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 CCNA_00862 CCNA_00862 xylonate dehydratase xylD
Query= SwissProt::B5ZZ34 (579 letters) >FitnessBrowser__Caulo:CCNA_00862 Length = 591 Score = 451 bits (1159), Expect = e-131 Identities = 242/572 (42%), Positives = 351/572 (61%), Gaps = 16/572 (2%) Query: 8 PRKLRSQEWYGGTSR---DVIYHRGWLKNQGYPHDLFDGRPVIGILNTWSDMTPCNGHLR 64 PR+ RS++W+ +Y ++ P +L G+P+IGI T SD++PCN Sbjct: 6 PRRFRSRDWFDNPDHIDMTALYLERFMNYGITPEELRSGKPIIGIAQTGSDISPCNRIHL 65 Query: 65 ELAEKVKAGVWEAGGFPLEVPVFSASENTFRPTAMMYRNLAALAVEEAIRGQPMDGCVLL 124 +L ++V+ G+ +AGG P+E PV EN RPTA + RNL+ L + E + G P+D VL Sbjct: 66 DLVQRVRDGIRDAGGIPMEFPVHPIFENCRRPTAALDRNLSYLGLVETLHGYPIDAVVLT 125 Query: 125 VGCDKTTPSLLMGAASCDLPSIVVTGGPMLNGYFRGERVGSGTHLWKFSEMVKAGEMTQA 184 GCDKTTP+ +M A + ++P+IV++GGPML+G+ E VGSGT +W+ + AGE+T+ Sbjct: 126 TGCDKTTPAGIMAATTVNIPAIVLSGGPMLDGWHENELVGSGTVIWRSRRKLAAGEITEE 185 Query: 185 EFLEAEASMSRSSGTCNTMGTASTMASMAEALGMALSGNAAIPGVDSRRKVMAQLTGRRI 244 EF++ AS + S+G CNTMGTASTM ++AEALG++L+G AAIP R MA TG+RI Sbjct: 186 EFIDRAASSAPSAGHCNTMGTASTMNAVAEALGLSLTGCAAIPAPYRERGQMAYKTGQRI 245 Query: 245 VQMVKDDLKPSEIMTKQAFENAIRTNAAIGGSTNAVIHLLAIAGRVGIDLSLDDWDRCGR 304 V + DD+KP +I+TKQAFENAI AA GGSTNA H++A+A G++++ DDW R Sbjct: 246 VDLAYDDVKPLDILTKQAFENAIALVAAAGGSTNAQPHIVAMARHAGVEITADDW-RAAY 304 Query: 305 DVPTIVNLMPSGKYLMEEFFYAGGLPVVLKRLGEAGLLHKDALTVSGETVWDEVKDVVNW 364 D+P IVN+ P+GKYL E F AGG P VL L + G LH D LTV+G+T+ + ++ Sbjct: 305 DIPLIVNMQPAGKYLGERFHRAGGAPAVLWELLQQGRLHGDVLTVTGKTMSENLQGRETS 364 Query: 365 NEDVILPAEKALTSSGGIVVLRGNLAPKGAVLKPSAASPHLL-----------VHKGRAV 413 + +VI P + L G +VL+GNL A++K S V + RA+ Sbjct: 365 DREVIFPYHEPLAEKAGFLVLKGNLF-DFAIMKSSVIGEEFRKRYLSQPGQEGVFEARAI 423 Query: 414 VFEDIDDYKAKINDDNLDIDENCIMVMKNCGPKGYPGMAEVGNMGLPPKVLKKGILDMVR 473 VF+ DDY +IND L+IDE CI+V++ GP G+PG AEV NM P +LKKGI+ + Sbjct: 424 VFDGSDDYHKRINDPALEIDERCILVIRGAGPIGWPGSAEVVNMQPPDHLLKKGIMSLPT 483 Query: 474 ISDARMSGTAYGTVVLHTSPEAAVGGPLAVVKNGDMIELDVPNRRLHLDISDEELARRLA 533 + D R SGTA +L+ SPE+A+GG L+ ++ GD I +D+ R + + +A R Sbjct: 484 LGDGRQSGTADSPSILNASPESAIGGGLSWLRTGDTIRIDLNTGRCDALVDEATIAARKQ 543 Query: 534 EWQPNHDLPTSGYAFLHQQHVEGADTGADLDF 565 + P + + +++ H DTG L+F Sbjct: 544 DGIPAVPATMTPWQEIYRAHASQLDTGGVLEF 575 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: 957 Number of extensions: 57 Number of successful extensions: 3 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: 591 Length adjustment: 37 Effective length of query: 542 Effective length of database: 554 Effective search space: 300268 Effective search space used: 300268 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