Align phosphogluconate dehydratase (characterized)
to candidate WP_084164617.1 N825_RS10340 dihydroxy-acid dehydratase
Query= CharProtDB::CH_024239 (603 letters) >NCBI__GCF_000576635.1:WP_084164617.1 Length = 577 Score = 200 bits (509), Expect = 1e-55 Identities = 162/486 (33%), Positives = 235/486 (48%), Gaps = 43/486 (8%) Query: 105 AGGVPAMCDGVTQGQDGME-LSLLSREVIAMSAAVGLSHNMFDGALFLGVCDKIVPGLTM 163 AGG P + G+ M ++L R + +M + + DG + L CDK P L M Sbjct: 75 AGGFPLEFPVSSLGEVTMRPTAMLFRNLASMDVEEAIRAHPLDGVVLLMGCDKTTPALLM 134 Query: 164 AALSFGHLPAVFVPSGPMASGLPNKEKV-------RIRQLYAEGKVDRMALLESEAASYH 216 A S LPA+ V GP G+ E + + + G++ E+EA Sbjct: 135 GAAS-ADLPAIGVSGGPQLRGVYRGEIIGSGTNIISMSEQLRAGEITLEEFHEAEAGMNR 193 Query: 217 APGTCTFYGTANTNQMVVEFMGMQLPGSSFVHPDSPLRDALTAAAARQVTRMTGNGNEWM 276 + G+C GTA+T +VE +G+ LPG++ + R+ L + R++ + + + Sbjct: 194 SAGSCMTMGTASTMASMVEALGLGLPGNAAIPAADARRNLLARMSGRRIVELA---RQDV 250 Query: 277 PIGKMIDEKVVVNGIVALLATGGSTNHTMHLVAMARAAGIQINWDDFSDLSDVVPLMARL 336 ++ + N I L A GGSTN +HL+A+A GI + DDF L + + L Sbjct: 251 KPSDILTRQAFENAIRTLAAIGGSTNAVVHLLALAGRVGIDLTLDDFDRLGRDIHCLVDL 310 Query: 337 YPNGPADINHFQAAGGVPVLVRELLKAGLLHEDVNTVAGFGLSRYTLEPWLNNGELD-WR 395 P+G + F AGG+P ++R L + GLLH+D TV G L W N GE W Sbjct: 311 MPSGRFLMEDFYYAGGLPAVLRALGERGLLHKDAMTVNGQTL-------WENVGEAPCW- 362 Query: 396 EGAEKSLDSNVIASFEQPFSHHGGTKVLSGNLG--RAVMKTSAVPVENQVIEAPAVVFES 453 + VI FE PF G +L+GNL AV+K SA E AVVFES Sbjct: 363 -------NREVITPFEAPFKPESGMAILTGNLAPDGAVIKPSAASPELMRHTGRAVVFES 415 Query: 454 QHDVMPAFEAGLLDRD--CVVVVRHQGPKA-NGMPELHKLMPPLGVLLDRCFKIALVTDG 510 ++ A + LD D CV+V+++ GPK GM E+ + P +L + ++D Sbjct: 416 VEEMHHAVDDEDLDIDASCVMVLKNCGPKGYPGMAEVGNMPLPAKLLRQGVRDMIRISDA 475 Query: 511 RLSG-ASGKVPSAIHVTPEAYDGGLLAKVRDGDIIRVNGQTGELTLLVDEAELAAR---- 565 R+SG A G V +HV PEA GG LA VR+GD+I ++ L L VD+AELAAR Sbjct: 476 RMSGTAYGTV--VLHVAPEATAGGPLALVRNGDMITLDVPARSLHLHVDDAELAARRAAW 533 Query: 566 ---EPH 568 EPH Sbjct: 534 TPPEPH 539 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: 850 Number of extensions: 50 Number of successful extensions: 8 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 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