Align phosphogluconate dehydratase (characterized)
to candidate WP_010961325.1 MCA_RS10195 dihydroxy-acid dehydratase
Query= CharProtDB::CH_024239 (603 letters) >NCBI__GCF_000008325.1:WP_010961325.1 Length = 562 Score = 222 bits (565), Expect = 4e-62 Identities = 157/462 (33%), Positives = 240/462 (51%), Gaps = 29/462 (6%) Query: 113 DGVTQGQDGMELSLLSREVIAMSAAVGLSHNMFDGALFLGVCDKIVPGLTMAALSFGHLP 172 DG++ G +GM+ SL+SREVIA S ++ +DG + +G CDK +PG + AL+ + P Sbjct: 85 DGISMGTEGMKYSLVSREVIADSIETVVACQGYDGVVAIGGCDKNMPGC-LIALARLNRP 143 Query: 173 AVFVPSGPMASGLPNKEKVRIRQLY------AEGKVDRMALLESEAASYHAPGTCTFYGT 226 AVFV G + G + +K+ + ++ A ++D L E+ + PG+C T Sbjct: 144 AVFVYGGTILPGCHDGKKLDVVSVFEAVGARANHRIDDAELHAIESNAIPGPGSCGGMYT 203 Query: 227 ANTNQMVVEFMGMQLPGSSFVHPDSPLRDALTAAAARQVTRMTGNGNEWMPIGKMIDEKV 286 ANT +E +GM LPGSS S ++ A QV ++ G + I + +K Sbjct: 204 ANTMASAIEALGMSLPGSSAQVAISRAKELDCERAGAQVLKLLDLGLKPRDI---MTKKA 260 Query: 287 VVNGIVALLATGGSTNHTMHLVAMARAAGIQINWDDFSDLSDVVPLMARLYPNGPADINH 346 N I ++A GGSTN +HL+AMA A G+ + DDF+ + VP++A L P+G + Sbjct: 261 FENAITVVIALGGSTNAVLHLLAMANACGVDLKLDDFTRIGRKVPMLADLKPSGRYSMAE 320 Query: 347 FQAAGGVPVLVRELLKAGLLHEDVNTVAGFGLSRYTLEPWLNNGELDWREGAEKSLDSNV 406 GG+ L++ LL AGLLH D TV G TLE L + D+ G ++ Sbjct: 321 LVEIGGIQPLMKTLLDAGLLHGDCMTVTG-----KTLEENLADAP-DYPAG------QDM 368 Query: 407 IASFEQPFSHHGGTKVLSGNLGRAVMKTSAVPVENQVIEAPAVVFESQHDVMPAFEAGLL 466 I S + P +L GNL E A VF+ + + A G + Sbjct: 369 IRSLDNPIKKDSHLVILKGNLAPEGAVAKITGKEGLSFTGTARVFDCEEAALTAILDGTI 428 Query: 467 DRDCVVVVRHQGPKANGMPELHKLMPPLGVLLDRCF--KIALVTDGRLSGAS-GKVPSAI 523 + V+V+R++GPK G P + +++ P ++ + ++AL+TDGR SG + G V Sbjct: 429 VKGDVIVIRYEGPK--GGPGMREMLSPTSAVMGKGLGKEVALITDGRFSGGTHGFVVG-- 484 Query: 524 HVTPEAYDGGLLAKVRDGDIIRVNGQTGELTLLVDEAELAAR 565 H+TPEAY GG LA VRDGD I ++ +T EL+L V + E+ R Sbjct: 485 HITPEAYTGGPLAIVRDGDTITIDAETRELSLHVTDDEIGRR 526 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: 835 Number of extensions: 34 Number of successful extensions: 6 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: 562 Length adjustment: 36 Effective length of query: 567 Effective length of database: 526 Effective search space: 298242 Effective search space used: 298242 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