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 8501301 DvMF_2034 dihydroxy-acid dehydratase (RefSeq)
Query= SwissProt::B5ZZ34 (579 letters) >FitnessBrowser__Miya:8501301 Length = 555 Score = 317 bits (813), Expect = 6e-91 Identities = 193/547 (35%), Positives = 301/547 (55%), Gaps = 22/547 (4%) Query: 27 HRGWLKNQGYPHDLFDGRPVIGILNTWSDMTPCNGHLRELAEKVKAGVWEAGGFPLEVPV 86 HR L G + + RP++G++N +++ P + HL +AE VKAGV AGG P+E P Sbjct: 15 HRSLLHALGLTREEIE-RPLVGVVNAANEVVPGHVHLHTIAEAVKAGVRAAGGTPMEFPA 73 Query: 87 FSASENTFRPTAMMY-----RNLAALAVEEAIRGQPMDGCVLLVGCDKTTPSLLMGAASC 141 + + M+ R + A ++E P D V + CDK+ P +LM Sbjct: 74 IAVCDGLAMNHEGMHFSLPSREIIADSIEIMATAHPFDALVFIPNCDKSVPGMLMAMLRM 133 Query: 142 DLPSIVVTGGPMLNGYFRGERVGSGTHLWKFSEM--VKAGEMTQAEFLEAEASMSRSSGT 199 D+PSI+V+GGPML G G G + F + V+ G+MT AE E + G+ Sbjct: 134 DIPSIMVSGGPMLAG---GTLAGRTDLISVFEAVGRVQRGDMTMAELDEMTETACPGCGS 190 Query: 200 CNTMGTASTMASMAEALGMALSGNAAIPGVDSRRKVMAQLTGRRIVQMVKDDLKPSEIMT 259 C M TA+TM MAE +G+AL GN IP V + R +A+ G +++++++ ++ P I+T Sbjct: 191 CAGMFTANTMNCMAETMGLALPGNGTIPAVTAARVRLAKHAGMKVMELLEKNITPRSIVT 250 Query: 260 KQAFENAIRTNAAIGGSTNAVIHLLAIAGRVGIDLSLDDWDRCGRDVPTIVNLMPSGKYL 319 +A NA+ + A+GGSTN V+HL A+ G G+DL+LD +D R P + L P+G + Sbjct: 251 PRAVANAVAVDMALGGSTNTVLHLPAVFGEAGLDLTLDIFDEVSRKTPNLCKLSPAGHHH 310 Query: 320 MEEFFYAGGLPVVLKRLGEAGLLHKDALTVSGETVWDEVKDVVN--WNEDVILPAEKALT 377 +++ AGG+P V+ L GL+ +TV+G+T+ + + ++ N DVI A+ + Sbjct: 311 IQDLHAAGGIPAVMAELTRKGLVDTSVMTVTGKTLAENLAELNARVLNPDVIRSADAPYS 370 Query: 378 SSGGIVVLRGNLAPKGAVLKPSAASPHLLVHKGRAVVFEDIDDYKAKINDDNLDIDENCI 437 + GGI +L+G+LAP+GAV+K SA +P ++V + A VF+ + A I I++ Sbjct: 371 AQGGIAILKGSLAPQGAVVKQSAVAPEMMVREAVARVFDSEGEAHAAIMGGK--INKGDA 428 Query: 438 MVMKNCGPKGYPGMAEVGNMGLPPKVLKKGI---LDMVRISDARMSGTAYGTVVLHTSPE 494 ++++ GP+G PGM E+ L P G+ D+ I+D R SG G + H SPE Sbjct: 429 IIIRYEGPRGGPGMREM----LSPTAAIAGMGLGADVALITDGRFSGGTRGAAIGHVSPE 484 Query: 495 AAVGGPLAVVKNGDMIELDVPNRRLHLDISDEELARRLAEWQPNHDLPTSGYAFLHQQHV 554 AA GG + +V+ GD I +D+P RRL L + + ELA R + P TS + + V Sbjct: 485 AADGGNIGLVREGDHILIDIPARRLDLLVDEAELAARRETFVPLEKPVTSPLLRRYARQV 544 Query: 555 EGADTGA 561 A TGA Sbjct: 545 TSAATGA 551 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: 861 Number of extensions: 48 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: 555 Length adjustment: 36 Effective length of query: 543 Effective length of database: 519 Effective search space: 281817 Effective search space used: 281817 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