Align Xylonate dehydratase (EC 4.2.1.82) (characterized)
to candidate 15969 b1851 phosphogluconate dehydratase (NCBI)
Query= reanno::pseudo6_N2E2:Pf6N2E2_1668 (594 letters) >FitnessBrowser__Keio:15969 Length = 603 Score = 183 bits (464), Expect = 2e-50 Identities = 147/472 (31%), Positives = 222/472 (47%), Gaps = 47/472 (9%) Query: 120 DGVVLTTGCDKTTPACLMAAATTD-LPAIVLSGGPMLDGHHKGELIGSGTVLWHARNLMA 178 DG + CDK P MAA + LPA+ + GPM G E + R L A Sbjct: 146 DGALFLGVCDKIVPGLTMAALSFGHLPAVFVPSGPMASGLPNKEKV-------RIRQLYA 198 Query: 179 AGEIDYEGFMEMTTAASPSVGHCNTMGTALSMNALAEALGMSLPGCASIPAPYRERGQMA 238 G++D +E A+ + G C GTA + + E +GM LPG + + R + Sbjct: 199 EGKVDRMALLESEAASYHAPGTCTFYGTANTNQMVVEFMGMQLPGSSFVHPDSPLRDALT 258 Query: 239 YATGKRICDLV---RQDIRPSQIMTRQAFENAIAVASALGASSNCPPHLIAIARHMGVEL 295 A +++ + + + +++ + N I A G S+N HL+A+AR G+++ Sbjct: 259 AAAARQVTRMTGNGNEWMPIGKMIDEKVVVNGIVALLATGGSTNHTMHLVAMARAAGIQI 318 Query: 296 SLEDWQRIGEDVPLLVNCMPAGKYLGEGFHRAGGVPSVMHELQKAGRLHEDCATVSGKTI 355 + +D+ + + VPL+ P G F AGGVP ++ EL KAG LHED TV+G + Sbjct: 319 NWDDFSDLSDVVPLMARLYPNGPADINHFQAAGGVPVLVRELLKAGLLHEDVNTVAGFGL 378 Query: 356 -----------GEI-----VSNSLTSNTDVIHPFDTPLKHRAGFIVLSGNFFDSAIMKMS 399 GE+ SL SN VI F+ P H G VLSGN A+MK S Sbjct: 379 SRYTLEPWLNNGELDWREGAEKSLDSN--VIASFEQPFSHHGGTKVLSGN-LGRAVMKTS 435 Query: 400 VVGEAFRKTYLSEPGAENSFEARAIVFEGPEDYHARIDDPALDIDERCILVIRGVGTVGY 459 V P EA A+VFE D + LD D C++V+R G Sbjct: 436 AV-----------PVENQVIEAPAVVFESQHDVMPAFEAGLLDRD--CVVVVRHQGPKA- 481 Query: 460 PGSAEVVNMAPPAALIKQGIDSLPCLGDGRQSGTSAS-PSILNMSPEAAVGGGLALLKTN 518 G E+ + PP ++ + + DGR SG S PS ++++PEA GG LA ++ Sbjct: 482 NGMPELHKLMPPLGVLLDRCFKIALVTDGRLSGASGKVPSAIHVTPEAYDGGLLAKVRDG 541 Query: 519 DRLKVDLNTRTVNLLIDDAEMAQRRREWIPNIPPSQT-PWQELYRQLVGQLS 569 D ++V+ T + LL+D+AE+A R IP++ S+ +EL+ L +LS Sbjct: 542 DIIRVNGQTGELTLLVDEAELAAREPH-IPDLSASRVGTGRELFSALREKLS 592 Lambda K H 0.319 0.135 0.407 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: 840 Number of extensions: 44 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: 594 Length of database: 603 Length adjustment: 37 Effective length of query: 557 Effective length of database: 566 Effective search space: 315262 Effective search space used: 315262 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 (21.7 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