Align L-arabinonate dehydratase; ArDHT; D-fuconate dehydratase; Galactonate dehydratase; L-arabonate dehydratase; EC 4.2.1.25; EC 4.2.1.67; EC 4.2.1.6 (characterized)
to candidate Ac3H11_3523 Xylonate dehydratase (EC 4.2.1.82)
Query= SwissProt::B5ZZ34 (579 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_3523 Length = 593 Score = 439 bits (1130), Expect = e-127 Identities = 239/572 (41%), Positives = 350/572 (61%), Gaps = 16/572 (2%) Query: 9 RKLRSQEWYGGTSRD---VIYHRGWLKNQGYPHDLFDGRPVIGILNTWSDMTPCNGHLRE 65 R RS+EW+ R +Y ++ P +L GRP+IGI T SD++PCN + Sbjct: 7 RPFRSREWFAAPERSDMTALYLERFMNYGLTPEELRSGRPIIGIAQTGSDLSPCNRIHLD 66 Query: 66 LAEKVKAGVWEAGGFPLEVPVFSASENTFRPTAMMYRNLAALAVEEAIRGQPMDGCVLLV 125 LA +V+ G+ +AGG P+E PV EN RPTA + RNLA L + E + G P+D VL Sbjct: 67 LARRVRDGIRDAGGIPMEFPVHPIFENCRRPTAALDRNLAYLGLVEILYGYPIDAVVLTT 126 Query: 126 GCDKTTPSLLMGAASCDLPSIVVTGGPMLNGYFRGERVGSGTHLWKFSEMVKAGEMTQAE 185 GCDKTTP+ +M A++ D+P+IV++GGPML+G+ G+ VGSGT +W+ + AGE+ + E Sbjct: 127 GCDKTTPAGVMAASTVDIPAIVLSGGPMLDGWHDGQLVGSGTVIWRSRRQLAAGEIDEEE 186 Query: 186 FLEAEASMSRSSGTCNTMGTASTMASMAEALGMALSGNAAIPGVDSRRKVMAQLTGRRIV 245 FL+ + + S+G CNTMGTASTM ++AEALG++L G AAIP R MA TGRRIV Sbjct: 187 FLQRACNSAPSAGHCNTMGTASTMNAVAEALGLSLPGCAAIPAPYRERGQMAYETGRRIV 246 Query: 246 QMVKDDLKPSEIMTKQAFENAIRTNAAIGGSTNAVIHLLAIAGRVGIDLSLDDWDRCGRD 305 +M +DL+PS I+T+++F NA+ + GGS+NA +H++A+A G+ L+ DW D Sbjct: 247 EMAYEDLRPSRILTRESFLNALSVVSVAGGSSNAQVHIMAMARHAGVQLTAQDWTDHAYD 306 Query: 306 VPTIVNLMPSGKYLMEEFFYAGGLPVVLKRLGEAGLLHKDALTVSGETVWDEVKDVVNWN 365 +P ++N+ P+G++L E FF AGG+P ++ L +AG LH D +V+G+TV + ++ + Sbjct: 307 LPLLLNMQPAGQFLGERFFRAGGVPALMWELQQAGKLHADCASVTGKTVGENLQGRETHD 366 Query: 366 EDVILPAEKALTSSGGIVVLRGNLAPKGAVLKPSAASPHLL-----------VHKGRAVV 414 +VI P L G +VL GNL G ++K S S + + RAVV Sbjct: 367 REVIRPFSNPLMHKAGFMVLSGNLFDFG-IMKTSVISEAFRQRYLSRPGQEGIFEARAVV 425 Query: 415 FEDIDDYKAKINDDNLDIDENCIMVMKNCGPKGYPGMAEVGNMGLPPKVLKKGILDMVRI 474 FE DDY A+IND L+IDE CI+VM+ GP G+PG AEV NM P ++K+GI + + Sbjct: 426 FEGADDYHARINDPALNIDEGCILVMRGAGPIGWPGSAEVVNMQPPDALIKRGINTLPTL 485 Query: 475 SDARMSGTAYGTVVLHTSPEAAVGGPLAVVKNGDMIELDVPNRRLHLDISDEELARRLAE 534 D R SGTA +L+ SPE+AVGG L+ +++GD + +D+ R ++ EE+ARR + Sbjct: 486 GDGRQSGTADSPSILNASPESAVGGGLSWLQSGDTVRIDLNTGRCDALVTPEEIARRKRD 545 Query: 535 W-QPNHDLPTSGYAFLHQQHVEGADTGADLDF 565 P S + L+++ GA LDF Sbjct: 546 LPAPPVPASQSPWEALYREKTGQLADGATLDF 577 Lambda K H 0.318 0.135 0.408 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: 988 Number of extensions: 55 Number of successful extensions: 2 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: 579 Length of database: 593 Length adjustment: 37 Effective length of query: 542 Effective length of database: 556 Effective search space: 301352 Effective search space used: 301352 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: 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