Align L-arabonate dehydratase (EC 4.2.1.25) (characterized)
to candidate Ga0059261_2649 Ga0059261_2649 Dihydroxyacid dehydratase/phosphogluconate dehydratase
Query= reanno::BFirm:BPHYT_RS19730 (577 letters) >FitnessBrowser__Korea:Ga0059261_2649 Length = 618 Score = 465 bits (1197), Expect = e-135 Identities = 258/539 (47%), Positives = 348/539 (64%), Gaps = 16/539 (2%) Query: 8 KKPLRSQAWFGLKDRDGF--LHRSWMKNQGIPHDEF-DGRPVIGICNTWSELTPCNAHFR 64 ++ LRS AWF D L+ N G+ E GRP+IGI T S+L+PCN H Sbjct: 26 ERKLRSAAWFDNPDNIDMTALYLERYLNFGLSLKELRSGRPIIGIAQTGSDLSPCNRHHL 85 Query: 65 ELAEYVKKGVHEAGGLPLEFPVMSLGETNLRPTAMLFRNLASMDVEESIRGNPMDGVILL 124 LAE V++G+ +AGG+ +EFPV + ET RPTA L RNLA + + E++ G P+DGV+L Sbjct: 86 VLAERVREGIRDAGGIAIEFPVHPIQETGKRPTAGLDRNLAYLGLVEALYGYPLDGVVLT 145 Query: 125 VGCDKTTPALLMGAASCNLPALAVSGGPMLNGRFRGKNIGSGTGVWQMSEEVRAGTMTQE 184 +GCDKTTPA LM AA+ N+PA+A+S GPMLNG +G+ GSGT VW+ + + AG + + Sbjct: 146 IGCDKTTPACLMAAATVNIPAIALSVGPMLNGWHKGERTGSGTIVWKARQMLAAGEIDDD 205 Query: 185 EFTEAESCMNRSRGHCMTMGTASTMASMVESLGMGLPHNAAIPAVDARRQVLAHLAGRRI 244 EF + S G+C TMGTA+TM S+ E+LGM LP +AAIPA RQ +A+ G R Sbjct: 206 EFIRLVASSAPSTGYCNTMGTATTMNSLAEALGMSLPGSAAIPAPHRDRQEVAYQTGLRA 265 Query: 245 VDMVREDLTMDKILTRQAFENAIRTNAAIGGSTNAVVHLIALAKRIGVELSLEDW-ELGS 303 V++VR D+ ILTR+AFENAI N+AIGGSTNA +HL A+A+ IGV+L ++ W E G Sbjct: 266 VELVRADVKPSDILTREAFENAIVVNSAIGGSTNAPIHLAAIARHIGVDLPIDAWQEKGH 325 Query: 304 NVPCLVNLQPSGEYLMEDFYYAGGLPAVLKQLGEQGLLHKEALTVNGKTLWDNVRNAANY 363 VP LVNLQP+GEYL ED+Y AGG+PAV+ QL + GL+H++A TVNGK++ N R A Sbjct: 326 AVPLLVNLQPAGEYLGEDYYRAGGVPAVVSQLIDAGLIHEDAGTVNGKSIGANCRGVAIE 385 Query: 364 DEKVITTFAEPFKPKAGIAVLKGNLAPNGAVIKPSAATASLLKH-----------RGRAV 412 DEKVI FA+P K AG VL+GNL A++K S + G AV Sbjct: 386 DEKVIRPFAQPLKDAAGFIVLRGNLF-ESAIMKTSVISDEFRDRYLSNPDDPDAFEGPAV 444 Query: 413 VFENIEELHAKIDDESLDIDEHCIMVLKGAGPKGYPGFAEVGNMPLPKKVLQKGITDMVR 472 VF+ E+ HA+IDD +L I ++ ++GAGP GYPG AEV NM P ++++GI + Sbjct: 445 VFDGPEDYHARIDDPALGITPETLLFMRGAGPVGYPGAAEVVNMRPPAYLIREGIHALPC 504 Query: 473 ISDGRMSGTAYGAVVLHVSPEAAAGGPLAFVQTGDMIELDVEERRLHLDVTDEELARRR 531 I DGR SGT+ +L+ SPEAAA G LA ++TGD + +D+ + + + ELA RR Sbjct: 505 IGDGRQSGTSGSPSILNASPEAAAMGGLALIRTGDRVRIDLGKGTADVLIPSAELAERR 563 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: 993 Number of extensions: 59 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: 577 Length of database: 618 Length adjustment: 37 Effective length of query: 540 Effective length of database: 581 Effective search space: 313740 Effective search space used: 313740 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