Align L-arabonate dehydratase (EC 4.2.1.25) (characterized)
to candidate 15969 b1851 phosphogluconate dehydratase (NCBI)
Query= reanno::BFirm:BPHYT_RS19730 (577 letters) >FitnessBrowser__Keio:15969 Length = 603 Score = 199 bits (507), Expect = 2e-55 Identities = 157/512 (30%), Positives = 252/512 (49%), Gaps = 42/512 (8%) Query: 47 IGICNTWSELTPCNAHFRELAEYVKKGVHEA-------GGLPLEFPVMSLGETNLRPTAM 99 I I +++++ + + E ++K +HEA GG+P ++ G+ + ++ Sbjct: 68 IAIITSYNDMLSAHQPYEHYPEIIRKALHEANAVGQVAGGVPAMCDGVTQGQDGME-LSL 126 Query: 100 LFRNLASMDVEESIRGNPMDGVILLVGCDKTTPALLMGAASC-NLPALAVSGGPMLNGRF 158 L R + +M + N DG + L CDK P L M A S +LPA+ V GPM +G Sbjct: 127 LSREVIAMSAAVGLSHNMFDGALFLGVCDKIVPGLTMAALSFGHLPAVFVPSGPMASGLP 186 Query: 159 RGKNIGSGTGVWQMSEEVRAGTMTQEEFTEAESCMNRSRGHCMTMGTASTMASMVESLGM 218 + + ++ + G + + E+E+ + G C GTA+T +VE +GM Sbjct: 187 NKEKV-------RIRQLYAEGKVDRMALLESEAASYHAPGTCTFYGTANTNQMVVEFMGM 239 Query: 219 GLPHNAAIPAVDARRQVLAHLAGRRIVDMV---REDLTMDKILTRQAFENAIRTNAAIGG 275 LP ++ + R L A R++ M E + + K++ + N I A GG Sbjct: 240 QLPGSSFVHPDSPLRDALTAAAARQVTRMTGNGNEWMPIGKMIDEKVVVNGIVALLATGG 299 Query: 276 STNAVVHLIALAKRIGVELSLEDW-ELGSNVPCLVNLQPSGEYLMEDFYYAGGLPAVLKQ 334 STN +HL+A+A+ G++++ +D+ +L VP + L P+G + F AGG+P ++++ Sbjct: 300 STNHTMHLVAMARAAGIQINWDDFSDLSDVVPLMARLYPNGPADINHFQAAGGVPVLVRE 359 Query: 335 LGEQGLLHKEALTVNGKTL-------WDN-----VRNAA--NYDEKVITTFAEPFKPKAG 380 L + GLLH++ TV G L W N R A + D VI +F +PF G Sbjct: 360 LLKAGLLHEDVNTVAGFGLSRYTLEPWLNNGELDWREGAEKSLDSNVIASFEQPFSHHGG 419 Query: 381 IAVLKGNLAPNGAVIKPSAATASLLKHRGRAVVFENIEELHAKIDDESLDIDEHCIMVLK 440 VL GNL AV+K SA AVVFE+ ++ + LD D C++V++ Sbjct: 420 TKVLSGNL--GRAVMKTSAVPVENQVIEAPAVVFESQHDVMPAFEAGLLDRD--CVVVVR 475 Query: 441 GAGPKGYPGFAEVGNMPLPKKVLQKGITDMVRISDGRMSGTAYGAV--VLHVSPEAAAGG 498 GPK G E+ + P VL + ++DGR+SG A G V +HV+PEA GG Sbjct: 476 HQGPKA-NGMPELHKLMPPLGVLLDRCFKIALVTDGRLSG-ASGKVPSAIHVTPEAYDGG 533 Query: 499 PLAFVQTGDMIELDVEERRLHLDVTDEELARR 530 LA V+ GD+I ++ + L L V + ELA R Sbjct: 534 LLAKVRDGDIIRVNGQTGELTLLVDEAELAAR 565 Lambda K H 0.318 0.135 0.401 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: 780 Number of extensions: 38 Number of successful extensions: 11 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: 577 Length of database: 603 Length adjustment: 37 Effective length of query: 540 Effective length of database: 566 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