Align phosphogluconate dehydratase (characterized)
to candidate Ac3H11_3523 Xylonate dehydratase (EC 4.2.1.82)
Query= CharProtDB::CH_024239 (603 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_3523 Length = 593 Score = 182 bits (462), Expect = 3e-50 Identities = 148/477 (31%), Positives = 221/477 (46%), Gaps = 45/477 (9%) Query: 146 DGALFLGVCDKIVPGLTMAALSFGHLPAVFVPSGPMASGLPNKEKV-------RIRQLYA 198 D + CDK P MAA S +PA+ + GPM G + + V R R+ A Sbjct: 120 DAVVLTTGCDKTTPAGVMAA-STVDIPAIVLSGGPMLDGWHDGQLVGSGTVIWRSRRQLA 178 Query: 199 EGKVDRMALLESEAASYHAPGTCTFYGTANTNQMVVEFMGMQLPGSSFVHPDSPLRDALT 258 G++D L+ S + G C GTA+T V E +G+ LPG + + R + Sbjct: 179 AGEIDEEEFLQRACNSAPSAGHCNTMGTASTMNAVAEALGLSLPGCAAIPAPYRERGQMA 238 Query: 259 AAAARQVTRMTGNGNEWMPIGKMIDEKVVVNGIVALLATGGSTNHTMHLVAMARAAGIQI 318 R++ M E + +++ + +N + + GGS+N +H++AMAR AG+Q+ Sbjct: 239 YETGRRIVEMA---YEDLRPSRILTRESFLNALSVVSVAGGSSNAQVHIMAMARHAGVQL 295 Query: 319 NWDDFSDLSDVVPLMARLYPNGPADINHFQAAGGVPVLVRELLKAGLLHEDVNTVAGFGL 378 D++D + +PL+ + P G F AGGVP L+ EL +AG LH D +V G + Sbjct: 296 TAQDWTDHAYDLPLLLNMQPAGQFLGERFFRAGGVPALMWELQQAGKLHADCASVTGKTV 355 Query: 379 SRYTLEPWLNNGELDWREGAEKSLDSNVIASFEQPFSHHGGTKVLSGNL-GRAVMKTSAV 437 L RE + D VI F P H G VLSGNL +MKTS + Sbjct: 356 GE----------NLQGRE----THDREVIRPFSNPLMHKAGFMVLSGNLFDFGIMKTSVI 401 Query: 438 -----------PVENQVIEAPAVVFESQHDVMPAFE--AGLLDRDCVVVVRHQGPKA-NG 483 P + + EA AVVFE D A +D C++V+R GP G Sbjct: 402 SEAFRQRYLSRPGQEGIFEARAVVFEGADDYHARINDPALNIDEGCILVMRGAGPIGWPG 461 Query: 484 MPELHKLMPPLGVLLDRCFKIALVTDGRLSGASGKVPSAIHVTPEAYDGGLLAKVRDGDI 543 E+ + PP ++ + + DGR SG + PS ++ +PE+ GG L+ ++ GD Sbjct: 462 SAEVVNMQPPDALIKRGINTLPTLGDGRQSGTADS-PSILNASPESAVGGGLSWLQSGDT 520 Query: 544 IRVNGQTGELTLLVDEAELAAREPHIPDLSASRVGTGRELFSAL-REKLSGAEQGAT 599 +R++ TG LV E+A R+ DL A V + + AL REK GAT Sbjct: 521 VRIDLNTGRCDALVTPEEIARRK---RDLPAPPVPASQSPWEALYREKTGQLADGAT 574 Lambda K H 0.318 0.134 0.392 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: 893 Number of extensions: 46 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: 603 Length of database: 593 Length adjustment: 37 Effective length of query: 566 Effective length of database: 556 Effective search space: 314696 Effective search space used: 314696 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 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