Align xylonate dehydratase (EC 4.2.1.82) (characterized)
to candidate AZOBR_RS15015 AZOBR_RS15015 dihydroxy-acid dehydratase
Query= BRENDA::P39358 (655 letters) >FitnessBrowser__azobra:AZOBR_RS15015 Length = 621 Score = 201 bits (512), Expect = 6e-56 Identities = 194/634 (30%), Positives = 305/634 (48%), Gaps = 95/634 (14%) Query: 72 GLRGAD-GKPVALALHQ------GHYEL-DIQMKAAAEVIKANH-ALPYAVYVSDPCDGR 122 G++ D GKP+ + GH L D+ A E+ KA A + D DG Sbjct: 26 GMKDGDFGKPIIAIANSFTQFVPGHVHLKDLGQLVAREIEKAGGVAKEFNTIAVD--DGI 83 Query: 123 TQGTTGMFDSLPYRNDASMVMRRLIRSLPDAKAVIGVASCDKGLPATMMALAAQHNIATV 182 G GM SLP R + + ++ + A A++ +++CDK P +MA A + NI V Sbjct: 84 AMGHDGMLYSLPSRELIADAVEYMVNA-HCADALVCISNCDKITPGMLMA-AMRLNIPAV 141 Query: 183 LVPGGATLPAKDGEDNGKVQT-----IGARFANGELSLQDAR-----RAGCKACASSGGG 232 V GG P + G+ N + +T I A A + ++ D R C C G Sbjct: 142 FVSGG---PMEAGKVNWRGKTKAVDLIDAMVAAADPTVSDEEAAVMERGSCPTC----GS 194 Query: 233 CQFLGTAGTSQVVAEGLGLAIPHSALAPSGEPVWREIARASARAALNLSQKGITT----- 287 C + TA + + E LGL++P + + +E+ A+ R A+ L ++ Sbjct: 195 CSGMFTANSMNCLTEALGLSLPGNGTILATHADRKELFLAAGRMAVELCRRWYQEEDATA 254 Query: 288 --REILTDKAIENAMTVHAAFGGSTNLLLHIPAIAHQAGCHIP-TVDDWIRINKRVPRLV 344 R I T +A ENAMT+ A GGSTN +LH+ A A + +P T+ D R+++RVP + Sbjct: 255 LPRGIATFEAFENAMTLDIAMGGSTNTVLHLLAAAQEG--QVPFTMADIDRLSRRVPNVC 312 Query: 345 SVLPNGPVYHPTVNAFMAGGVPEVMLHLRSLGLLHEDVMTVTGSTLKENLDWWE------ 398 V P H + AGG+ ++ L GLL+ DV TV TL + LD W+ Sbjct: 313 KVAPAVSDVH-IEDVHKAGGIFGILGELDRGGLLNRDVATVHAKTLGDALDRWDVKRTQD 371 Query: 399 ---HS---------------ERRQRFKQLLLDQEQINADEVIMSPQQAKARGLTSTITFP 440 H+ + +R+ +L LD+++ VI S A ++ + F Sbjct: 372 EGVHTMFKAAPGGIPTTIAFSQEKRWPELDLDRDK----GVIRSVDSAFSKDGGLAVLF- 426 Query: 441 VGNIAPEGSVIKSTAIDPSMIDEQGIYYHKGVAKVYLSEKSAIYDIKHDKIKAGDILVII 500 GNIA +G ++K+ +D S + G A+V+ S+ +A+ I D +KAGD++VI Sbjct: 427 -GNIAEKGCIVKTAGVDASNL------VFAGPARVFESQDAAVEAILGDTVKAGDVVVIR 479 Query: 501 GVGP-SGTGMEETYQVTSALKHLSYGKHVSLITDARFSGVSTGACIGHVGPEALAGGPIG 559 GP G GM+E TS LK GK +L+TD RFSG ++G IGH PEA GG IG Sbjct: 480 YEGPRGGPGMQEMLYPTSYLKSKGLGKACALVTDGRFSGGTSGLSIGHASPEAAQGGAIG 539 Query: 560 KLRTGDLIEIKIDCRELHGEVNFLGTRSDEQLPSQEEATAILNA---RPSHQDLLPDPEL 616 ++ GD IEI I R+++ + SDE+L + +A A +P++++ + P L Sbjct: 540 LVQDGDRIEIDIPNRKINLAL------SDEELQRRRDAENAKGADAWKPANRNRVVSPAL 593 Query: 617 PDDTRLWAMLQAVSGGTWTGCIYDVNKI-GAALR 649 R +A A++ G + DV+++ G A++ Sbjct: 594 ----RAYA---ALTTSADRGAVRDVSQVEGIAMK 620 Lambda K H 0.317 0.135 0.400 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: 974 Number of extensions: 50 Number of successful extensions: 6 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: 655 Length of database: 621 Length adjustment: 38 Effective length of query: 617 Effective length of database: 583 Effective search space: 359711 Effective search space used: 359711 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 54 (25.4 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