Align L-arabonate dehydratase (EC 4.2.1.25) (characterized)
to candidate WP_012385795.1 BIND_RS14500 dihydroxy-acid dehydratase
Query= reanno::BFirm:BPHYT_RS19730 (577 letters) >NCBI__GCF_000019845.1:WP_012385795.1 Length = 599 Score = 480 bits (1236), Expect = e-140 Identities = 278/595 (46%), Positives = 370/595 (62%), Gaps = 25/595 (4%) Query: 8 KKP--LRSQAWFGLKDRDGF--LHRSWMKNQGIPHDEFD-GRPVIGICNTWSELTPCNAH 62 KKP LRS+AWF L+ N G+ E G+P+IGI T S+L+PCN Sbjct: 5 KKPEELRSRAWFDNPANPDMTALYLERYLNYGLTAKELQSGKPIIGIAQTGSDLSPCNRP 64 Query: 63 FRELAEYVKKGVHEAGGLPLEFPVMSLGETNLRPTAMLFRNLASMDVEESIRGNPMDGVI 122 ELA+ V++G+ EAGG+ +EFPV + ET RPTA L RNLA + + E + G P+DGV+ Sbjct: 65 HLELAKRVREGIREAGGIAIEFPVHPIQETGKRPTAALDRNLAYLGLVEILYGYPLDGVV 124 Query: 123 LLVGCDKTTPALLMGAASCNLPALAVSGGPMLNGRFRGKNIGSGTGVWQMSEEVRAGTMT 182 L GCDKTTPA LM AA+ +LPA+ ++GGPMLNG F G+ GSGT +W+ E + G + Sbjct: 125 LTTGCDKTTPACLMAAATVDLPAIVLTGGPMLNGWFNGERTGSGTIIWKARELLAKGEID 184 Query: 183 QEEFTEAESCMNRSRGHCMTMGTASTMASMVESLGMGLPHNAAIPAVDARRQVLAHLAGR 242 ++F E + S G+C TMGTA+TM S+ E+LGM LP AAIPA R +A+ G+ Sbjct: 185 YQKFIELVASSAPSAGYCNTMGTATTMNSLAEALGMSLPGCAAIPAPYRERGQIAYETGK 244 Query: 243 RIVDMVREDLTMDKILTRQAFENAIRTNAAIGGSTNAVVHLIALAKRIGVELSLEDWE-L 301 RIVDMV EDL I+TRQA EN I N+AIGGSTNA +H+ A+A+ +GV L ++DWE + Sbjct: 245 RIVDMVFEDLKPSDIITRQALENVIIVNSAIGGSTNAPIHINAIARHVGVPLEVDDWERV 304 Query: 302 GSNVPCLVNLQPSGEYLMEDFYYAGGLPAVLKQLGEQGLLHKEALTVNGKTLWDNVRNAA 361 G VP +VNLQP+G YL EDF+ AGG+PAV+ +L GL+H+ ALTVNG+T+ DN A Sbjct: 305 GGQVPLIVNLQPAGTYLGEDFHRAGGVPAVVHELMRHGLIHENALTVNGRTMGDNCHERA 364 Query: 362 NYDEKVITTFAEPFKPKAGIAVLKGNLAPNG----AVIKPSAATASLLK------HRGRA 411 D VI TF P AG V++GNL + VI T L GRA Sbjct: 365 ALDADVIRTFETALVPAAGFKVVRGNLFDSAIMKTCVISDEFRTRYLSNPQDPDAFEGRA 424 Query: 412 VVFENIEELHAKIDDESLDIDEHCIMVLKGAGPKGYPGFAEVGNMPLPKKVLQKGITDMV 471 VVF+ E+ H +IDD SL+IDEHC++ ++G G G+PG AEV NM P +LQ+ IT + Sbjct: 425 VVFDGPEDYHQRIDDPSLNIDEHCLLFIRGTGAIGFPGSAEVVNMRAPSYLLQRNITSLP 484 Query: 472 RISDGRMSGTAYGAVVLHVSPEAAAGGPLAFVQTGDMIELDVEERRLHLDVTDEELARRR 531 I DGR SGT+ +L+ SPEAAAGG LA ++TGD + +D+ + R + ++DEELA+RR Sbjct: 485 CIGDGRQSGTSGSPSILNASPEAAAGGGLALLRTGDRVRIDLLKGRADILISDEELAQRR 544 Query: 532 AAWQAPEAPK-----RGYYKLYVEHVLQADQGADLDFLVG----SSGAPVPRDSH 577 A +QA K + ++ V Q QG L V +S VPRDSH Sbjct: 545 ADFQAHGGYKYPPSQTPWQEIQRGIVDQLAQGMVLKPAVKYQRVASTYGVPRDSH 599 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: 981 Number of extensions: 56 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: 599 Length adjustment: 37 Effective length of query: 540 Effective length of database: 562 Effective search space: 303480 Effective search space used: 303480 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