Align Phosphogluconate dehydratase; 6-phosphogluconate dehydratase; EC 4.2.1.12 (characterized)
to candidate 14407 b0269 CP4-6 prophage; predicted dehydratase (NCBI)
Query= SwissProt::P21909 (607 letters) >FitnessBrowser__Keio:14407 Length = 655 Score = 189 bits (480), Expect = 3e-52 Identities = 168/500 (33%), Positives = 241/500 (48%), Gaps = 38/500 (7%) Query: 80 LSAHEPYYRYPEQMKVFAREV--GATVQVAGGVPAMCDGVTQGQPGMEESLFSRDVIALA 137 L H ++ QM+ A+E+ + A V CDG +QG GM +SL R+ A+ Sbjct: 83 LGYHTGHWEIGMQMQAAAKEITRNGGIPFAAFVSDPCDGRSQGTHGMFDSLPYRNDAAIV 142 Query: 138 TSVSLSHGMFEGAALLGI--CDKIVPGLLMGALRFGHLPTILVPSG---PMTTGIPNKEK 192 L + A++G+ CDK +P ++ LPTILVP G P T G + Sbjct: 143 FR-RLIRSLPTRRAVIGVATCDKGLPATMIALAAMHDLPTILVPGGATLPPTVGEDAGKV 201 Query: 193 IRIRQLYAQGKIGQKELLDMEA-ACYHAEGTCTFYGTANTNQMVMEVLGLHMPGSAFVTP 251 I +A ++ +E ++ AC G C F GTA T+Q+V E LGL +P SA Sbjct: 202 QTIGARFANHELSLQEAAELGCRACASPGGGCQFLGTAGTSQVVAEALGLALPHSALAPS 261 Query: 252 GTPLRQALTRAAVHRVAELGWKGDDYRPLGKIIDEKSIVNAIVGLLATGGSTNHTMHIPA 311 G + + R + V+EL +G R I+ +K+I NA+V A GGSTN +HIPA Sbjct: 262 GQAVWLEIARQSARAVSELDSRGITTR---DILSDKAIENAMVIHAAFGGSTNLLLHIPA 318 Query: 312 IARAAG-VIVNWNDFHDLSEVVPLIARIYPNGP---RDINEFQNAGGMAYVIKELLSANL 367 IA AAG I + + ++ VP + + PNGP + F AGG+ V+ L L Sbjct: 319 IAHAAGCTIPDVEHWTRINRKVPRLVSVLPNGPDYHPTVRAFL-AGGVPEVMLHLRDLGL 377 Query: 368 LNRDVTTI----AKGGIEEYAKAPALNDAGELVWKPAGEPGDDTILRPVSNPFAKDGGLR 423 L+ D T+ +E + + + + + G DD IL P AK GL Sbjct: 378 LHLDAMTVTGQTVGENLEWWQASERRARFRQCLREQDGVEPDDVILPPEK---AKAKGLT 434 Query: 424 ----LLEGNLG--RAMYKASAVDPK------FWTIEAPVRVFSDQDDVQKAFKAGELNKD 471 GN+ ++ KA+A+DP + VRVF + KA K E+ + Sbjct: 435 STVCFPTGNIAPEGSVIKATAIDPSVVGEDGVYHHTGRVRVFVSEAQAIKAIKREEIVQG 494 Query: 472 VIVVVRFQGPRANGMPELHKLTPALGVLQDNGYKVALVTDGRMSGATGKVPVALHVSPEA 531 I+VV GP GM E ++LT AL + G V+L+TD R SG + HVSPEA Sbjct: 495 DIMVVIGGGPSGTGMEETYQLTSALKHI-SWGKTVSLITDARFSGVSTGACFG-HVSPEA 552 Query: 532 LGGGAIGKLRDGDIVRISVE 551 L GG IGKLRD DI+ I+V+ Sbjct: 553 LAGGPIGKLRDNDIIEIAVD 572 Lambda K H 0.318 0.136 0.403 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: 1047 Number of extensions: 60 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: 607 Length of database: 655 Length adjustment: 38 Effective length of query: 569 Effective length of database: 617 Effective search space: 351073 Effective search space used: 351073 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 54 (25.4 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