Align Xylonate dehydratase (EC 4.2.1.82) (characterized)
to candidate CA265_RS15795 CA265_RS15795 dihydroxy-acid dehydratase
Query= reanno::pseudo6_N2E2:Pf6N2E2_1668 (594 letters) >FitnessBrowser__Pedo557:CA265_RS15795 Length = 560 Score = 258 bits (658), Expect = 6e-73 Identities = 170/527 (32%), Positives = 271/527 (51%), Gaps = 30/527 (5%) Query: 32 MNYGMTREELQSGRPIIGIAQTGSDLTPCNRHHLELAQRVKAGIRDAGGIPMEFPVHPIA 91 M YG+ + + +GIA G D CN H +LA+ VK G+ + + F ++ Sbjct: 23 MLYGIGLTDADMAKAQVGIASMGYDGNTCNMHLNDLAKDVKKGVWKNDLVGLVFNTIGVS 82 Query: 92 EQSRRPT-----AALDRNLAYLGLVEILHGYPLDGVVLTTGCDKTTPACLMAAATTDLPA 146 + T + + R++ + I G DG++ GCDK P +MA A D P+ Sbjct: 83 DGMSNGTDGMRYSLVSRDVIADSIETICGGQYYDGIISIPGCDKNMPGAIMAMARLDRPS 142 Query: 147 IVLSGGPMLDGHHKGELIGSGTVLWHARNLMAAGEIDYEGFMEMTTAASPSVGHCNTMGT 206 I++ GG + GH+KGE + + + A G + E + + P G C M T Sbjct: 143 IMVYGGTIAPGHYKGEELNIVSA-FEALGQKICGNLSEEDYQGIIKHTCPGAGACGGMYT 201 Query: 207 ALSMNALAEALGMSLPGCASIPAPYRERGQMAYATGKRICDLVRQDIRPSQIMTRQAFEN 266 A +M + EALGMSLP +S PA E+ Q GK I L+ +DI+PS IMTR+AFEN Sbjct: 202 ANTMASAIEALGMSLPYSSSNPAISEEKKQECLDAGKYIKILLEKDIKPSDIMTRKAFEN 261 Query: 267 AIAVASALGASSNCPPHLIAIARHMGVELSLEDWQRIGEDVPLLVNCMPAGKYLGEGFHR 326 AI LG S+N H IA+ + +G+E++ +D+QR+ + P+L + P+GKYL + H+ Sbjct: 262 AIRSIIILGGSTNAVLHFIAMGKAIGIEITQDDFQRMSDVTPVLADFKPSGKYLMQDLHQ 321 Query: 327 AGGVPSVMHELQKAGRLHEDCATVSGKTIGE---IVSNSLTSNTDVIHPFDTPLKHRAGF 383 GG+P+V+ L G LH DC TV+GKT+ E V + + + +I P+K Sbjct: 322 YGGIPAVLKYLLNEGLLHGDCLTVTGKTVAENLADVKSIMDYDQKIIQKLSEPIKATGHL 381 Query: 384 IVLSGNFFD-SAIMKMSVVGEAFRKTYLSEPGAE-NSFEARAIVFEGPEDYHARIDDPAL 441 +L GN + ++ K+S G E FE A VF+G D A I + Sbjct: 382 QILYGNLAEKGSVAKIS--------------GKEGEKFEGPARVFDGEHDLIAGISSGRV 427 Query: 442 DIDERCILVIRGVGTVGYPGSAEVVNMAPPAALIKQGI-DSLPCLGDGRQSGTSASPSIL 500 + ++VI+ G VG PG E+ + P +A+I G+ S+ + DGR SG + + Sbjct: 428 QPGD--VIVIKNSGPVGAPGMPEM--LKPTSAIIGAGLGKSVALITDGRFSGGTHGFVVG 483 Query: 501 NMSPEAAVGGGLALLKTNDRLKVDLNTRTVNLLIDDAEMAQRRREWI 547 +++PE+ GG + L++ DR+ +D +NL + D +A+RR+ ++ Sbjct: 484 HITPESYKGGLIGLVEDEDRILIDAVNNIINLQVSDEVIAERRKNYV 530 Lambda K H 0.319 0.135 0.407 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: 845 Number of extensions: 47 Number of successful extensions: 4 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: 594 Length of database: 560 Length adjustment: 36 Effective length of query: 558 Effective length of database: 524 Effective search space: 292392 Effective search space used: 292392 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 (21.7 bits) S2: 53 (25.0 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