Align L-arabonate dehydratase (EC 4.2.1.25) (characterized)
to candidate 3606698 Dshi_0129 dihydroxy-acid dehydratase (RefSeq)
Query= reanno::WCS417:GFF2156 (578 letters) >FitnessBrowser__Dino:3606698 Length = 577 Score = 309 bits (791), Expect = 2e-88 Identities = 189/526 (35%), Positives = 287/526 (54%), Gaps = 17/526 (3%) Query: 24 YRSWMKNQGIADHQFHGKPIIGICNTWSELTPCNAHFRQIAEHVKRGVIEAGGFPVEFPV 83 +RS+ G+ + + H +P++G+ W+E PCN + A+ VK GV +A G P EF Sbjct: 25 HRSYYYAMGMTEEEIH-QPLVGVATCWNEAAPCNIALSRQAQAVKMGVKQASGTPREFTT 83 Query: 84 FS------NGESNLRPTAMLTRNLASMDVEEAIRGNPIDGVVLLTGCDKTTPALLMGAAS 137 + G +R +++ +R + VE +RG+ D +V L GCDK+ P ++M Sbjct: 84 ITVTDGIAMGHEGMR-SSLASREAIADTVELTMRGHCYDAIVGLAGCDKSLPGMMMAMVR 142 Query: 138 CDVPAIVVTGGPMLNGKHKGQDIGSGTVVWQLSEQVKAGTITLDDFLAAEGGMSRSAGTC 197 +VP++ + GG +L G+ G+D+ V + + +AG T + E SAG C Sbjct: 143 LNVPSVFIYGGSILPGRLNGEDVTVQDVFEAVGKH-QAGNYTDAELEVLERVACPSAGAC 201 Query: 198 NTMGTASTMACMAEALGTSLPHNAAIPAVDARRYVLAHMSGMRAVEMVREDLKLSKILTK 257 TA+TMAC++EA+G +LP++A PA R SG ++++ + ++ I+T+ Sbjct: 202 GGQFTANTMACVSEAIGLALPNSAGAPAPYESRDQYGEASGRAVMDLIEKGIRARDIVTR 261 Query: 258 EAFENAIRVNAAIGGSTNAVIHLKAIAGRIGVELDLDDWTRIGRGMPTIVDLQPSGRFLM 317 ++ ENA R+ A GGSTNA +HL AIA G+E L D I R P VDL+P G+++ Sbjct: 262 KSLENAARIVACTGGSTNAGLHLPAIAHEAGIEFTLQDVCDIFRDTPYFVDLKPGGKYVA 321 Query: 318 EEFYYAGGLPAVLRRLGEANLIPHPNALTVNGKSLGENTQDSPIYGQDEVIRTLDNPIRA 377 ++ Y AGG+P V+R L A LI H + +TV G S+GE + VI +D P+ Sbjct: 322 KDMYEAGGVPVVMRELRRAGLI-HEDCMTVTGYSIGEELDKVTLEADGRVIYPVDTPLST 380 Query: 378 DGGICVLRGNLAPLGAVLKPSAASPALMQHRGRAVVFE-NFDMYKARINDPELDVDANSI 436 GG+ L GNLAP GA++K + S + G A VFE D ++A N + D + Sbjct: 381 TGGVVGLEGNLAPEGAIVKIAGMSDDQLVFTGPARVFECEEDAFEAVQNRAYAEGD---V 437 Query: 437 LVMKNCGPKGYPGMAEVGNMGLPAKLLAQGVTDMVR-ISDARMSGTAYGTVVLHVAPEAA 495 V++N GP G PGM E+ + A L QG+ V I+D R SG G V HV PEAA Sbjct: 438 FVIRNEGPAGGPGMREM--LATTAALSGQGMGKKVALITDGRFSGATRGFCVGHVGPEAA 495 Query: 496 AGGPLATVKEGDWIELDCANGRLHLDIPDAELAARMADLAPPQKLI 541 GGP+A +K+GD I +D G L + + + ELAAR + P++ I Sbjct: 496 HGGPIAMLKDGDMITIDALKGELSVALSEDELAARKDAWSGPRETI 541 Lambda K H 0.319 0.136 0.413 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: 892 Number of extensions: 51 Number of successful extensions: 7 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: 578 Length of database: 577 Length adjustment: 36 Effective length of query: 542 Effective length of database: 541 Effective search space: 293222 Effective search space used: 293222 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 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