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_01488 CCNA_01488 dihydroxyacid dehydratase
Query= SwissProt::B5ZZ34 (579 letters) >FitnessBrowser__Caulo:CCNA_01488 Length = 600 Score = 450 bits (1158), Expect = e-131 Identities = 252/574 (43%), Positives = 354/574 (61%), Gaps = 19/574 (3%) Query: 9 RKLRSQEWYGGTSR---DVIYHRGWLKNQGYPHDLFDGRPVIGILNTWSDMTPCNGHLRE 65 R LRS+ W+ +Y +L +L G+P+IGI T SD++PCN H Sbjct: 9 RALRSRAWFDNPDNIDMTALYLERYLNFGLTLEELQSGKPIIGIAQTGSDLSPCNRHHLV 68 Query: 66 LAEKVKAGVWEAGGFPLEVPVFSASENTFRPTAMMYRNLAALAVEEAIRGQPMDGCVLLV 125 LAE+V+ G+ AGG LE PV E RPTA + RNL+ L + E + G P+DG VL + Sbjct: 69 LAERVREGIRSAGGIALEFPVHPIQETGKRPTAGLDRNLSYLGLVELLYGYPLDGVVLTI 128 Query: 126 GCDKTTPSLLMGAASCDLPSIVVTGGPMLNGYFRGERVGSGTHLWKFSEMVKAGEMTQAE 185 GCDKTTP+ LM AA+ ++P+I ++ GPMLNG+ +G+R GSGT +WK EM+ AGE+ A Sbjct: 129 GCDKTTPACLMAAATVNIPAIALSVGPMLNGWHKGKRTGSGTIVWKAREMLAAGEIDNAG 188 Query: 186 FLEAEASMSRSSGTCNTMGTASTMASMAEALGMALSGNAAIPGVDSRRKVMAQLTGRRIV 245 F++ AS + S+G CNTMGTA+TM S+ EALGM+L G+AAIP R+ A TG RIV Sbjct: 189 FIKLVASSAPSTGYCNTMGTATTMNSLTEALGMSLPGSAAIPAPYRDRQENAYRTGLRIV 248 Query: 246 QMVKDDLKPSEIMTKQAFENAIRTNAAIGGSTNAVIHLLAIAGRVGIDLSLDDWDRCGRD 305 +MV +DLKPS+I+T++AF NAI N+AIGGSTNA IHL A+A + +DL+L+DW+ G+D Sbjct: 249 EMVAEDLKPSDILTREAFLNAIVVNSAIGGSTNAPIHLNALARHMDVDLTLEDWETAGKD 308 Query: 306 VPTIVNLMPSGKYLMEEFFYAGGLPVVLKRLGEAGLLHKDALTVSGETVWDEVKDVVNWN 365 VP +VNL P+G+YL E+++ AGG+P V +L E GL+H+DA VSG+++ ++ + V + Sbjct: 309 VPLLVNLQPAGEYLGEDYYRAGGVPAVFGQLIEQGLIHQDARAVSGQSIGEQYRGAVIED 368 Query: 366 EDVILPAEKALTSSGGIVVLRGNLAPKGAVLKPSAASPHLLVH-----------KGRAVV 414 EDVI P + L G ++RGNL A++K S S +G A+V Sbjct: 369 EDVIRPFARPLVEHAGFAIMRGNLF-NSAIMKTSVISEEFRARYLSNPDDPDAFEGNAIV 427 Query: 415 FEDIDDYKAKINDDNLDIDENCIMVMKNCGPKGYPGMAEVGNMGLPPKVLKKGILDMVRI 474 F+ +DY +I+D L I I+ M+ GP GYPG AEV NM P ++K+GI + I Sbjct: 428 FDGPEDYHHRIDDPALGITAYSILFMRGAGPIGYPGSAEVVNMRAPNYLIKQGIHQLPCI 487 Query: 475 SDARMSGTAYGTVVLHTSPEAAVGGPLAVVKNGDMIELDVPNRRLHLDISDEELA--RRL 532 D R SGT+ +L+ SPEAA GG LA++K GD + D+ R+ + +S E+ RR Sbjct: 488 GDGRQSGTSGSPSILNASPEAAAGGGLALLKTGDRVRFDLRKSRVDVLVSASEVVERRRA 547 Query: 533 AEWQPNHDLPTSGYAFLHQQH--VEGADTGADLD 564 E + P S + Q V DTGA L+ Sbjct: 548 LEAAGGYAYPESQTPWQEIQRAVVGQMDTGAVLE 581 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: 928 Number of extensions: 59 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: 600 Length adjustment: 37 Effective length of query: 542 Effective length of database: 563 Effective search space: 305146 Effective search space used: 305146 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