Align Phosphogluconate dehydratase; 6-phosphogluconate dehydratase; EC 4.2.1.12 (characterized)
to candidate 18321 b4297 KpLE2 phage-like element; predicted dehydratase (NCBI)
Query= SwissProt::P21909 (607 letters) >FitnessBrowser__Keio:18321 Length = 655 Score = 188 bits (477), Expect = 7e-52 Identities = 156/500 (31%), Positives = 243/500 (48%), Gaps = 38/500 (7%) Query: 80 LSAHEPYYRYPEQMKVFAREVGAT--VQVAGGVPAMCDGVTQGQPGMEESLFSRDVIALA 137 L+ H+ +Y QMK A + A + A V CDG TQG GM +SL R+ ++ Sbjct: 83 LALHQGHYELDIQMKAAAEVIKANHALPYAVYVSDPCDGRTQGTTGMFDSLPYRNDASMV 142 Query: 138 TSVSLSHGMFEGAALLGI--CDKIVPGLLMGALRFGHLPTILVPSGPMTTGIPNKEKIRI 195 L + + A++G+ CDK +P +M ++ T+LVP G ++ ++ Sbjct: 143 MR-RLIRSLPDAKAVIGVASCDKGLPATMMALAAQHNIATVLVPGGATLPAKDGEDNGKV 201 Query: 196 RQLYAQGKIGQKELLDMEAA----CYHAEGTCTFYGTANTNQMVMEVLGLHMPGSAFVTP 251 + + A+ G+ L D A C + G C F GTA T+Q+V E LGL +P SA Sbjct: 202 QTIGARFANGELSLQDARRAGCKACASSGGGCQFLGTAGTSQVVAEGLGLAIPHSALAPS 261 Query: 252 GTPLRQALTRAAVHRVAELGWKGDDYRPLGKIIDEKSIVNAIVGLLATGGSTNHTMHIPA 311 G P+ + + RA+ L KG R +I+ +K+I NA+ A GGSTN +HIPA Sbjct: 262 GEPVWREIARASARAALNLSQKGITTR---EILTDKAIENAMTVHAAFGGSTNLLLHIPA 318 Query: 312 IARAAGV-IVNWNDFHDLSEVVPLIARIYPNGP---RDINEFQNAGGMAYVIKELLSANL 367 IA AG I +D+ +++ VP + + PNGP +N F AGG+ V+ L S L Sbjct: 319 IAHQAGCHIPTVDDWIRINKRVPRLVSVLPNGPVYHPTVNAFM-AGGVPEVMLHLRSLGL 377 Query: 368 LNRDVTTIA----KGGIEEYAKAPALNDAGELVWKPAGEPGDDTILRPVSNPFAKDGGL- 422 L+ DV T+ K ++ + + +L+ D+ I+ P AK GL Sbjct: 378 LHEDVMTVTGSTLKENLDWWEHSERRQRFKQLLLDQEQINADEVIMSPQQ---AKARGLT 434 Query: 423 ---RLLEGNLG--RAMYKASAVDPK------FWTIEAPVRVFSDQDDVQKAFKAGELNKD 471 GN+ ++ K++A+DP + + +V+ + K ++ Sbjct: 435 STITFPVGNIAPEGSVIKSTAIDPSMIDEQGIYYHKGVAKVYLSEKSAIYDIKHDKIKAG 494 Query: 472 VIVVVRFQGPRANGMPELHKLTPALGVLQDNGYKVALVTDGRMSGATGKVPVALHVSPEA 531 I+V+ GP GM E +++T AL L G V+L+TD R SG + + HV PEA Sbjct: 495 DILVIIGVGPSGTGMEETYQVTSALKHL-SYGKHVSLITDARFSGVSTGACIG-HVGPEA 552 Query: 532 LGGGAIGKLRDGDIVRISVE 551 L GG IGKLR GD++ I ++ Sbjct: 553 LAGGPIGKLRTGDLIEIKID 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: 981 Number of extensions: 56 Number of successful extensions: 8 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 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