Align Phosphogluconate dehydratase; EC 4.2.1.12; 6-phosphogluconate dehydratase (uncharacterized)
to candidate WP_106713510.1 CU102_RS23445 dihydroxy-acid dehydratase
Query= curated2:P31961 (608 letters) >NCBI__GCF_003010955.1:WP_106713510.1 Length = 578 Score = 185 bits (469), Expect = 5e-51 Identities = 165/548 (30%), Positives = 251/548 (45%), Gaps = 47/548 (8%) Query: 68 VAIVSAYNDMLSAHQPFERFPGLIKQALHEIGSVGQFAGGVPAMCDGVTQGEPGME-LSL 126 VAI++ ++D H F+ +K+ + + AGG P ++ E ++ ++ Sbjct: 46 VAILNTWSDAQPCHMHFKDRVEWVKRGVLQ-------AGGFPMELPALSLSENFVKPTTM 98 Query: 127 ASRDVIAMSTAIALSHNMFDAALCLGVCDKIVPGLLIGSLRFGHLPTVFVPAGPMPTG-I 185 R+++AM L + D A+ +G CDK P L++G+L G LP +F+PAGPM G Sbjct: 99 LYRNMLAMEAEELLRSHPVDGAVLMGGCDKTTPALIMGALSMG-LPFIFLPAGPMLRGNY 157 Query: 186 SNKEKAAVRQLFA------EGKATREELLASEMASYHAPGTCTFYGTANTNQLLVEVMGL 239 + K + F G ++ E E + G C GTA+T + E MGL Sbjct: 158 AGKYLGSGTDGFKYWDERRAGTISKVEWQGIEGGIARSYGHCMTMGTASTMTAIAEAMGL 217 Query: 240 HLPGASFVNPNTPLRDELTREAARQASRLTPENGNYVPMAEIVDEKAIVNSVVALLATGG 299 LPGAS + ++ + R+ + E+ + IV A+ N+V +ATG Sbjct: 218 TLPGASSIPAADAGHQRMSTQCGRRIVEMIWED---LTPVRIVTPVAVENAVTVAMATGC 274 Query: 300 STNHTLHLLAIAQAAGIQLTWQDMSELSHVVPTLARIYPNGQADI-NHFQAAGGMSFLIR 358 STN +H++A+A+ AGI L D+ + P +A I P+G + + F AGG+ L++ Sbjct: 275 STNAIIHVIAMARRAGIPLELDDLDRIGRTTPVIANIRPSGTSYLMEDFYYAGGLRALMK 334 Query: 359 QLLDGGLLHEDVQTVAGPGLRRYTREPFLEDGRLVWREGPERSLDEAILRPLDKPFSAEG 418 QL G L TV G L E +W +E ++RPL P EG Sbjct: 335 QL--GDKLDSSAITVTGTPLTDGLEEV------KIW--------NEDVIRPLTNPVYHEG 378 Query: 419 GLRLMEGNL--GRGVMKVSAVAPEHQVVEAPVRIFHDQASLAAAFKAGE--LERDLVAVV 474 L +++GNL V+K +A P+ + + P + A L + L D V V+ Sbjct: 379 SLAVLKGNLCPDGAVIKPAACDPKFHLHKGPALVADSYAELKKIIDDPDYPLTPDTVLVL 438 Query: 475 RFQGPRAN-GMPELHKLTPFLGVLQDRGFK-VALVTDGRMSGASGKVPAAIHVSPEAIAG 532 R GP+ GMPE + P L G + + ++D RMSG S +H +PEA G Sbjct: 439 RNAGPQGGPGMPE-WGMIPMPKALLKLGLRDMMRISDARMSGTSFGA-CVLHAAPEAYVG 496 Query: 533 GPLARLRDGDRVRVDGVNGELRVLVDDAEWQARSLEPAPQDGNLGCGRELFAFMRNAMSS 592 GPLA LR GD V +D L +LV D E AR P G G L + Sbjct: 497 GPLALLRTGDMVEMDIPARSLNMLVTDEELNARRAAWMPPPPRYGRGYGL--MFSKHIEQ 554 Query: 593 AEEGACSF 600 A++G C F Sbjct: 555 ADKG-CDF 561 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: 831 Number of extensions: 51 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: 578 Length adjustment: 37 Effective length of query: 571 Effective length of database: 541 Effective search space: 308911 Effective search space used: 308911 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