Align Phosphogluconate dehydratase; EC 4.2.1.12; 6-phosphogluconate dehydratase (uncharacterized)
to candidate 8501301 DvMF_2034 dihydroxy-acid dehydratase (RefSeq)
Query= curated2:P31961 (608 letters) >FitnessBrowser__Miya:8501301 Length = 555 Score = 245 bits (626), Expect = 3e-69 Identities = 185/550 (33%), Positives = 269/550 (48%), Gaps = 57/550 (10%) Query: 33 KGPHRGTLPCGNLAHGVAACGESDKQTLRLMNQANVAIVSAYNDMLSAHQPFERFPGLIK 92 K PHR +L H + E ++ L V +V+A N+++ H +K Sbjct: 12 KAPHR------SLLHALGLTREEIERPL-------VGVVNAANEVVPGHVHLHTIAEAVK 58 Query: 93 QALHEIGSVGQFAGGVP------AMCDGVTQGEPGMELSLASRDVIAMSTAIALSHNMFD 146 + AGG P A+CDG+ GM SL SR++IA S I + + FD Sbjct: 59 AGVRA-------AGGTPMEFPAIAVCDGLAMNHEGMHFSLPSREIIADSIEIMATAHPFD 111 Query: 147 AALCLGVCDKIVPGLLIGSLRFGHLPTVFVPAGPMPTGISNKEKAAVRQLF-AEGKATRE 205 A + + CDK VPG+L+ LR +P++ V GPM G + + + +F A G+ R Sbjct: 112 ALVFIPNCDKSVPGMLMAMLRMD-IPSIMVSGGPMLAGGTLAGRTDLISVFEAVGRVQRG 170 Query: 206 ELLASE---MASYHAPG--TCTFYGTANTNQLLVEVMGLHLPGASFVNPNTPLRDELTRE 260 ++ +E M PG +C TANT + E MGL LPG + T R L + Sbjct: 171 DMTMAELDEMTETACPGCGSCAGMFTANTMNCMAETMGLALPGNGTIPAVTAARVRLAKH 230 Query: 261 AARQASRLTPENGNYVPMAEIVDEKAIVNSVVALLATGGSTNHTLHLLAIAQAAGIQLTW 320 A + L +N + IV +A+ N+V +A GGSTN LHL A+ AG+ LT Sbjct: 231 AGMKVMELLEKN---ITPRSIVTPRAVANAVAVDMALGGSTNTVLHLPAVFGEAGLDLTL 287 Query: 321 QDMSELSHVVPTLARIYPNGQADINHFQAAGGMSFLIRQLLDGGLLHEDVQTVAGPGLRR 380 E+S P L ++ P G I AAGG+ ++ +L GL+ V TV G L Sbjct: 288 DIFDEVSRKTPNLCKLSPAGHHHIQDLHAAGGIPAVMAELTRKGLVDTSVMTVTGKTLAE 347 Query: 381 YTREPFLEDGRLVWREGPERSLDEAILRPLDKPFSAEGGLRLMEGNLG--RGVMKVSAVA 438 E R L+ ++R D P+SA+GG+ +++G+L V+K SAVA Sbjct: 348 NLAEL------------NARVLNPDVIRSADAPYSAQGGIAILKGSLAPQGAVVKQSAVA 395 Query: 439 PEHQVVEAPVRIFHDQASLAAAFKAGELERDLVAVVRFQGPRAN-GMPELHKLTPFLGVL 497 PE V EA R+F + AA G++ + ++R++GPR GM E+ L+P + Sbjct: 396 PEMMVREAVARVFDSEGEAHAAIMGGKINKGDAIIIRYEGPRGGPGMREM--LSPTAAIA 453 Query: 498 -QDRGFKVALVTDGRMSGASGKVPAAI-HVSPEAIAGGPLARLRDGDRVRVDGVNGELRV 555 G VAL+TDGR SG G AAI HVSPEA GG + +R+GD + +D L + Sbjct: 454 GMGLGADVALITDGRFSG--GTRGAAIGHVSPEAADGGNIGLVREGDHILIDIPARRLDL 511 Query: 556 LVDDAEWQAR 565 LVD+AE AR Sbjct: 512 LVDEAELAAR 521 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: 927 Number of extensions: 69 Number of successful extensions: 7 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: 555 Length adjustment: 36 Effective length of query: 572 Effective length of database: 519 Effective search space: 296868 Effective search space used: 296868 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