Align Phosphogluconate dehydratase; EC 4.2.1.12; 6-phosphogluconate dehydratase (uncharacterized)
to candidate WP_086508318.1 BZY95_RS01905 dihydroxy-acid dehydratase
Query= curated2:P31961 (608 letters) >NCBI__GCF_002151265.1:WP_086508318.1 Length = 561 Score = 214 bits (546), Expect = 6e-60 Identities = 160/495 (32%), Positives = 234/495 (47%), Gaps = 36/495 (7%) Query: 113 DGVTQGEPGMELSLASRDVIAMSTAIALSHNMFDAALCLGVCDKIVPGLLIGSLRFGHLP 172 DG+ G GM+ SL SR+VIA S FD + +G CDK +PG L+G R P Sbjct: 87 DGIANGTEGMKYSLVSREVIADSIETVAGCEGFDGLVAIGGCDKNMPGCLMGLARLNR-P 145 Query: 173 TVFVPAGPMPTGISNKEKAAVRQLF---AEGKATREELLASEMASYHAPGTCTFYGTANT 229 +VFV G + G ++ + +V + + G EL E + PG+C TANT Sbjct: 146 SVFVYGGTIQPGKNHTDIVSVFEAMGAHSRGDLELIELKQIEETAIPGPGSCGGMYTANT 205 Query: 230 NQLLVEVMGLHLPGASFVNPNTPLRDELTREAARQASRLTPENGNYVPMAEIVDEKAIVN 289 +E +G+ LPG+S N + + + A L + + ++I+ +A N Sbjct: 206 MASAIEALGMSLPGSSAQNAVSQAKRDDCEAAGAAVLELLERD---IKPSDIMTRQAFEN 262 Query: 290 SVVALLATGGSTNHTLHLLAIAQAAGIQLTWQDMSELSHVVPTLARIYPNGQADINHFQA 349 +V ++A GGSTN LHL+A+A G+ L+ D +E+ VP LA + P+G+ ++ Sbjct: 263 AVTVVIALGGSTNAVLHLIAMANTVGVPLSLVDFTEIGRRVPVLADLRPSGRYMMSELVE 322 Query: 350 AGGMSFLIRQLLDGGLLHEDVQTVAGPGLRRYTRE--PFLEDGRLVWREGPERSLDEAIL 407 GG+ L++ LLD GLLH D TV G L P+ + D+ I+ Sbjct: 323 IGGIQPLMKTLLDAGLLHGDCLTVTGRTLAENLANVAPYPD--------------DQKII 368 Query: 408 RPLDKPFSAEGGLRLMEGNLGRGVMKVSAVAPEHQVVEAPVRIFHDQASLAAAFKAGELE 467 LD P AE LR++ GNL E R+F + A G + Sbjct: 369 AALDAPLKAESHLRILFGNLAPEGAVAKITGKEGTRFSGTARVFGSEEEAQARINDGTVV 428 Query: 468 RDLVAVVRFQGPRAN-GMPELHKLTPFLGVL-QDRGFKVALVTDGRMSGASGKVPAAIHV 525 V V+R++GPR GM E+ LTP ++ + G VAL+TDGR SG S HV Sbjct: 429 AGDVVVIRYEGPRGGPGMREM--LTPTSAIMGRGLGDSVALITDGRFSGGSHGFVVG-HV 485 Query: 526 SPEAIAGGPLARLRDGDRVRVDGVNGELRVLVDDAEWQARSL---EPAPQDGNLGCGREL 582 +PEA GGPLA + DGD + +D + V + D E R +PAP+ R + Sbjct: 486 TPEAFDGGPLALVEDGDMITIDAEADTIDVDLSDEELMRRRAAWQQPAPR-----YTRGV 540 Query: 583 FAFMRNAMSSAEEGA 597 A +SSA GA Sbjct: 541 LAKYARTVSSASTGA 555 Lambda K H 0.319 0.135 0.397 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: 829 Number of extensions: 41 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: 608 Length of database: 561 Length adjustment: 36 Effective length of query: 572 Effective length of database: 525 Effective search space: 300300 Effective search space used: 300300 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 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