Align L-arabonate dehydratase (EC 4.2.1.25) (characterized)
to candidate Ac3H11_3523 Xylonate dehydratase (EC 4.2.1.82)
Query= reanno::BFirm:BPHYT_RS19730 (577 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_3523 Length = 593 Score = 454 bits (1168), Expect = e-132 Identities = 247/589 (41%), Positives = 366/589 (62%), Gaps = 20/589 (3%) Query: 8 KKPLRSQAWFGLKDRDGF--LHRSWMKNQGIPHDEF-DGRPVIGICNTWSELTPCNAHFR 64 ++P RS+ WF +R L+ N G+ +E GRP+IGI T S+L+PCN Sbjct: 6 RRPFRSREWFAAPERSDMTALYLERFMNYGLTPEELRSGRPIIGIAQTGSDLSPCNRIHL 65 Query: 65 ELAEYVKKGVHEAGGLPLEFPVMSLGETNLRPTAMLFRNLASMDVEESIRGNPMDGVILL 124 +LA V+ G+ +AGG+P+EFPV + E RPTA L RNLA + + E + G P+D V+L Sbjct: 66 DLARRVRDGIRDAGGIPMEFPVHPIFENCRRPTAALDRNLAYLGLVEILYGYPIDAVVLT 125 Query: 125 VGCDKTTPALLMGAASCNLPALAVSGGPMLNGRFRGKNIGSGTGVWQMSEEVRAGTMTQE 184 GCDKTTPA +M A++ ++PA+ +SGGPML+G G+ +GSGT +W+ ++ AG + +E Sbjct: 126 TGCDKTTPAGVMAASTVDIPAIVLSGGPMLDGWHDGQLVGSGTVIWRSRRQLAAGEIDEE 185 Query: 185 EFTEAESCMNRSRGHCMTMGTASTMASMVESLGMGLPHNAAIPAVDARRQVLAHLAGRRI 244 EF + S GHC TMGTASTM ++ E+LG+ LP AAIPA R +A+ GRRI Sbjct: 186 EFLQRACNSAPSAGHCNTMGTASTMNAVAEALGLSLPGCAAIPAPYRERGQMAYETGRRI 245 Query: 245 VDMVREDLTMDKILTRQAFENAIRTNAAIGGSTNAVVHLIALAKRIGVELSLEDW-ELGS 303 V+M EDL +ILTR++F NA+ + GGS+NA VH++A+A+ GV+L+ +DW + Sbjct: 246 VEMAYEDLRPSRILTRESFLNALSVVSVAGGSSNAQVHIMAMARHAGVQLTAQDWTDHAY 305 Query: 304 NVPCLVNLQPSGEYLMEDFYYAGGLPAVLKQLGEQGLLHKEALTVNGKTLWDNVRNAANY 363 ++P L+N+QP+G++L E F+ AGG+PA++ +L + G LH + +V GKT+ +N++ + Sbjct: 306 DLPLLLNMQPAGQFLGERFFRAGGVPALMWELQQAGKLHADCASVTGKTVGENLQGRETH 365 Query: 364 DEKVITTFAEPFKPKAGIAVLKGNLAPNGAVIKPSAATASLLKH-----------RGRAV 412 D +VI F+ P KAG VL GNL G ++K S + + + RAV Sbjct: 366 DREVIRPFSNPLMHKAGFMVLSGNLFDFG-IMKTSVISEAFRQRYLSRPGQEGIFEARAV 424 Query: 413 VFENIEELHAKIDDESLDIDEHCIMVLKGAGPKGYPGFAEVGNMPLPKKVLQKGITDMVR 472 VFE ++ HA+I+D +L+IDE CI+V++GAGP G+PG AEV NM P ++++GI + Sbjct: 425 VFEGADDYHARINDPALNIDEGCILVMRGAGPIGWPGSAEVVNMQPPDALIKRGINTLPT 484 Query: 473 ISDGRMSGTAYGAVVLHVSPEAAAGGPLAFVQTGDMIELDVEERRLHLDVTDEELARRRA 532 + DGR SGTA +L+ SPE+A GG L+++Q+GD + +D+ R VT EE+ARR+ Sbjct: 485 LGDGRQSGTADSPSILNASPESAVGGGLSWLQSGDTVRIDLNTGRCDALVTPEEIARRKR 544 Query: 533 AWQAPEAP--KRGYYKLYVEHVLQADQGADLDFLVGSS--GAPVPRDSH 577 AP P + + LY E Q GA LDF + PR +H Sbjct: 545 DLPAPPVPASQSPWEALYREKTGQLADGATLDFALAFQRISEKTPRHNH 593 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: 925 Number of extensions: 57 Number of successful extensions: 4 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: 593 Length adjustment: 37 Effective length of query: 540 Effective length of database: 556 Effective search space: 300240 Effective search space used: 300240 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