Align xylonate dehydratase (EC 4.2.1.82) (characterized)
to candidate BWI76_RS00975 BWI76_RS00975 dihydroxy-acid dehydratase
Query= BRENDA::Q9A9Z2 (595 letters) >FitnessBrowser__Koxy:BWI76_RS00975 Length = 616 Score = 177 bits (448), Expect = 1e-48 Identities = 163/565 (28%), Positives = 260/565 (46%), Gaps = 76/565 (13%) Query: 39 GITPEELRSGKPIIGIAQTGSDISPCNRIHL-DLVQRVRDGIRDAGGIPMEFPVHPIFEN 97 G+T ++ GKPII + + + P +HL DL + V + I AGG+ EF + + Sbjct: 26 GMTDDDF--GKPIIAVVNSFTQFVP-GHVHLRDLGKLVAEQIEAAGGVAKEFNTIAVDDG 82 Query: 98 CRRPTAALDRNLSYLGLVETLHGYPI-----DAVVLTTGCDKTTPAGIMAATTVNIPAIV 152 + +L L+ Y + DA+V + CDK TP +MA+ +NIP I Sbjct: 83 IAMGHGGMLYSLPSRELIADSVEYMVNAHCADAMVCISNCDKITPGMLMASLRLNIPVIF 142 Query: 153 LSGGPMLDGWHE--NELVGSGTVIWRSRRKLAAGEITEEEFIDRAASSAPSAGHCNTMGT 210 +SGGPM G + ++++ V + + A ++++++ S+ P+ G C+ M T Sbjct: 143 VSGGPMEAGKTKLSDQIIKLDLV--DAMIQGADPKVSDDQSDQVERSACPTCGSCSGMFT 200 Query: 211 ASTMNAVAEALGLSLTGCAAIPAPYRERGQMAYKTGQRIVDLA-----YDDVK--PLDIL 263 A++MN + EALGLS G ++ A + +R Q+ G RIV+L DD P +I Sbjct: 201 ANSMNCLTEALGLSQPGNGSLLATHADRKQLFLNAGSRIVELTKRYYEQDDASALPRNIA 260 Query: 264 TKQAFENAIALVAAAGGSTNAQPHIVAMARHAGVEITADDW-RAAYDIPLIVNMQPA-GK 321 K AFENA+ L A GGSTN H++A A+ A ++ T D + + +P + + P+ K Sbjct: 261 NKAAFENAMTLDIAMGGSTNTVLHLLAAAQEAEIDFTMSDIDKLSRKVPQLCKVAPSTQK 320 Query: 322 YLGERFHRAGGAPAVLWELLQQGRLHGDVLTVTGKTMSENLQGRE---TSDREV------ 372 Y E HRAGG +L EL + G L+ DV V G ++ + L+ + T D V Sbjct: 321 YHMEDVHRAGGVLGILGELERAGLLNRDVKNVLGLSLPQTLEQYDITVTQDEAVKKMFRA 380 Query: 373 ----------------------------IFPYHEPLAEKAGFLVLKGNLFD-FAIMKSSV 403 I ++ G VL GN + I+K++ Sbjct: 381 GPAGIRTTQAFSQNCRWDTLDDDRAEGCIRSLEHAYSKDGGLAVLYGNFAENGCIVKTAG 440 Query: 404 IGEEFRKRYLSQPGQEGVFEARAIVFDGSDDYHKRINDPALEIDERCILVIRGAGPIGWP 463 + + K F A V++ D I + + ++VIR GP G P Sbjct: 441 VDDSILK-----------FTGPAKVYESQDAAVDAILGGKIVAGD--VVVIRYEGPKGGP 487 Query: 464 GSAEVVNMQPPDHLLKKGI-MSLPTLGDGRQSGTADSPSILNASPESAIGGGLSWLRTGD 522 G E+ + P L G+ + + DGR SG SI + SPE+A GG ++ + GD Sbjct: 488 GMQEM--LYPTTFLKSMGLGKACALITDGRFSGGTSGLSIGHVSPEAASGGNIAIIEDGD 545 Query: 523 TIRIDLNTGRCDALVDEATIAARKQ 547 I ID+ + +A IAAR++ Sbjct: 546 MIAIDIPNRGIQLQLSDAEIAARRE 570 Lambda K H 0.319 0.136 0.411 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: 832 Number of extensions: 40 Number of successful extensions: 7 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 595 Length of database: 616 Length adjustment: 37 Effective length of query: 558 Effective length of database: 579 Effective search space: 323082 Effective search space used: 323082 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 Apr 09 2024. 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