Align Phosphogluconate dehydratase; EC 4.2.1.12 (uncharacterized)
to candidate WP_091380796.1 BLU33_RS19300 dihydroxy-acid dehydratase
Query= curated2:P56111 (608 letters) >NCBI__GCF_900105165.1:WP_091380796.1 Length = 560 Score = 181 bits (460), Expect = 6e-50 Identities = 160/470 (34%), Positives = 233/470 (49%), Gaps = 53/470 (11%) Query: 113 DGITQGYDGMELSLFSRDVIALSTAVGLSHNVFDGAFFLGVCDKIVPGLLIGALSFGNLA 172 DG++ G +GM SL SRD+IA S + +DG L CDK +PG ++ A+ N Sbjct: 82 DGMSNGTEGMRYSLVSRDIIADSIEAVVGAQYYDGVITLPGCDKNMPGSIM-AMGRLNRP 140 Query: 173 SVFVPSGPMVSG------IENYKKAKARQDFAMGKINREELLKVEMQSYHDVGTCTFYGT 226 S+ V G + G + +A G I+ E+ + V + G C T Sbjct: 141 SIMVYGGTIKPGHWKGEDLNIVSAFEALGQKMAGTISPEDFMGVIKNACPSAGACGGIYT 200 Query: 227 ANSNQMMMEFMGLHVANSSFINPNNPLRKVLVEESAKRLASGKVLP--LAKLIDEKSIL- 283 AN+ +E +G+ + SS +NP + E+ A+ LA+GK + LAK I I+ Sbjct: 201 ANTMAAAIEALGMSLPYSS----SNPA--LSEEKKAECLAAGKAIKILLAKDIKPTDIMT 254 Query: 284 -----NALIGLMATGGSTNHTLHLIAIARSCGVILNWDDFDAVSNLIPLLAKVYPNGSAD 338 NA++ +M GGSTN LHLIA+A+S G+ + DDF AVSN IP+LA + P+G Sbjct: 255 REAFENAIVVIMVLGGSTNAVLHLIAMAKSVGIKITQDDFQAVSNRIPVLADMKPSGKYM 314 Query: 339 VNAFEACGGLVFVIKELLKEGLLFEDTHTIMDTETQKGMQNYTKTPFLENNQLVYKDAIN 398 + GG+ V+K +G L T+ T EN Q + Sbjct: 315 MEDLHKVGGVPAVMKYCWDQGWLHGHCLTV------------TGKTIAENLQEI------ 356 Query: 399 HSLNTD---ILRPVSDPFAANGGLKILKGNL--GRAVIKISAIKDEHRKVKARAIVFKTQ 453 S+N D I+ PV +P A G L+IL GNL G +V KI+ E + A VF + Sbjct: 357 PSINFDTQKIILPVENPIKATGHLQILYGNLAEGGSVAKITG--KEGTSFEGPARVFDGE 414 Query: 454 SEFLERFKNKELERDFVAVLPFQGPK-SNGMPELHKLTTNL-GALQDMGYKVALVTDGRM 511 E + ++ +E+ V V+ GPK + GMPE+ K T+ + GA +G VAL+TDGR Sbjct: 415 FELIHGIQSGRVEKGDVVVIRNVGPKGAPGMPEMLKPTSAIFGA--GLGSSVALITDGRF 472 Query: 512 SGAS-GKVPSAIHLSPEGALNGAIIKIKDGDLIELDAPNNALNVLEKDFE 560 SG + G V H++PE G I +KD D I +DA N +NV+ D E Sbjct: 473 SGGTHGFVVG--HITPEAYDGGGIAFVKDNDRIFIDAINRTINVMISDEE 520 Lambda K H 0.318 0.135 0.386 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: 747 Number of extensions: 43 Number of successful extensions: 5 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: 608 Length of database: 560 Length adjustment: 36 Effective length of query: 572 Effective length of database: 524 Effective search space: 299728 Effective search space used: 299728 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