Align phosphogluconate dehydratase (characterized)
to candidate RR42_RS18585 RR42_RS18585 dihydroxy-acid dehydratase
Query= CharProtDB::CH_024239 (603 letters) >FitnessBrowser__Cup4G11:RR42_RS18585 Length = 577 Score = 186 bits (471), Expect = 3e-51 Identities = 154/513 (30%), Positives = 242/513 (47%), Gaps = 45/513 (8%) Query: 68 IAIITSYNDMLSAHQPYEHYPEIIRKALHEANAVGQVAGGVPAMCDGVTQGQDGME-LSL 126 I I +Y+++ + + E ++ + EA GG P ++ G+ + ++ Sbjct: 47 IGICNTYSELTPCNSHFRTLAEQVKIGVWEA-------GGFPLEFPVMSLGETMLRPTAM 99 Query: 127 LSREVIAMSAAVGLSHNMFDGALFLGVCDKIVPGLTMAALSFGHLPAVFVPSGPMASGL- 185 L R + +M + N DG + L CDK P L M A S LP + V GPM SG Sbjct: 100 LFRNLASMDVEESIRGNPIDGVVLLMGCDKTTPALMMGAASCD-LPTIGVSGGPMLSGKF 158 Query: 186 ------PNKEKVRIRQLYAEGKVDRMALLESEAASYHAPGTCTFYGTANTNQMVVEFMGM 239 + ++ + G++ + E+E+ + + G C GTA+T +VE +GM Sbjct: 159 RGGELGSGTDVWKMSEQVRAGQMSQEDFFEAESCMHRSHGHCMTMGTASTMASMVEALGM 218 Query: 240 QLPGSSFVHPDSPLRDALTAAAARQVTRMTGNGNEWMPIGKMIDEKVVVNGIVALLATGG 299 LPG++ + R+ L A+ R++ M + + + K++ N I A GG Sbjct: 219 SLPGNAAIPAVDGRRNVLARASGRRIVEMVKDN---LVMSKILTRDAFENAIRVNAAIGG 275 Query: 300 STNHTMHLVAMARAAGIQINWDDFSDLSDVVPLMARLYPNGPADINHFQAAGGVPVLVRE 359 STN +HL+A+A G+++ +D+ L +P + L P+G + F AGG+P ++RE Sbjct: 276 STNAVIHLLAIAGRIGVELKLEDWDALGHELPCLLDLQPSGRHLMEDFYYAGGLPAVIRE 335 Query: 360 LLKAGLLHEDVNTVAGFGLSRYTLEPWLNNGELDWREGAE-KSLDSNVIASFEQPFSHHG 418 L +L D TV NG+ W + + + VI +F PF + Sbjct: 336 L--ESVLARDALTV---------------NGKTLWDNCKDAPNWNREVIHAFGAPFKANA 378 Query: 419 GTKVLSGNL--GRAVMKTSAVPVENQVIEAPAVVFESQHDVMPAFEAGLLDRD--CVVVV 474 G VL GNL AV+K SA AVVFE+ + + LD D CV+V+ Sbjct: 379 GIAVLRGNLCPDGAVIKPSAATPALLKHTGRAVVFENSEHMHQRLDDESLDVDETCVLVL 438 Query: 475 RHQGPKA-NGMPELHKLMPPLGVLLDRCFKIALVTDGRLSG-ASGKVPSAIHVTPEAYDG 532 ++ GP+ GM E + P VL + V+D R+SG A G V +HV PEA G Sbjct: 439 KNCGPRGYPGMAEAGNMPLPPKVLRKGITDMVRVSDARMSGTAYGTV--VLHVAPEAAAG 496 Query: 533 GLLAKVRDGDIIRVNGQTGELTLLVDEAELAAR 565 G LA V+DGD++ ++ +L L VDEAEL R Sbjct: 497 GPLALVKDGDMVELDVPMRKLHLHVDEAELQRR 529 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: 845 Number of extensions: 48 Number of successful extensions: 7 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 1 Length of query: 603 Length of database: 577 Length adjustment: 37 Effective length of query: 566 Effective length of database: 540 Effective search space: 305640 Effective search space used: 305640 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