 L-fuconate dehydratase
Query= BRENDA::Q8ZL58 (398 letters) >FitnessBrowser__Putida:PP_2831 Length = 411 Score = 97.1 bits (240), Expect = 8e-25 Identities = 83/296 (28%), Positives = 129/296 (43%), Gaps = 61/296 (20%) Query: 76 VGFSYSKRAGGQGIYAHAKEIADNLLGEDPNDIDKIYTKLLWAGASVGRSGMAVQAISPI 135 VG + + + G + H ++D+ +L W G G +A AI Sbjct: 49 VGLTLEEISADMGAFWHRFTVSDS--------------QLRWLGPEKGVIHLATAAIIN- 93 Query: 136 DIALWDMKAKRAGLPLAKLLG--------------------------------------- 156 A+WD+ AK G P+ KLL Sbjct: 94 --AVWDLWAKHEGKPVWKLLADMTPEQLVRCLDFSYVTDVLTPEEAIALLRRQAPGKAER 151 Query: 157 -AH--RDSVQCYNTSGGFLHTPLDQVLKNVVISRENGIGGIKLKVGQPNCAEDIRRLTAV 213 AH R+ Y T+ G+L +++ K + +G IK K+G + EDIRR + + Sbjct: 152 EAHMLREGYPGYTTAPGWLGYSEEKMRKLAREAVADGWTHIKQKIGA-DLEEDIRRASIL 210 Query: 214 REALGDEFPLMVDANQQWDRETAIRMGRKMEQFNLIWIEEPLDAYDIEGHAQLAAAL-DT 272 R+ +G E LM+DANQ W E ++ R++ F +WIEEP DI GHA + + Sbjct: 211 RDEIGWERTLMMDANQVWGVEESVANMRRLAAFEPLWIEEPTSPDDILGHATIRQRIAPI 270 Query: 273 PIATGEMLTSFREHEQLILGNASDFVQPDAPRVGGISPFLKIMDLAAKHGRKLAPH 328 +ATGE + +Q+ A DF Q DA R+GG++ L ++ +AAK+ + PH Sbjct: 271 GVATGEHCHNRVMFKQMFQAGALDFCQLDAARLGGLNEVLIVLLMAAKYDVPVCPH 326 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: 417 Number of extensions: 22 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: 411 Length adjustment: 31 Effective length of query: 367 Effective length of database: 380 Effective search space: 139460 Effective search space used: 139460 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