Align L-talarate dehydratase (EC 4.2.1.156); galactarate dehydratase (EC 4.2.1.42) (characterized)
to candidate AZOBR_RS26635 AZOBR_RS26635 mandelate racemase
Query= BRENDA::Q8ZL58 (398 letters) >FitnessBrowser__azobra:AZOBR_RS26635 Length = 393 Score = 147 bits (372), Expect = 4e-40 Identities = 120/384 (31%), Positives = 178/384 (46%), Gaps = 42/384 (10%) Query: 40 LATPVSDAKVLTGRQKPLTEVAIIIAEIRSRDGFEGVGFSYSKRAGGQGIYAHAKE---- 95 L TP++ AK Q E ++ I + DG G G GGQ A E Sbjct: 11 LKTPLN-AKTFYSSQAAFPERNSLLVRITTDDGLVGWG------EGGQYGPAEPPESCII 63 Query: 96 --IADNLLGEDPNDIDKIYTKLLWAGASVGRSGMAVQAISPIDIALWDMKAKRAGLPLAK 153 +A L+G + +++ L G+ G ++A+S IDIALWD+ K P+ Sbjct: 64 DVLAPRLIGRRADQPVRVFEDLYSFCRDFGQKGTYIEALSAIDIALWDLWGKSLNRPVHA 123 Query: 154 LLG-AHRDSVQCYNTS----GGFLHTP--LDQVLKNVVISRENGIGGIKLKVGQPNCAED 206 L+G A RD V Y T F TP + + + RE G+ IK+K+G A+D Sbjct: 124 LMGGAFRDKVAAYGTGCYYPDYFRDTPRMMAALAEEAQRYREAGLPAIKIKIGLLPIAQD 183 Query: 207 IRRLTAVREALGDEFPLMVDANQQWDRETAIRMGRKMEQFNLIWIEEPLDAYDIEGHAQL 266 I R+ VR+ LG + +MVDAN ++ AIR+GR +E+F++ W EEP+ D +G+ ++ Sbjct: 184 IERVALVRDVLGPDTLIMVDANHAYNTAGAIRIGRALERFDVRWFEEPVPPEDRQGYRRV 243 Query: 267 AAALDTPIATGEMLTSFREHEQLILGNASDFVQPDAPRVGGISPFLKIMDLAAKHGRKLA 326 ++D PIA GE + +L+ G D QPD GG + + KI+ L HG Sbjct: 244 RDSIDVPIAGGECEYTRYGFRELLAGGCIDIAQPDLCCAGGFTEWQKILALTTAHGVMTV 303 Query: 327 PH-----FAMEVHLHLSAAYPL------------EPWLEHFEWLNPLFNEQL----ELRD 365 PH A+ L A PL EP +E NPL ++ L L D Sbjct: 304 PHIWGSGIALAAALQALATAPLVPYTALGVPLQNEPMVEFDRTHNPLRDDLLIDNFTLVD 363 Query: 366 GRMWISDRHGLGFTLS-EQARRWT 388 G + + GLG + +Q R+T Sbjct: 364 GCLALPGGAGLGVEVDPDQLARYT 387 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: 406 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: 393 Length adjustment: 31 Effective length of query: 367 Effective length of database: 362 Effective search space: 132854 Effective search space used: 132854 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