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 Pf6N2E2_1668 Xylonate dehydratase (EC 4.2.1.82)
Query= SwissProt::B5ZZ34 (579 letters) >FitnessBrowser__pseudo6_N2E2:Pf6N2E2_1668 Length = 594 Score = 479 bits (1234), Expect = e-139 Identities = 258/569 (45%), Positives = 360/569 (63%), Gaps = 15/569 (2%) Query: 10 KLRSQEWYGGTSR---DVIYHRGWLKNQGYPHDLFDGRPVIGILNTWSDMTPCNGHLREL 66 +LRS++W+ + +Y ++ +L GRP+IGI T SD+TPCN H EL Sbjct: 8 RLRSEQWFNDPAHADMTALYVERYMNYGMTREELQSGRPIIGIAQTGSDLTPCNRHHLEL 67 Query: 67 AEKVKAGVWEAGGFPLEVPVFSASENTFRPTAMMYRNLAALAVEEAIRGQPMDGCVLLVG 126 A++VKAG+ +AGG P+E PV +E + RPTA + RNLA L + E + G P+DG VL G Sbjct: 68 AQRVKAGIRDAGGIPMEFPVHPIAEQSRRPTAALDRNLAYLGLVEILHGYPLDGVVLTTG 127 Query: 127 CDKTTPSLLMGAASCDLPSIVVTGGPMLNGYFRGERVGSGTHLWKFSEMVKAGEMTQAEF 186 CDKTTP+ LM AA+ DLP+IV++GGPML+G+ +GE +GSGT LW ++ AGE+ F Sbjct: 128 CDKTTPACLMAAATTDLPAIVLSGGPMLDGHHKGELIGSGTVLWHARNLMAAGEIDYEGF 187 Query: 187 LEAEASMSRSSGTCNTMGTASTMASMAEALGMALSGNAAIPGVDSRRKVMAQLTGRRIVQ 246 +E + S S G CNTMGTA +M ++AEALGM+L G A+IP R MA TG+RI Sbjct: 188 MEMTTAASPSVGHCNTMGTALSMNALAEALGMSLPGCASIPAPYRERGQMAYATGKRICD 247 Query: 247 MVKDDLKPSEIMTKQAFENAIRTNAAIGGSTNAVIHLLAIAGRVGIDLSLDDWDRCGRDV 306 +V+ D++PS+IMT+QAFENAI +A+G S+N HL+AIA +G++LSL+DW R G DV Sbjct: 248 LVRQDIRPSQIMTRQAFENAIAVASALGASSNCPPHLIAIARHMGVELSLEDWQRIGEDV 307 Query: 307 PTIVNLMPSGKYLMEEFFYAGGLPVVLKRLGEAGLLHKDALTVSGETVWDEVKDVVNWNE 366 P +VN MP+GKYL E F AGG+P V+ L +AG LH+D TVSG+T+ + V + + N Sbjct: 308 PLLVNCMPAGKYLGEGFHRAGGVPSVMHELQKAGRLHEDCATVSGKTIGEIVSNSLTSNT 367 Query: 367 DVILPAEKALTSSGGIVVLRGNLAPKGAVLKPSAASPHLL-----------VHKGRAVVF 415 DVI P + L G +VL GN A++K S + RA+VF Sbjct: 368 DVIHPFDTPLKHRAGFIVLSGNFF-DSAIMKMSVVGEAFRKTYLSEPGAENSFEARAIVF 426 Query: 416 EDIDDYKAKINDDNLDIDENCIMVMKNCGPKGYPGMAEVGNMGLPPKVLKKGILDMVRIS 475 E +DY A+I+D LDIDE CI+V++ G GYPG AEV NM P ++K+GI + + Sbjct: 427 EGPEDYHARIDDPALDIDERCILVIRGVGTVGYPGSAEVVNMAPPAALIKQGIDSLPCLG 486 Query: 476 DARMSGTAYGTVVLHTSPEAAVGGPLAVVKNGDMIELDVPNRRLHLDISDEELARRLAEW 535 D R SGT+ +L+ SPEAAVGG LA++K D +++D+ R ++L I D E+A+R EW Sbjct: 487 DGRQSGTSASPSILNMSPEAAVGGGLALLKTNDRLKVDLNTRTVNLLIDDAEMAQRRREW 546 Query: 536 QPNHDLPTSGYAFLHQQHVEGADTGADLD 564 PN + + L++Q V TG L+ Sbjct: 547 IPNIPPSQTPWQELYRQLVGQLSTGGCLE 575 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: 990 Number of extensions: 57 Number of successful extensions: 2 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: 594 Length adjustment: 37 Effective length of query: 542 Effective length of database: 557 Effective search space: 301894 Effective search space used: 301894 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