Align L-arabonate dehydratase (EC 4.2.1.25) (characterized)
to candidate CCNA_01488 CCNA_01488 dihydroxyacid dehydratase
Query= reanno::BFirm:BPHYT_RS19730 (577 letters) >FitnessBrowser__Caulo:CCNA_01488 Length = 600 Score = 473 bits (1217), Expect = e-138 Identities = 275/602 (45%), Positives = 376/602 (62%), Gaps = 27/602 (4%) Query: 1 MADSNQTKKPLRSQAWFGLKDRDGF--LHRSWMKNQGIPHDEFD-GRPVIGICNTWSELT 57 M+ N ++ LRS+AWF D L+ N G+ +E G+P+IGI T S+L+ Sbjct: 1 MSVPNVPRRALRSRAWFDNPDNIDMTALYLERYLNFGLTLEELQSGKPIIGIAQTGSDLS 60 Query: 58 PCNAHFRELAEYVKKGVHEAGGLPLEFPVMSLGETNLRPTAMLFRNLASMDVEESIRGNP 117 PCN H LAE V++G+ AGG+ LEFPV + ET RPTA L RNL+ + + E + G P Sbjct: 61 PCNRHHLVLAERVREGIRSAGGIALEFPVHPIQETGKRPTAGLDRNLSYLGLVELLYGYP 120 Query: 118 MDGVILLVGCDKTTPALLMGAASCNLPALAVSGGPMLNGRFRGKNIGSGTGVWQMSEEVR 177 +DGV+L +GCDKTTPA LM AA+ N+PA+A+S GPMLNG +GK GSGT VW+ E + Sbjct: 121 LDGVVLTIGCDKTTPACLMAAATVNIPAIALSVGPMLNGWHKGKRTGSGTIVWKAREMLA 180 Query: 178 AGTMTQEEFTEAESCMNRSRGHCMTMGTASTMASMVESLGMGLPHNAAIPAVDARRQVLA 237 AG + F + + S G+C TMGTA+TM S+ E+LGM LP +AAIPA RQ A Sbjct: 181 AGEIDNAGFIKLVASSAPSTGYCNTMGTATTMNSLTEALGMSLPGSAAIPAPYRDRQENA 240 Query: 238 HLAGRRIVDMVREDLTMDKILTRQAFENAIRTNAAIGGSTNAVVHLIALAKRIGVELSLE 297 + G RIV+MV EDL ILTR+AF NAI N+AIGGSTNA +HL ALA+ + V+L+LE Sbjct: 241 YRTGLRIVEMVAEDLKPSDILTREAFLNAIVVNSAIGGSTNAPIHLNALARHMDVDLTLE 300 Query: 298 DWE-LGSNVPCLVNLQPSGEYLMEDFYYAGGLPAVLKQLGEQGLLHKEALTVNGKTLWDN 356 DWE G +VP LVNLQP+GEYL ED+Y AGG+PAV QL EQGL+H++A V+G+++ + Sbjct: 301 DWETAGKDVPLLVNLQPAGEYLGEDYYRAGGVPAVFGQLIEQGLIHQDARAVSGQSIGEQ 360 Query: 357 VRNAANYDEKVITTFAEPFKPKAGIAVLKGNLAPNGAVIKPSAATASLLKH--------- 407 R A DE VI FA P AG A+++GNL N A++K S + Sbjct: 361 YRGAVIEDEDVIRPFARPLVEHAGFAIMRGNLF-NSAIMKTSVISEEFRARYLSNPDDPD 419 Query: 408 --RGRAVVFENIEELHAKIDDESLDIDEHCIMVLKGAGPKGYPGFAEVGNMPLPKKVLQK 465 G A+VF+ E+ H +IDD +L I + I+ ++GAGP GYPG AEV NM P ++++ Sbjct: 420 AFEGNAIVFDGPEDYHHRIDDPALGITAYSILFMRGAGPIGYPGSAEVVNMRAPNYLIKQ 479 Query: 466 GITDMVRISDGRMSGTAYGAVVLHVSPEAAAGGPLAFVQTGDMIELDVEERRLHLDVTDE 525 GI + I DGR SGT+ +L+ SPEAAAGG LA ++TGD + D+ + R+ + V+ Sbjct: 480 GIHQLPCIGDGRQSGTSGSPSILNASPEAAAGGGLALLKTGDRVRFDLRKSRVDVLVSAS 539 Query: 526 ELARRRAAWQA------PEAPKRGYYKLYVEHVLQADQGADLDFLVG----SSGAPVPRD 575 E+ RR A +A PE+ + + ++ V Q D GA L+ V + +PRD Sbjct: 540 EVVERRRALEAAGGYAYPES-QTPWQEIQRAVVGQMDTGAVLEPAVKYQRIAQTKGLPRD 598 Query: 576 SH 577 +H Sbjct: 599 NH 600 Lambda K H 0.318 0.135 0.401 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: 909 Number of extensions: 51 Number of successful extensions: 5 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: 577 Length of database: 600 Length adjustment: 37 Effective length of query: 540 Effective length of database: 563 Effective search space: 304020 Effective search space used: 304020 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