Align Xylonate dehydratase (EC 4.2.1.82) (characterized)
to candidate Ga0059261_2649 Ga0059261_2649 Dihydroxyacid dehydratase/phosphogluconate dehydratase
Query= reanno::pseudo6_N2E2:Pf6N2E2_1668 (594 letters) >FitnessBrowser__Korea:Ga0059261_2649 Length = 618 Score = 754 bits (1947), Expect = 0.0 Identities = 370/595 (62%), Positives = 459/595 (77%), Gaps = 4/595 (0%) Query: 4 TPKHRLRSEQWFNDPAHADMTALYVERYMNYGMTREELQSGRPIIGIAQTGSDLTPCNRH 63 T + +LRS WF++P + DMTALY+ERY+N+G++ +EL+SGRPIIGIAQTGSDL+PCNRH Sbjct: 24 TEERKLRSAAWFDNPDNIDMTALYLERYLNFGLSLKELRSGRPIIGIAQTGSDLSPCNRH 83 Query: 64 HLELAQRVKAGIRDAGGIPMEFPVHPIAEQSRRPTAALDRNLAYLGLVEILHGYPLDGVV 123 HL LA+RV+ GIRDAGGI +EFPVHPI E +RPTA LDRNLAYLGLVE L+GYPLDGVV Sbjct: 84 HLVLAERVREGIRDAGGIAIEFPVHPIQETGKRPTAGLDRNLAYLGLVEALYGYPLDGVV 143 Query: 124 LTTGCDKTTPACLMAAATTDLPAIVLSGGPMLDGHHKGELIGSGTVLWHARNLMAAGEID 183 LT GCDKTTPACLMAAAT ++PAI LS GPML+G HKGE GSGT++W AR ++AAGEID Sbjct: 144 LTIGCDKTTPACLMAAATVNIPAIALSVGPMLNGWHKGERTGSGTIVWKARQMLAAGEID 203 Query: 184 YEGFMEMTTAASPSVGHCNTMGTALSMNALAEALGMSLPGCASIPAPYRERGQMAYATGK 243 + F+ + +++PS G+CNTMGTA +MN+LAEALGMSLPG A+IPAP+R+R ++AY TG Sbjct: 204 DDEFIRLVASSAPSTGYCNTMGTATTMNSLAEALGMSLPGSAAIPAPHRDRQEVAYQTGL 263 Query: 244 RICDLVRQDIRPSQIMTRQAFENAIAVASALGASSNCPPHLIAIARHMGVELSLEDWQRI 303 R +LVR D++PS I+TR+AFENAI V SA+G S+N P HL AIARH+GV+L ++ WQ Sbjct: 264 RAVELVRADVKPSDILTREAFENAIVVNSAIGGSTNAPIHLAAIARHIGVDLPIDAWQEK 323 Query: 304 GEDVPLLVNCMPAGKYLGEGFHRAGGVPSVMHELQKAGRLHEDCATVSGKTIGEIVSNSL 363 G VPLLVN PAG+YLGE ++RAGGVP+V+ +L AG +HED TV+GK+IG Sbjct: 324 GHAVPLLVNLQPAGEYLGEDYYRAGGVPAVVSQLIDAGLIHEDAGTVNGKSIGANCRGVA 383 Query: 364 TSNTDVIHPFDTPLKHRAGFIVLSGNFFDSAIMKMSVVGEAFRKTYLSEPGAENSFEARA 423 + VI PF PLK AGFIVL GN F+SAIMK SV+ + FR YLS P ++FE A Sbjct: 384 IEDEKVIRPFAQPLKDAAGFIVLRGNLFESAIMKTSVISDEFRDRYLSNPDDPDAFEGPA 443 Query: 424 IVFEGPEDYHARIDDPALDIDERCILVIRGVGTVGYPGSAEVVNMAPPAALIKQGIDSLP 483 +VF+GPEDYHARIDDPAL I +L +RG G VGYPG+AEVVNM PPA LI++GI +LP Sbjct: 444 VVFDGPEDYHARIDDPALGITPETLLFMRGAGPVGYPGAAEVVNMRPPAYLIREGIHALP 503 Query: 484 CLGDGRQSGTSASPSILNMSPEAAVGGGLALLKTNDRLKVDLNTRTVNLLIDDAEMAQRR 543 C+GDGRQSGTS SPSILN SPEAA GGLAL++T DR+++DL T ++LI AE+A+RR Sbjct: 504 CIGDGRQSGTSGSPSILNASPEAAAMGGLALIRTGDRVRIDLGKGTADVLIPSAELAERR 563 Query: 544 REWIP----NIPPSQTPWQELYRQLVGQLSTGGCLEPATLHLRVIARSGEPRHSH 594 R PPSQTPWQE+ R+LVGQ+ +G LE A R+ G PR +H Sbjct: 564 RVLAEAGGYRFPPSQTPWQEIQRKLVGQMESGAILEGAERFQRIAQTQGLPRDNH 618 Lambda K H 0.319 0.135 0.407 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: 1171 Number of extensions: 48 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: 594 Length of database: 618 Length adjustment: 37 Effective length of query: 557 Effective length of database: 581 Effective search space: 323617 Effective search space used: 323617 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 (21.7 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