Align xylonate dehydratase (EC 4.2.1.82) (characterized)
to candidate AZOBR_RS15015 AZOBR_RS15015 dihydroxy-acid dehydratase
Query= BRENDA::Q9A9Z2 (595 letters) >FitnessBrowser__azobra:AZOBR_RS15015 Length = 621 Score = 185 bits (470), Expect = 4e-51 Identities = 181/601 (30%), Positives = 266/601 (44%), Gaps = 97/601 (16%) Query: 48 GKPIIGIAQTGSDISPCNRIHL-DLVQRVRDGIRDAGGIPMEFPVHPIFENCRRPTAALD 106 GKPII IA + + P +HL DL Q V I AGG+ EF + + + Sbjct: 33 GKPIIAIANSFTQFVP-GHVHLKDLGQLVAREIEKAGGVAKEFNTIAVDDGIAMGHDGML 91 Query: 107 RNLSYLGLVETLHGYPI-----DAVVLTTGCDKTTPAGIMAATTVNIPAIVLSGGPMLDG 161 +L L+ Y + DA+V + CDK TP +MAA +NIPA+ +SGGPM Sbjct: 92 YSLPSRELIADAVEYMVNAHCADALVCISNCDKITPGMLMAAMRLNIPAVFVSGGPM--- 148 Query: 162 WHENELVGSGTVIWRSRRK--------LAAGE--ITEEEFIDRAASSAPSAGHCNTMGTA 211 +G V WR + K +AA + +++EE S P+ G C+ M TA Sbjct: 149 -------EAGKVNWRGKTKAVDLIDAMVAAADPTVSDEEAAVMERGSCPTCGSCSGMFTA 201 Query: 212 STMNAVAEALGLSLTGCAAIPAPYRERGQMAYKTGQRIVDLA---YDD----VKPLDILT 264 ++MN + EALGLSL G I A + +R ++ G+ V+L Y + P I T Sbjct: 202 NSMNCLTEALGLSLPGNGTILATHADRKELFLAAGRMAVELCRRWYQEEDATALPRGIAT 261 Query: 265 KQAFENAIALVAAAGGSTNAQPHIVAMARHAGVEIT-ADDWRAAYDIPLIVNMQPAGKYL 323 +AFENA+ L A GGSTN H++A A+ V T AD R + +P + + PA + Sbjct: 262 FEAFENAMTLDIAMGGSTNTVLHLLAAAQEGQVPFTMADIDRLSRRVPNVCKVAPAVSDV 321 Query: 324 G-ERFHRAGGAPAVLWELLQQGRLHGDVLTVTGKTMSENL----------QGRET----- 367 E H+AGG +L EL + G L+ DV TV KT+ + L +G T Sbjct: 322 HIEDVHKAGGIFGILGELDRGGLLNRDVATVHAKTLGDALDRWDVKRTQDEGVHTMFKAA 381 Query: 368 ----------------------SDREVIFPYHEPLAEKAGFLVLKGNLFDFAIMKSSVIG 405 D+ VI ++ G VL GN+ + K ++ Sbjct: 382 PGGIPTTIAFSQEKRWPELDLDRDKGVIRSVDSAFSKDGGLAVLFGNIAE----KGCIV- 436 Query: 406 EEFRKRYLSQPGQEGVFEARAIVFDGSDDYHKRINDPALEIDERCILVIRGAGPIGWPGS 465 + VF A VF+ D + I ++ + ++VIR GP G PG Sbjct: 437 -----KTAGVDASNLVFAGPARVFESQDAAVEAILGDTVKAGD--VVVIRYEGPRGGPGM 489 Query: 466 AEVVNMQPPDHLLKKGI-MSLPTLGDGRQSGTADSPSILNASPESAIGGGLSWLRTGDTI 524 E+ + P +L KG+ + + DGR SG SI +ASPE+A GG + ++ GD I Sbjct: 490 QEM--LYPTSYLKSKGLGKACALVTDGRFSGGTSGLSIGHASPEAAQGGAIGLVQDGDRI 547 Query: 525 RIDLNTGRCD-ALVDEATIAARKQDGIPAVPA--------TMTPWQEIYRAHASQLDTGG 575 ID+ + + AL DE R + A ++P Y A + D G Sbjct: 548 EIDIPNRKINLALSDEELQRRRDAENAKGADAWKPANRNRVVSPALRAYAALTTSADRGA 607 Query: 576 V 576 V Sbjct: 608 V 608 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: 924 Number of extensions: 52 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: 621 Length adjustment: 37 Effective length of query: 558 Effective length of database: 584 Effective search space: 325872 Effective search space used: 325872 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