Align L-talarate dehydratase (EC 4.2.1.156); galactarate dehydratase (EC 4.2.1.42) (characterized)
to candidate AZOBR_RS17545 AZOBR_RS17545 mandelate racemase
Query= BRENDA::Q8ZL58 (398 letters) >FitnessBrowser__azobra:AZOBR_RS17545 Length = 390 Score = 136 bits (342), Expect = 1e-36 Identities = 105/349 (30%), Positives = 172/349 (49%), Gaps = 25/349 (7%) Query: 54 QKPLTEVAIIIAEIRSRDGFEGVGFSYSKRAGGQGIYAH------AKEIADNLLGEDPND 107 Q + VA+I +R G GF+ + R G G+ D+L+ E + Sbjct: 26 QMTCSTVAVITDVVRDGKPVIGYGFNSNGRYGAGGLMRERFIPRLTSAAPDSLIDEANGN 85 Query: 108 ID--KIYTKLLWAGASVGRSGMAVQAISPIDIALWDMKAKRAGLPLAKLL------GAHR 159 +D KI+ +L+ G G A+ ID+A+WD AK AG PL +LL G Sbjct: 86 LDPFKIWARLM-TNEKPGGHGERSVAMGTIDMAVWDAVAKIAGKPLYRLLADRYRGGVAD 144 Query: 160 DSVQCYNTSGGFLHTPLDQVLKNVVIS-RENGIGGIKLKVGQPNCAEDIRRLTAVREALG 218 +SV Y G + + L+N + S R+ G +K+K+G + +D+RR+ AV E +G Sbjct: 145 ESVWVYAAGGYYYPGKGVEALQNEMRSYRDRGYNVVKMKIGATSLEDDLRRIEAVLEVVG 204 Query: 219 DEFPLMVDANQQWDRETAIRMGRKMEQFNLIWIEEPLDAYDIEGHAQLAAALDTPIATGE 278 D L VDAN ++D +TAI ++ +NL W EE D D A+LA D P+ATGE Sbjct: 205 DGRNLCVDANGRFDLKTAIAYAEALKPYNLFWYEEAGDPLDYALQAELANHYDRPMATGE 264 Query: 279 MLTSFREHEQLI----LGNASDFVQPDAPRVGGISPFLKIMDLAAKHG---RKLAPHFAM 331 L S ++ LI + D++Q D G+ +++ +D+ A++G R++ PH Sbjct: 265 NLFSHQDARNLIRHGGMRPDRDWLQFDCALSYGLVEYMRTLDMLAENGWSSRRVVPHGGH 324 Query: 332 EVHLHLSAAYPLEPWLEHFEWLNPL--FNEQLELRDGRMWISDRHGLGF 378 ++ L+++A L + + P F + + + DGR+ + G+GF Sbjct: 325 QMSLNIAAGLHLGGNESYPDVFKPFCGFADSIAVEDGRVRLPALPGIGF 373 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: 400 Number of extensions: 17 Number of successful extensions: 3 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: 390 Length adjustment: 31 Effective length of query: 367 Effective length of database: 359 Effective search space: 131753 Effective search space used: 131753 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