Align L-arabinonate dehydratase; ArDHT; D-fuconate dehydratase; Galactonate dehydratase; L-arabonate dehydratase; EC 4.2.1.25; EC 4.2.1.67; EC 4.2.1.6 (characterized)
to candidate 14407 b0269 CP4-6 prophage; predicted dehydratase (NCBI)
Query= SwissProt::B5ZZ34 (579 letters) >FitnessBrowser__Keio:14407 Length = 655 Score = 186 bits (471), Expect = 3e-51 Identities = 175/552 (31%), Positives = 264/552 (47%), Gaps = 72/552 (13%) Query: 42 DGRPVIGILNTWSDMTPCNGHLRELAEKVKAGVWEA---GGFPLEVPVFSASENTFRPT- 97 DGRP+ +T GH E+ +++A E GG P V + + T Sbjct: 77 DGRPIALGYHT--------GHW-EIGMQMQAAAKEITRNGGIPFAAFVSDPCDGRSQGTH 127 Query: 98 ----AMMYRNLAALAVEEAIRGQPMDGCVLLVG-CDKTTPSLLMG-AASCDLPSIVVTGG 151 ++ YRN AA+ IR P V+ V CDK P+ ++ AA DLP+I+V GG Sbjct: 128 GMFDSLPYRNDAAIVFRRLIRSLPTRRAVIGVATCDKGLPATMIALAAMHDLPTILVPGG 187 Query: 152 PMLNGYFRGERVGSGTHLWKFSEMVKAGEMTQAEFLEAEASMSRS-SGTCNTMGTASTMA 210 L GE G + E++ E E S G C +GTA T Sbjct: 188 ATLPPTV-GEDAGK---VQTIGARFANHELSLQEAAELGCRACASPGGGCQFLGTAGTSQ 243 Query: 211 SMAEALGMALSGNAAIPGVDSRRKVMAQLTGRRIVQMVKDDLKPSEIMTKQAFENAIRTN 270 +AEALG+AL +A P + +A+ + R + ++ + +I++ +A ENA+ + Sbjct: 244 VVAEALGLALPHSALAPSGQAVWLEIARQSARAVSELDSRGITTRDILSDKAIENAMVIH 303 Query: 271 AAIGGSTNAVIHLLAIAGRVGIDL-SLDDWDRCGRDVPTIVNLMPSGK--YLMEEFFYAG 327 AA GGSTN ++H+ AIA G + ++ W R R VP +V+++P+G + F AG Sbjct: 304 AAFGGSTNLLLHIPAIAHAAGCTIPDVEHWTRINRKVPRLVSVLPNGPDYHPTVRAFLAG 363 Query: 328 GLPVVLKRLGEAGLLHKDALTVSGETVWDEV------------------KDVVNWNEDVI 369 G+P V+ L + GLLH DA+TV+G+TV + + +D V +DVI Sbjct: 364 GVPEVMLHLRDLGLLHLDAMTVTGQTVGENLEWWQASERRARFRQCLREQDGVE-PDDVI 422 Query: 370 LPAEKA----LTSSGGIVVLRGNLAPKGAVLKPSAASPHLL------VHKGRAVVFEDID 419 LP EKA LTS+ + GN+AP+G+V+K +A P ++ H GR VF + Sbjct: 423 LPPEKAKAKGLTST--VCFPTGNIAPEGSVIKATAIDPSVVGEDGVYHHTGRVRVF--VS 478 Query: 420 DYKAKINDDNLDIDENCIMVMKNCGPKGYPGMAEVGNMGLPPKVLKKGILDMVRISDARM 479 + +A +I + IMV+ GP G GM E + K + G + I+DAR Sbjct: 479 EAQAIKAIKREEIVQGDIMVVIGGGPSG-TGMEETYQLTSALKHISWG-KTVSLITDARF 536 Query: 480 SGTAYGTVVLHTSPEAAVGGPLAVVKNGDMIELDVPNRRL----------HLDISDEELA 529 SG + G H SPEA GGP+ +++ D+IE+ V L ++ EE A Sbjct: 537 SGVSTGACFGHVSPEALAGGPIGKLRDNDIIEIAVDRLTLTGSVNFIGTADNPLTPEEGA 596 Query: 530 RRLAEWQPNHDL 541 R LA Q + DL Sbjct: 597 RELARRQTHPDL 608 Lambda K H 0.318 0.135 0.408 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: 1028 Number of extensions: 66 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: 579 Length of database: 655 Length adjustment: 37 Effective length of query: 542 Effective length of database: 618 Effective search space: 334956 Effective search space used: 334956 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: 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