Align Phosphogluconate dehydratase; EC 4.2.1.12; 6-phosphogluconate dehydratase (uncharacterized)
to candidate WP_012676391.1 PERMA_RS02785 dihydroxy-acid dehydratase
Query= curated2:P31961 (608 letters) >NCBI__GCF_000021565.1:WP_012676391.1 Length = 557 Score = 263 bits (671), Expect = 2e-74 Identities = 177/552 (32%), Positives = 283/552 (51%), Gaps = 46/552 (8%) Query: 25 EMVRAAASKGPHRGTLPCGNLAHGVAACGESDKQTLRLMNQANVAIVSAYNDMLSAHQPF 84 ++V+ + PHR L ACG +D+ + + I ++Y D++ H Sbjct: 4 DIVKKGFERAPHRSLL---------RACGLTDED----FKKPFIGIANSYIDIIPGHVHL 50 Query: 85 ERFPGLIKQALHEIGSVGQFAGGVPAMCDGVTQGEPGMELSLASRDVIAMSTAIALSHNM 144 F ++K+A+ E G V F V + DG+ G GM SL SR++IA S + + Sbjct: 51 REFAQIVKEAVREAGGV-PFEFNVIGVDDGIAMGHSGMHYSLPSRELIADSIETVVEAHK 109 Query: 145 FDAALCLGVCDKIVPGLLIGSLRFGHLPTVFVPAGPMPTG-ISNKEKAAVRQLF------ 197 DA +C+ CDKIVPG+++ + R ++P +FV GPM G + + + F Sbjct: 110 LDALVCIPNCDKIVPGMIMAAARL-NIPVIFVSGGPMAAGHLPDGRPIDLATAFEAVGAV 168 Query: 198 AEGKATREELLASEMASYHAPGTCTFYGTANTNQLLVEVMGLHLPGASFVNPNTPLRDEL 257 + G T EL E + + G+C+ TAN+ L EV+G+ LPG + P R EL Sbjct: 169 SRGLMTENELRVIEENACPSCGSCSGMFTANSMNCLSEVLGIALPGNGSILATDPRRQEL 228 Query: 258 TREAARQASRLTPENGNYVPMAEIVDEKAIVNSVVALLATGGSTNHTLHLLAIAQAAGIQ 317 R+A Q +L + + +IV+E+ I N+ +A GGS+N LHLLAIA AGI Sbjct: 229 ARKAGEQIVKLVEAD---LKFRDIVNEETIENAFTLDIAMGGSSNTVLHLLAIANEAGID 285 Query: 318 LTWQDMSELSHVVPTLARIYPNGQADINHFQAAGGMSFLIRQLLDGGLLHEDVQTVAGPG 377 + + ++S PTL ++ P Q + AGG+S ++++L GLLH D TV+ Sbjct: 286 FPVEKIDQISRRTPTLCKLAPASQYHMEDLDRAGGISAILKELSKKGLLHLDRPTVS--- 342 Query: 378 LRRYTREPFLEDGRLVWREGPERSLDEAILRPLDKPFSAEGGLRLMEGNLG--RGVMKVS 435 T +ED + D ++RP+ P+S GGL ++ GN+ GV+K + Sbjct: 343 --LKTLGEVIEDAEI---------KDPDVIRPIHNPYSETGGLAVLFGNIAPYGGVVKAA 391 Query: 436 AVAPEHQVVEAPVRIFHDQASLAAAFKAGELERDLVAVVRFQGPRAN-GMPELHKLTPFL 494 AV P+ V F + A G+++ V V+R++GPR GM E+ L+P Sbjct: 392 AVDPKIMVHRGKAVCFDSEEEAIAGITGGKVKAGDVVVIRYEGPRGGPGMREM--LSPTS 449 Query: 495 GVL-QDRGFKVALVTDGRMSGASGKVPAAIHVSPEAIAGGPLARLRDGDRVRVDGVNGEL 553 ++ G KV+L+TDGR SGA+ + H+SPEA AGGP+ ++DGD + +D N ++ Sbjct: 450 AIMGMGLGDKVSLITDGRFSGAT-RGACIGHISPEAAAGGPIGIIKDGDEILIDIPNRKI 508 Query: 554 RVLVDDAEWQAR 565 +L+ + E++ R Sbjct: 509 ELLISEEEFKKR 520 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: 785 Number of extensions: 49 Number of successful extensions: 8 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: 557 Length adjustment: 36 Effective length of query: 572 Effective length of database: 521 Effective search space: 298012 Effective search space used: 298012 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 Apr 09 2024. 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