Align L-arabonate dehydratase (EC 4.2.1.25) (characterized)
to candidate WP_012114021.1 XAUT_RS10055 dihydroxy-acid dehydratase
Query= reanno::BFirm:BPHYT_RS19730 (577 letters) >NCBI__GCF_000017645.1:WP_012114021.1 Length = 604 Score = 489 bits (1259), Expect = e-142 Identities = 275/592 (46%), Positives = 375/592 (63%), Gaps = 27/592 (4%) Query: 11 LRSQAWFGLKDRDGF--LHRSWMKNQGIPHDEFD-GRPVIGICNTWSELTPCNAHFRELA 67 LRSQ WF D G L+ N G+ +E G+P+IGI T S+L+PCN H +LA Sbjct: 15 LRSQLWFDNPDNPGMTALYLERYLNFGLTREELQSGKPIIGIAQTGSDLSPCNRHHLDLA 74 Query: 68 EYVKKGVHEAGGLPLEFPVMSLGETNLRPTAMLFRNLASMDVEESIRGNPMDGVILLVGC 127 + V+ G+ GG+P EFPV + ET RPTA L RNLA + + E + G P+DGV+L GC Sbjct: 75 KRVRDGIEAMGGVPFEFPVHPIQETGKRPTAALDRNLAYLGLVEILYGYPLDGVVLTTGC 134 Query: 128 DKTTPALLMGAASCNLPALAVSGGPMLNGRFRGKNIGSGTGVWQMSEEVRAGTMTQEEFT 187 DKTTPA +M AA+ N+PA+ +SGGPMLNG ++G+ GSGT VW+ E AG + EF Sbjct: 135 DKTTPACIMAAATVNIPAIVLSGGPMLNGWWKGERTGSGTVVWKNRERFAAGEIDYNEFM 194 Query: 188 EAESCMNRSRGHCMTMGTASTMASMVESLGMGLPHNAAIPAVDARRQVLAHLAGRRIVDM 247 + + S GHC TMGTASTM ++ E+LGM LP AAIPA R +A+ G+RIVDM Sbjct: 195 DVVASSAPSVGHCNTMGTASTMNALAEALGMSLPGCAAIPAPYRERGQIAYDTGKRIVDM 254 Query: 248 VREDLTMDKILTRQAFENAIRTNAAIGGSTNAVVHLIALAKRIGVELSLEDWE-LGSNVP 306 V EDL ILTR+AFENAIR N+AIGGSTNA +HL A+A+ +GV L+++DW+ +G +P Sbjct: 255 VWEDLKPSDILTREAFENAIRVNSAIGGSTNAPIHLNAIARHVGVPLNVDDWQAVGHKIP 314 Query: 307 CLVNLQPSGEYLMEDFYYAGGLPAVLKQLGEQGLLHKEALTVNGKTLWDNVRNAANYDEK 366 LVNLQP+GEYL E+F+ AGG+PAV+ +L E+G +H+ ALTVNG+++ +N + ++D + Sbjct: 315 LLVNLQPAGEYLGEEFHRAGGVPAVVAELIEKGKIHEGALTVNGRSIGENCKGKLSWDRE 374 Query: 367 VITTFAEPFKPKAGIAVLKGNLAPNGAVIKPSAATASLLKH-----------RGRAVVFE 415 VI T+ P K AG VL GNL N AV+K S + GRAVVFE Sbjct: 375 VIKTYDAPLKEDAGFIVLHGNLF-NNAVMKTSVISPEFRDRFLSNPNDPEAFEGRAVVFE 433 Query: 416 NIEELHAKIDDESLDIDEHCIMVLKGAGPKGYPGFAEVGNMPLPKKVLQKGITDMVRISD 475 E+ H +IDD SL IDE+ ++ ++G GP GYPG AEV NM P +++KGI + I D Sbjct: 434 GPEDYHHRIDDPSLGIDEYTLLFIRGTGPLGYPGGAEVVNMQPPTALIKKGIHALPCIGD 493 Query: 476 GRMSGTAYGAVVLHVSPEAAAGGPLAFVQTGDMIELDVEERRLHLDVTDEELARRRAAWQ 535 GR SGT+ +L+ SPEAAAGG LA ++TGD + +D+ + ++ EELA+RRA Q Sbjct: 494 GRQSGTSGSPSILNASPEAAAGGGLALLKTGDRVRIDLNTCTADILISPEELAQRRADLQ 553 Query: 536 A------PEAPKRGYYKLYVEHVLQADQGADLDFLVG----SSGAPVPRDSH 577 P++ + + ++ V Q D+G L V + VPRD+H Sbjct: 554 GHGGFPMPQS-QTPWQEIQRSMVAQFDEGMVLKPAVKYQRVAQTMGVPRDNH 604 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: 1023 Number of extensions: 60 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: 604 Length adjustment: 37 Effective length of query: 540 Effective length of database: 567 Effective search space: 306180 Effective search space used: 306180 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 24 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