Align L-arabonate dehydratase; L-arabinonate dehydratase; EC 4.2.1.25 (characterized)
to candidate N515DRAFT_0569 N515DRAFT_0569 dihydroxy-acid dehydratase
Query= SwissProt::Q1JUQ1 (583 letters) >FitnessBrowser__Dyella79:N515DRAFT_0569 Length = 568 Score = 287 bits (735), Expect = 7e-82 Identities = 195/540 (36%), Positives = 284/540 (52%), Gaps = 30/540 (5%) Query: 25 RSWMKNQGIPDHEFDGRPIIGICNTWSELTPCNAHFRKLAEHVKRGISEAGGFPVEFPVF 84 R+ ++ G+ D +P++ + +TWS ++PCN + R+LAE V GI AGG P+EF Sbjct: 16 RAMLRATGLDDGAI-AKPLVAVVHTWSNVSPCNLNLRELAEQVAEGIRAAGGTPIEFNTI 74 Query: 85 S------NGESNLRPSAMLTRNLASMDVEEAIRGNPIDAVVLLAGCDKTTPALLMGAASC 138 + G +R S +++R + + +E A+ G+ +DA+V+L GCDKT PA M A Sbjct: 75 AVTDGIAMGTPGMRAS-LISREVITDSIELAVDGHCLDAMVVLCGCDKTIPAAAMAMARL 133 Query: 139 DVPAIVVSGGPMLNGKLEGKNIGSGTAVWQLHEALKA---GEIDVHHFLSAEAGMSRSAG 195 D+PA+ + GG + +G + I + Q+ EA+ A G+ID + E AG Sbjct: 134 DIPAVALYGGTIAHGTHDAHPI----TIQQVFEAVGAHGAGKIDDAELAAVERDACPGAG 189 Query: 196 TCNTMGTASTMACMAEALGVALPHNAAIPAVDSRRYVLAHMSGIRIVEMALEGLVLSKIL 255 C TA+TMA + LG++ IPA + A G +++ E ++ Sbjct: 190 ACGGQFTANTMAMVLTTLGLSPMGFNDIPATHPAKAAAARRCGELVMDCLREQRTPRALI 249 Query: 256 TRAAFENAIRANAAIGGSTNAVIHLKAIAGRIGVPLELEDWMRIGRDTPTIVDLMPSGRF 315 R + NA R AA GSTNAV+HL AIA G P LED+ + TP I DL+P GR+ Sbjct: 250 NRTSLRNAARMVAATAGSTNAVLHLLAIAREAGAPWTLEDFEPASKHTPVIADLLPGGRY 309 Query: 316 PMEEFYYAGGLPAVLRRLGEGGLLPNPDALTVNGKSLWDNVREAPNYD-EEVIRPLDRPL 374 E + AGG V + L G+L D TV G+SL++ AP + ++VI P+ +PL Sbjct: 310 TAVEMFGAGGAARVAQELIAAGML--DDVPTVTGRSLFEEAAAAPRAEQQDVILPVGQPL 367 Query: 375 IADGGIRILRGNLAPRGAVLKPSAASPELLKHRGRAVVFENLDHYKATINDEALDIDASS 434 GG IL GNLAP G +LK A G A VFE+ + A + I Sbjct: 368 KPRGGYSILYGNLAPEGCILK--LAGKGATHFEGTARVFESEEQAFAAVQQGR--IAKGD 423 Query: 435 VMVLKNCGPRGYPGMAEVGNMGLPPKLLRQGV-KDMVRISDARMSGTAYGTVVLHVAPEA 493 V+V++N GP G PGM E+ +G+ L+ +G+ D+ I+D R SG +G +V H+APEA Sbjct: 424 VIVIRNEGPAGGPGMREM--LGVTAALIGRGLGDDVALITDGRFSGATHGFMVGHMAPEA 481 Query: 494 AAGGPLAAVRNGDWIELDCEAGTLHLDITDDELHRRLSDVDPTAAPGVAGQLGKGGYARL 553 GGP+A +R+GD I +D AG + TD +L R P A G L K YARL Sbjct: 482 VRGGPIALLRDGDRIRID--AGLREI-ATDADLAERRQHWTPPAPKVTTGALAK--YARL 536 Lambda K H 0.319 0.136 0.412 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: 804 Number of extensions: 39 Number of successful extensions: 7 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: 583 Length of database: 568 Length adjustment: 36 Effective length of query: 547 Effective length of database: 532 Effective search space: 291004 Effective search space used: 291004 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