Align Phosphogluconate dehydratase; EC 4.2.1.12; 6-phosphogluconate dehydratase (uncharacterized)
to candidate WP_008506433.1 BIBO1_RS10395 dihydroxy-acid dehydratase
Query= curated2:P31961 (608 letters) >NCBI__GCF_000182725.1:WP_008506433.1 Length = 611 Score = 206 bits (524), Expect = 2e-57 Identities = 162/545 (29%), Positives = 253/545 (46%), Gaps = 54/545 (9%) Query: 68 VAIVSAYNDMLSAHQPFERFPGLIKQALHEIGSVGQFAGGVPAMCDGVTQGEPGMELSLA 127 +A+V+++ + H + L+ + + G V + + A+ DG+ G GM SL Sbjct: 37 IAVVNSFTQFVPGHVHLKDLGQLVAREIESAGGVAKEFNTI-AVDDGIAMGHDGMLYSLP 95 Query: 128 SRDVIAMSTAIALSHNMFDAALCLGVCDKIVPGLLIGSLRFGHLPTVFVPAGPMPTG--- 184 SR++IA S ++ + DA +C+ CDKI PG+L+ +LR ++P VFV GPM G Sbjct: 96 SRELIADSVEYMVNAHCADAMVCISNCDKITPGMLMAALRL-NIPVVFVSGGPMEAGKVV 154 Query: 185 ----ISNKEKAAVRQLFAEGKATREELLASEMASYHAPGTCTFYGTANTNQLLVEVMGLH 240 + + A+ T E++ A E ++ G+C+ TAN+ L E +GL Sbjct: 155 WEDSVKKLDLVDAMVAAADDHYTDEQVKAIERSACPTCGSCSGMFTANSMNCLTEALGLS 214 Query: 241 LPGASFVNPNTPLRDELTREAARQ----ASRLTPENGNYVPMAEIVDEKAIVNSVVALLA 296 LPG R L EA A R ++ V I A N++ +A Sbjct: 215 LPGNGSTLATHADRKRLFVEAGHLIVDLARRYYEQDDESVLPRSIATFSAFENAMTLDIA 274 Query: 297 TGGSTNHTLHLLAIAQAAGIQLTWQDMSELSHVVPTLARIYPNGQA----DINHFQAAGG 352 GGSTN LHLLA AQ A I T D+ LS VP L ++ P + D++H AGG Sbjct: 275 MGGSTNTVLHLLAAAQEAEIDFTMADIDRLSRRVPVLCKVAPAVSSVHMEDVHH---AGG 331 Query: 353 MSFLIRQLLDGGLLHEDVQTVAGPGLRR------------------YTREP--------F 386 + ++ QL + GLL + TV L + Y+ P F Sbjct: 332 IMGILGQLDNAGLLTTSIPTVHSETLAKALDHWDVTRTNSEMVHKFYSAAPGGVPTQVAF 391 Query: 387 LEDGRLVWREGPERSLDEAILRPLDKPFSAEGGLRLMEGNLGRG--VMKVSAVAPEHQVV 444 ++ R + + ++ ++R + FS +GGL ++ GNL ++K + V Sbjct: 392 SQERRF---DKVDTDREKGVIRSKEHAFSQDGGLAVLYGNLAEDGCIVKTAGVDDSILKF 448 Query: 445 EAPVRIFHDQASLAAAFKAGELERDLVAVVRFQGPRAN-GMPELHKLTPFLGVLQDRGFK 503 P RIF Q S G+++ + ++R++GPR GM E+ T +L + G Sbjct: 449 SGPARIFESQDSAVLGILNGKIKPGDIVLIRYEGPRGGPGMQEMLYPTSYLKS-KGLGKA 507 Query: 504 VALVTDGRMSGASGKVPAAIHVSPEAIAGGPLARLRDGDRVRVDGVNGELRVLVDDAEWQ 563 AL+TDGR SG S + HVSPEA GG + +R+GD + +D N ++ + VDDA Sbjct: 508 CALITDGRFSGGSSGLSIG-HVSPEAAEGGTIGLVREGDIIDIDIPNRKIHLTVDDATLA 566 Query: 564 ARSLE 568 R E Sbjct: 567 ERRAE 571 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: 867 Number of extensions: 46 Number of successful extensions: 9 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: 608 Length of database: 611 Length adjustment: 37 Effective length of query: 571 Effective length of database: 574 Effective search space: 327754 Effective search space used: 327754 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