Align L-arabonate dehydratase (EC 4.2.1.25) (characterized)
to candidate CCNA_00862 CCNA_00862 xylonate dehydratase xylD
Query= reanno::BFirm:BPHYT_RS19730 (577 letters) >FitnessBrowser__Caulo:CCNA_00862 Length = 591 Score = 457 bits (1175), Expect = e-133 Identities = 251/591 (42%), Positives = 364/591 (61%), Gaps = 18/591 (3%) Query: 4 SNQTKKPLRSQAWFGLKDRDGF--LHRSWMKNQGIPHDEF-DGRPVIGICNTWSELTPCN 60 SN+T + RS+ WF D L+ N GI +E G+P+IGI T S+++PCN Sbjct: 2 SNRTPRRFRSRDWFDNPDHIDMTALYLERFMNYGITPEELRSGKPIIGIAQTGSDISPCN 61 Query: 61 AHFRELAEYVKKGVHEAGGLPLEFPVMSLGETNLRPTAMLFRNLASMDVEESIRGNPMDG 120 +L + V+ G+ +AGG+P+EFPV + E RPTA L RNL+ + + E++ G P+D Sbjct: 62 RIHLDLVQRVRDGIRDAGGIPMEFPVHPIFENCRRPTAALDRNLSYLGLVETLHGYPIDA 121 Query: 121 VILLVGCDKTTPALLMGAASCNLPALAVSGGPMLNGRFRGKNIGSGTGVWQMSEEVRAGT 180 V+L GCDKTTPA +M A + N+PA+ +SGGPML+G + +GSGT +W+ ++ AG Sbjct: 122 VVLTTGCDKTTPAGIMAATTVNIPAIVLSGGPMLDGWHENELVGSGTVIWRSRRKLAAGE 181 Query: 181 MTQEEFTEAESCMNRSRGHCMTMGTASTMASMVESLGMGLPHNAAIPAVDARRQVLAHLA 240 +T+EEF + + S GHC TMGTASTM ++ E+LG+ L AAIPA R +A+ Sbjct: 182 ITEEEFIDRAASSAPSAGHCNTMGTASTMNAVAEALGLSLTGCAAIPAPYRERGQMAYKT 241 Query: 241 GRRIVDMVREDLTMDKILTRQAFENAIRTNAAIGGSTNAVVHLIALAKRIGVELSLEDWE 300 G+RIVD+ +D+ ILT+QAFENAI AA GGSTNA H++A+A+ GVE++ +DW Sbjct: 242 GQRIVDLAYDDVKPLDILTKQAFENAIALVAAAGGSTNAQPHIVAMARHAGVEITADDWR 301 Query: 301 LGSNVPCLVNLQPSGEYLMEDFYYAGGLPAVLKQLGEQGLLHKEALTVNGKTLWDNVRNA 360 ++P +VN+QP+G+YL E F+ AGG PAVL +L +QG LH + LTV GKT+ +N++ Sbjct: 302 AAYDIPLIVNMQPAGKYLGERFHRAGGAPAVLWELLQQGRLHGDVLTVTGKTMSENLQGR 361 Query: 361 ANYDEKVITTFAEPFKPKAGIAVLKGNLAPNGAVIKPSAATASLLKH-----------RG 409 D +VI + EP KAG VLKGNL + A++K S K Sbjct: 362 ETSDREVIFPYHEPLAEKAGFLVLKGNLF-DFAIMKSSVIGEEFRKRYLSQPGQEGVFEA 420 Query: 410 RAVVFENIEELHAKIDDESLDIDEHCIMVLKGAGPKGYPGFAEVGNMPLPKKVLQKGITD 469 RA+VF+ ++ H +I+D +L+IDE CI+V++GAGP G+PG AEV NM P +L+KGI Sbjct: 421 RAIVFDGSDDYHKRINDPALEIDERCILVIRGAGPIGWPGSAEVVNMQPPDHLLKKGIMS 480 Query: 470 MVRISDGRMSGTAYGAVVLHVSPEAAAGGPLAFVQTGDMIELDVEERRLHLDVTDEEL-A 528 + + DGR SGTA +L+ SPE+A GG L++++TGD I +D+ R V + + A Sbjct: 481 LPTLGDGRQSGTADSPSILNASPESAIGGGLSWLRTGDTIRIDLNTGRCDALVDEATIAA 540 Query: 529 RRRAAWQAPEAPKRGYYKLYVEHVLQADQGADLDFLV--GSSGAPVPRDSH 577 R++ A A + ++Y H Q D G L+F V A +PR +H Sbjct: 541 RKQDGIPAVPATMTPWQEIYRAHASQLDTGGVLEFAVKYQDLAAKLPRHNH 591 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: 900 Number of extensions: 45 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: 591 Length adjustment: 36 Effective length of query: 541 Effective length of database: 555 Effective search space: 300255 Effective search space used: 300255 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