Align Phosphogluconate dehydratase; EC 4.2.1.12; 6-phosphogluconate dehydratase (uncharacterized)
to candidate SMc00884 SMc00884 dihydroxy-acid dehydratase
Query= curated2:P31961 (608 letters) >FitnessBrowser__Smeli:SMc00884 Length = 574 Score = 199 bits (507), Expect = 2e-55 Identities = 161/510 (31%), Positives = 250/510 (49%), Gaps = 44/510 (8%) Query: 105 AGGVPAMCDGVTQGEPGME-LSLASRDVIAMSTAIALSHNMFDAALCLGVCDKIVPGLLI 163 AGG P + GE M ++ R+++AM A+ D + LG CDK PG L+ Sbjct: 74 AGGFPVEFPVSSLGETQMRPTAMLFRNLLAMDVEEAIRAYGIDGVVLLGGCDKTTPGQLM 133 Query: 164 GSLRFGHLPTVFVPAGPMPTGI-------SNKEKAAVRQLFAEGKATREELLASEMASYH 216 G+ LPT+ V +GPM G S + + G+ + +E +A+E Sbjct: 134 GAASVD-LPTIVVSSGPMLNGKWKGKDIGSGTDVWKFSEAVRAGEMSLQEFMAAESGMSR 192 Query: 217 APGTCTFYGTANTNQLLVEVMGLHLPGASFVNPNTPLRDELTREAARQASRLTPENGNYV 276 +PG C GTA T +VE MGL LP + + R L+ ++ + E+ + Sbjct: 193 SPGVCMTMGTATTMASIVEAMGLSLPTNAALPAVDARRMALSHMTGKRIVEMVHED---L 249 Query: 277 PMAEIVDEKAIVNSVVALLATGGSTNHTLHLLAIAQAAGIQLTWQDMSELSHVVPTLARI 336 +++I+ ++ N ++A A GGSTN +H+LAIA AGI L +D + VP + Sbjct: 250 RLSKILTKENFENGIIANAAVGGSTNAVVHMLAIAGRAGIDLCLEDFDRVGGQVPCIVNC 309 Query: 337 YPNGQADINHFQAAGGMSFLIRQLLDGGLLHEDVQTVAGPGLRRYTREPFLEDGRLVWRE 396 P+G+ I AGG+ ++ ++ LLH D TV G + +Y W E Sbjct: 310 MPSGKYLIEDLAYAGGLPAVMNRIQH--LLHPDAPTVFGVPISKY------------W-E 354 Query: 397 GPERSLDEAILRPLDKPFSAEGGLRLMEGNLGRG--VMKVSAVAPEHQVVEAPVRIFHDQ 454 E D+ ++RPLD P A G+R+++GNL V+K SA + E P +F Sbjct: 355 AAEVYNDD-VIRPLDNPLRAAAGIRVLKGNLAPNGAVIKPSAASEHLLAHEGPAYVFDTI 413 Query: 455 ASLAAAFKAGELE--RDLVAVVRFQGPRAN-GMPELHKLTPFLGVLQDRGFK-VALVTDG 510 L A +L D + V++ GP+ GM E+ + P L ++G + + ++D Sbjct: 414 EDLRAKIDDPDLPVTEDTILVLKGCGPKGYPGMAEVGNM-PIPRRLVEKGVRDMVRISDA 472 Query: 511 RMSG-ASGKVPAAIHVSPEAIAGGPLARLRDGDRVRVDGVNGELRVLVDDAEWQAR--SL 567 RMSG A G V +HVSPEA AGGPLA +R GDR+R+D + GEL +LV + E AR + Sbjct: 473 RMSGTAFGTV--VLHVSPEANAGGPLAIVRTGDRIRLDALKGELNLLVSEEELAARMAAW 530 Query: 568 EPAPQDGNLGCGRELFAFMRNAMSSAEEGA 597 +P Q + G + + + A++GA Sbjct: 531 QPPEQKWHRG----YYKLYHDTVLQADKGA 556 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: 814 Number of extensions: 49 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: 574 Length adjustment: 37 Effective length of query: 571 Effective length of database: 537 Effective search space: 306627 Effective search space used: 306627 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 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