Align Xylonate dehydratase (EC 4.2.1.82) (characterized)
to candidate WP_008410930.1 DESHY_RS05080 dihydroxy-acid dehydratase
Query= reanno::pseudo5_N2C3_1:AO356_28760 (594 letters) >NCBI__GCF_000315365.1:WP_008410930.1 Length = 552 Score = 289 bits (740), Expect = 2e-82 Identities = 199/548 (36%), Positives = 285/548 (52%), Gaps = 27/548 (4%) Query: 35 GMTREELQSGRPIIGIAQTGSDLTPCNRHHLELAQRVKAGIRDAGGIPMEFPVHPIAEQS 94 G+ EEL RP+IG+ + +++ P + H ++A+ VKAG+R AGG P+EFPV + + Sbjct: 23 GLLDEELS--RPLIGVVNSFNEVVPGHIHLRDIAEAVKAGVRMAGGTPLEFPVIAVCDGI 80 Query: 95 RRPTAALDRNLAYLGLV----EIL-HGYPLDGVVLTTGCDKTTPACLMAAATTDLPAIVL 149 + +LA ++ EI+ +P DG+VL CDK P LMAAA ++PA+V+ Sbjct: 81 AMGHPGMRYSLASREIIADSIEIMAQAHPFDGLVLIPNCDKVVPGMLMAAARLNIPAVVV 140 Query: 150 SGGPMLDGHHKGELIGSGTVLWHARNLMAAGEIDYEGFMEMTTAASPSVGHCNTMGTALS 209 SGGPML G + + + S T ++ A + AG + E E+ A P G C M TA S Sbjct: 141 SGGPMLAGRFQNQDV-SVTQMFEAVGAVQAGRLTPEELAELEENACPGCGSCAGMFTANS 199 Query: 210 MNALAEALGMSLPGCASIPAPYRERGQMAYATGKRICELVLQDIRPSQIMTRQAFENAIA 269 MN L EALGM+LPG +IPA R ++A A G R LV +++RP I+T F N +A Sbjct: 200 MNCLTEALGMALPGNGTIPAVSAARRRLAKAAGLRAVALVRENLRPRDILTMANFRNGLA 259 Query: 270 VASALGASSNCPPHLIAIARHMGVELSLDDWQRIGEDVPLLVNCMPAGKYLGEGFHRAGG 329 V ALG S+N HL AIAR G+EL+LD I E P L PAG++ + AGG Sbjct: 260 VDMALGCSTNTVLHLPAIAREAGIELNLDLINEISERTPHLCKLSPAGRHHIQDLDAAGG 319 Query: 330 VPSVMHELQKAGRLHEDCATVSGRTIGEIVSSSLTSNADVIHPFDTPLKHRAGFIVLSGN 389 + +VM EL G ++ + TVSG T+G+++ + + VI P G VL GN Sbjct: 320 IQAVMKELLNNGLINPNIKTVSGLTVGQLLEQAKVKDRQVIRSVQEPYSSTGGLAVLRGN 379 Query: 390 FF-DSAIMKMSVVG-EAFRKTYLSEPGAENSFEARAIVFEGPEDYHARIDDPALDIDERC 447 + A++K + V E R T A VF+G E I A I Sbjct: 380 LAPNGAVVKRAAVAPEMLRHT------------GPARVFDGEEAAITAI--MAGQIKPGD 425 Query: 448 ILVIRGVGTVGYPGSAEVVNMAPPAALIKQGID-SLPCLGDGRQSGTSASPSILNMSPEA 506 ++VIR G G PG E+ +AP + L G+D + L DGR SG S SI ++SPEA Sbjct: 426 VVVIRYEGPKGGPGMREM--LAPTSVLAGMGLDKEVALLTDGRFSGASRGASIGHISPEA 483 Query: 507 AVGGGLALLQTNDRLKVDLNTRTVNLLIDDEEMARRRLEWTPNIPPSQTPWQELYRQLVG 566 A GG +ALLQ D +++D+ + +D+ + +R W P P + Y + V Sbjct: 484 AEGGLIALLQDGDMIEIDIPNYRLAAKLDETVIKQRLEAWQPPAPKVTEGYLARYAKQVS 543 Query: 567 QLSTGGCL 574 G L Sbjct: 544 SAGQGAVL 551 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: 867 Number of extensions: 36 Number of successful extensions: 5 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 1 Length of query: 594 Length of database: 552 Length adjustment: 36 Effective length of query: 558 Effective length of database: 516 Effective search space: 287928 Effective search space used: 287928 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 24 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