Align Phosphogluconate dehydratase; EC 4.2.1.12; 6-phosphogluconate dehydratase (uncharacterized)
to candidate WP_008410930.1 DESHY_RS05080 dihydroxy-acid dehydratase
Query= curated2:P31961 (608 letters) >NCBI__GCF_000315365.1:WP_008410930.1 Length = 552 Score = 250 bits (639), Expect = 1e-70 Identities = 181/568 (31%), Positives = 290/568 (51%), Gaps = 62/568 (10%) Query: 25 EMVRAAASKGPHRGTLPCGNLAHGVAACGESDKQTLRLMNQANVAIVSAYNDMLSAHQPF 84 ++++ ++ PHR L A G D++ R + + +V+++N+++ H Sbjct: 4 DVMKEGLARAPHRSLLK---------ALGLLDEELSRPL----IGVVNSFNEVVPGHIHL 50 Query: 85 ERFPGLIKQALHEIGSVGQFAGGVP------AMCDGVTQGEPGMELSLASRDVIAMSTAI 138 +K + + AGG P A+CDG+ G PGM SLASR++IA S I Sbjct: 51 RDIAEAVKAGV-------RMAGGTPLEFPVIAVCDGIAMGHPGMRYSLASREIIADSIEI 103 Query: 139 ALSHNMFDAALCLGVCDKIVPGLLIGSLRFGHLPTVFVPAGPMPTGISNKEKAAVRQLFA 198 + FD + + CDK+VPG+L+ + R ++P V V GPM G + +V Q+F Sbjct: 104 MAQAHPFDGLVLIPNCDKVVPGMLMAAARL-NIPAVVVSGGPMLAGRFQNQDVSVTQMFE 162 Query: 199 E------GKATREELLASEMASYHAPGTCTFYGTANTNQLLVEVMGLHLPGASFVNPNTP 252 G+ T EEL E + G+C TAN+ L E +G+ LPG + + Sbjct: 163 AVGAVQAGRLTPEELAELEENACPGCGSCAGMFTANSMNCLTEALGMALPGNGTIPAVSA 222 Query: 253 LRDELTREAARQASRLTPENGNYVPMAEIVDEKAIVNSVVALLATGGSTNHTLHLLAIAQ 312 R L + A +A L EN + +I+ N + +A G STN LHL AIA+ Sbjct: 223 ARRRLAKAAGLRAVALVREN---LRPRDILTMANFRNGLAVDMALGCSTNTVLHLPAIAR 279 Query: 313 AAGIQLTWQDMSELSHVVPTLARIYPNGQADINHFQAAGGMSFLIRQLLDGGLLHEDVQT 372 AGI+L ++E+S P L ++ P G+ I AAGG+ ++++LL+ GL++ +++T Sbjct: 280 EAGIELNLDLINEISERTPHLCKLSPAGRHHIQDLDAAGGIQAVMKELLNNGLINPNIKT 339 Query: 373 VAGPGLRRYTREPFLEDGRLVWREGPERSLDEAILRPLDKPFSAEGGLRLMEGNL--GRG 430 V+G T LE ++ D ++R + +P+S+ GGL ++ GNL Sbjct: 340 VSG-----LTVGQLLEQAKV---------KDRQVIRSVQEPYSSTGGLAVLRGNLAPNGA 385 Query: 431 VMKVSAVAPEHQVVEAPVRIFHDQASLAAAFKAGELERDLVAVVRFQGPRANGMPELHKL 490 V+K +AVAPE P R+F + + A AG+++ V V+R++GP+ G P + ++ Sbjct: 386 VVKRAAVAPEMLRHTGPARVFDGEEAAITAIMAGQIKPGDVVVIRYEGPK--GGPGMREM 443 Query: 491 TPFLGVLQDRGF--KVALVTDGRMSGASGKVPAAIHVSPEAIAGGPLARLRDGDRVRVDG 548 VL G +VAL+TDGR SGAS + + H+SPEA GG +A L+DGD + +D Sbjct: 444 LAPTSVLAGMGLDKEVALLTDGRFSGAS-RGASIGHISPEAAEGGLIALLQDGDMIEIDI 502 Query: 549 VNGELRVLVDDAEWQARSLE----PAPQ 572 N L +D+ + R LE PAP+ Sbjct: 503 PNYRLAAKLDETVIKQR-LEAWQPPAPK 529 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: 897 Number of extensions: 63 Number of successful extensions: 9 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: 552 Length adjustment: 36 Effective length of query: 572 Effective length of database: 516 Effective search space: 295152 Effective search space used: 295152 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