Align L-talarate dehydratase (EC 4.2.1.156); galactarate dehydratase (EC 4.2.1.42) (characterized)
to candidate RR42_RS34985 RR42_RS34985 mandelate racemase
Query= BRENDA::Q8ZL58 (398 letters) >FitnessBrowser__Cup4G11:RR42_RS34985 Length = 368 Score = 230 bits (587), Expect = 4e-65 Identities = 133/349 (38%), Positives = 187/349 (53%), Gaps = 9/349 (2%) Query: 31 VKLSLAFLPLATPVSDA-KVLTGRQKPLTEVAIIIAEIRSRDGFEGVGFSYSKRAGGQGI 89 V+L LP P SDA + ++ P+ IR DG EG G++Y+ GG + Sbjct: 8 VELLQVDLPPRVPRSDAIQSFVMQETPMVR-------IRCDDGAEGTGYAYTIGTGGSSV 60 Query: 90 YAHAKE-IADNLLGEDPNDIDKIYTKLLWAGASVGRSGMAVQAISPIDIALWDMKAKRAG 148 A ++ +A L+G DP I+ I+ +LL+A + + A++ ID ALWD + +R G Sbjct: 61 MALLRDHLAPRLIGRDPAQIEAIWRELLFATHATSVGAITSLALAAIDTALWDWRCRRDG 120 Query: 149 LPLAKLLGAHRDSVQCYNTSGGFLHTPLDQVLKNVVISRENGIGGIKLKVGQPNCAEDIR 208 PL G + V Y T GG+LH D ++ V +RE G G KLKVG+ +ED+ Sbjct: 121 QPLWLAAGGAQPRVPVYTTEGGWLHLDADTLVSEAVAAREAGFRGAKLKVGRARASEDVA 180 Query: 209 RLTAVREALGDEFPLMVDANQQWDRETAIRMGRKMEQFNLIWIEEPLDAYDIEGHAQLAA 268 RL AVR+A+GD F LMVDANQ + AIR + + W EEPL A DI GH +LAA Sbjct: 181 RLAAVRDAVGDGFELMVDANQCFTAAEAIRRAPHYAELGIAWFEEPLPADDIGGHVRLAA 240 Query: 269 ALDTPIATGEMLTSFREHEQLILGNASDFVQPDAPRVGGISPFLKIMDLAAKHGRKLAPH 328 + PIA GE L S + + + A VQ D R+GGI+P+LK+ LA H + PH Sbjct: 241 STSVPIAVGESLYSPGQFAEYVRQGACGIVQADVARIGGITPWLKVAHLAEAHNLSICPH 300 Query: 329 FAMEVHLHLSAAYPLEPWLEHFEWLNPLFNEQLELRDGRMWISDRHGLG 377 F ME+H+ L AA P W+E+ L+ + + + G D GLG Sbjct: 301 FLMELHVSLCAAVPNAAWVEYIPQLDEIAASSVRIEAGHAIAPDAPGLG 349 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: 434 Number of extensions: 17 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: 368 Length adjustment: 30 Effective length of query: 368 Effective length of database: 338 Effective search space: 124384 Effective search space used: 124384 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