Align L-talarate dehydratase (EC 4.2.1.156); galactarate dehydratase (EC 4.2.1.42) (characterized)
to candidate RR42_RS22655 RR42_RS22655 mandelate racemase
Query= BRENDA::Q8ZL58 (398 letters) >FitnessBrowser__Cup4G11:RR42_RS22655 Length = 385 Score = 518 bits (1334), Expect = e-151 Identities = 254/382 (66%), Positives = 303/382 (79%), Gaps = 2/382 (0%) Query: 18 TRTAAETG--DRIEWVKLSLAFLPLATPVSDAKVLTGRQKPLTEVAIIIAEIRSRDGFEG 75 T+ +TG D I ++LS +LPLATP+SDAKVLTGRQKP+TE+AI+ AEI + G +G Sbjct: 3 TQHQPKTGANDNIASIRLSSVYLPLATPISDAKVLTGRQKPMTEIAILFAEIETEGGDKG 62 Query: 76 VGFSYSKRAGGQGIYAHAKEIADNLLGEDPNDIDKIYTKLLWAGASVGRSGMAVQAISPI 135 +GFSY+KRAGG G +AHA+EIA L+GED NDI +++ KL+WAGASVGRSG+A QAI Sbjct: 63 LGFSYAKRAGGPGQFAHAREIAPALIGEDANDIARLWNKLIWAGASVGRSGLATQAIGAF 122 Query: 136 DIALWDMKAKRAGLPLAKLLGAHRDSVQCYNTSGGFLHTPLDQVLKNVVISRENGIGGIK 195 D+ALWD+KA+RA LPLAKLLGAHRDSV+CYNTSGGFLHTPLDQ+L N S E GIGGIK Sbjct: 123 DVALWDLKARRANLPLAKLLGAHRDSVKCYNTSGGFLHTPLDQLLMNASKSVEKGIGGIK 182 Query: 196 LKVGQPNCAEDIRRLTAVREALGDEFPLMVDANQQWDRETAIRMGRKMEQFNLIWIEEPL 255 LKVGQP+CA DI+R+ VR+ LGD F LMVDANQQWDR TA RM R +EQFNLIWIEEPL Sbjct: 183 LKVGQPDCAADIQRVETVRKHLGDGFALMVDANQQWDRPTAQRMCRILEQFNLIWIEEPL 242 Query: 256 DAYDIEGHAQLAAALDTPIATGEMLTSFREHEQLILGNASDFVQPDAPRVGGISPFLKIM 315 DAYD EGHA LAA DTPIATGEMLTS EH LI A+D++ PD PRVGGI+PFL + Sbjct: 243 DAYDSEGHAALAAQFDTPIATGEMLTSVAEHWDLIRHRAADYLMPDGPRVGGITPFLTVA 302 Query: 316 DLAAKHGRKLAPHFAMEVHLHLSAAYPLEPWLEHFEWLNPLFNEQLELRDGRMWISDRHG 375 LA G +APHFAME+H+HL+AAYP EPW+EHFEWL PLFNE+LE++DGRM + R G Sbjct: 303 TLADHAGLMIAPHFAMELHVHLAAAYPREPWVEHFEWLEPLFNERLEIKDGRMLVPTRPG 362 Query: 376 LGFTLSEQARRWTQLTCEFGKR 397 +G +LS Q WT+ EFG + Sbjct: 363 IGVSLSGQVAGWTREQAEFGAK 384 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: 556 Number of extensions: 19 Number of successful extensions: 1 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: 385 Length adjustment: 31 Effective length of query: 367 Effective length of database: 354 Effective search space: 129918 Effective search space used: 129918 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