Align Phosphogluconate dehydratase; EC 4.2.1.12; 6-phosphogluconate dehydratase (uncharacterized)
to candidate PfGW456L13_3725 Dihydroxy-acid dehydratase (EC 4.2.1.9)
Query= curated2:P31961 (608 letters) >FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_3725 Length = 560 Score = 219 bits (558), Expect = 2e-61 Identities = 156/493 (31%), Positives = 243/493 (49%), Gaps = 32/493 (6%) Query: 113 DGVTQGEPGMELSLASRDVIAMSTAIALSHNMFDAALCLGVCDKIVPGLLIGSLRFGHLP 172 DG+ G GM+ SL SR+VIA S + FD + +G CDK +PG LIG R P Sbjct: 86 DGIANGTEGMKYSLVSREVIADSIEVVTGCEGFDGLVTIGGCDKNMPGCLIGMARLNR-P 144 Query: 173 TVFVPAGPMPTGISNKEKAAVRQLF---AEGKATREELLASEMASYHAPGTCTFYGTANT 229 ++FV G + G + + +V + A G + ++ E + PG+C TANT Sbjct: 145 SIFVYGGTIQPGAGHTDIISVFEAVGQHARGDISEIQVKQIEEVAIPGPGSCGGMYTANT 204 Query: 230 NQLLVEVMGLHLPGASFVNPNTPLRDELTREAARQASRLTPENGNYVPMAEIVDEKAIVN 289 +E +G+ LPG+S + + + A +Q L + + +I+ KA N Sbjct: 205 MASAIEALGMSLPGSSSQDAIGADKASDSFRAGQQVMELLKLD---LKPRDIMTRKAFEN 261 Query: 290 SVVALLATGGSTNHTLHLLAIAQAAGIQLTWQDMSELSHVVPTLARIYPNGQADINHFQA 349 ++ ++A GSTN LHLLA+A A ++LT D EL V P +A + P+G+ ++ A Sbjct: 262 AIRVVIALAGSTNAVLHLLAMANAVDVELTLDDFVELGKVSPVVADLRPSGKYMMSELVA 321 Query: 350 AGGMSFLIRQLLDGGLLHEDVQTVAGPGLRRYTREPFLEDGRLVWREGPERSLDEAILRP 409 GG+ L++++LD G+LH DV TV G L P+ + ++RP Sbjct: 322 IGGIQPLMKRMLDAGMLHGDVLTVTGQTLAENLASV------------PDYPAGQDVIRP 369 Query: 410 LDKPFSAEGGLRLMEGNLGRGVMKVSAVAPEHQVVEAPVRIFHDQASLAAAFKAGELERD 469 D+P + L ++ GNL E E R++H + A GE++ Sbjct: 370 FDQPIKKDSHLVILRGNLSPTGAVAKITGKEGLRFEGTARVYHGEEGALAGILNGEVQPG 429 Query: 470 LVAVVRFQGPRAN-GMPELHKLTPFLGVL-QDRGFKVALVTDGRMSGASGKVPAAIHVSP 527 V V+R++GP+ GM E+ L+P V+ + G +VAL+TDGR SG S H++P Sbjct: 430 EVIVIRYEGPKGGPGMREM--LSPTSAVMGKGLGKEVALITDGRFSGGSHGFVVG-HITP 486 Query: 528 EAIAGGPLARLRDGDRVRVDGVNGELRVLVDD---AEWQARSLEPAPQDGNLGCGRELFA 584 EA GGP+A + +GDR+ +D + V V D AE ++R + P + R + A Sbjct: 487 EAFEGGPIALVENGDRIIIDAETRLITVDVSDAVLAERKSRWVRPESK-----YKRGVLA 541 Query: 585 FMRNAMSSAEEGA 597 +SSA EGA Sbjct: 542 KYAKTVSSASEGA 554 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: 808 Number of extensions: 48 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: 560 Length adjustment: 36 Effective length of query: 572 Effective length of database: 524 Effective search space: 299728 Effective search space used: 299728 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