Align L-talarate dehydratase (EC 4.2.1.156); galactarate dehydratase (EC 4.2.1.42) (characterized)
to candidate SM_b21107 SM_b21107 mandelate racemase or evolutionary related enzyme of the mandelate racemase muconate lactonizing enzyme family protein
Query= BRENDA::Q8ZL58 (398 letters) >FitnessBrowser__Smeli:SM_b21107 Length = 370 Score = 221 bits (563), Expect = 3e-62 Identities = 129/373 (34%), Positives = 201/373 (53%), Gaps = 12/373 (3%) Query: 27 RIEWVKLSLAFLPLATPVSDA-KVLTGRQKPLTEVAIIIAEIRSRDGFEGVGFSYSKRAG 85 RIE +L + LP +DA + ++ P I I DG G G+SY+ G Sbjct: 3 RIEKTELRMVDLPPKNKRTDAIQSFVSQETP-------IVTITDADGATGTGYSYTIGTG 55 Query: 86 GQGIYAHAKE-IADNLLGEDPNDIDKIYTKLLWAGASVGRSGMAVQAISPIDIALWDMKA 144 G + + + LLGED + I+ ++ K+ +A + + A++ +D ALWD++A Sbjct: 56 GSSVMRLLSDHLVPILLGEDADCIEALWQKMEFATHATTIGAITALALAAVDTALWDLRA 115 Query: 145 KRAGLPLAKLLGAHRDSVQCYNTSGGFLHTPLDQVLKNVVISRENGIGGIKLKVGQPNCA 204 K+ LPL KL G ++S Y T GG+LH ++ + + ++ NG G K+K+G+P+ A Sbjct: 116 KKQKLPLWKLAGGAKESCPLYTTEGGWLHIEKQALVDDALQAKANGFSGSKVKIGKPSGA 175 Query: 205 EDIRRLTAVREALGDEFPLMVDANQQWDRETAIRMGRKMEQFNLIWIEEPLDAYDIEGHA 264 ED RL+A+R ALGD F +M D NQ + + AIR ++ + +L WIEEPL A D++GH Sbjct: 176 EDYDRLSAMRAALGDGFEIMTDCNQGFTVDEAIRRAARLRELDLAWIEEPLPADDLDGHI 235 Query: 265 QLAAALDTPIATGEMLTSFREHEQLILGNASDFVQPDAPRVGGISPFLKIMDLAAKHGRK 324 +L + TPIA GE + S R + + A VQ D R+GGI+P+LK+ A Sbjct: 236 RLTRSTPTPIAVGESIYSIRHFREYMQKGACSIVQVDVARIGGITPWLKVAHAAEAFDIP 295 Query: 325 LAPHFAMEVHLHLSAAYPLEPWLEHFEWLNPLFNEQLELRDGRMWISDRHGLGFTL---S 381 + PHF ME+H+ L A P ++E+ L+ L +E+R+GR G+G + Sbjct: 296 VCPHFLMELHVSLVCAVPNGKYVEYIPQLDDLTQMGMEIREGRAIAPSNPGIGIAWDWEA 355 Query: 382 EQARRWTQLTCEF 394 +AR + T EF Sbjct: 356 VKARSVAEFTREF 368 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: 407 Number of extensions: 16 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: 370 Length adjustment: 30 Effective length of query: 368 Effective length of database: 340 Effective search space: 125120 Effective search space used: 125120 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