Align L-arabonate dehydratase (EC 4.2.1.25) (characterized)
to candidate 8501301 DvMF_2034 dihydroxy-acid dehydratase (RefSeq)
Query= reanno::Smeli:SM_b20890 (579 letters) >FitnessBrowser__Miya:8501301 Length = 555 Score = 337 bits (864), Expect = 8e-97 Identities = 204/547 (37%), Positives = 307/547 (56%), Gaps = 22/547 (4%) Query: 27 HRSWMKNQGLPADTFDGRPIIGICNTWSELTPCNAHLRDLAERVKRGVYEAGGFPVEFPV 86 HRS + GL + + RP++G+ N +E+ P + HL +AE VK GV AGG P+EFP Sbjct: 15 HRSLLHALGLTREEIE-RPLVGVVNAANEVVPGHVHLHTIAEAVKAGVRAAGGTPMEFPA 73 Query: 87 FSTGES-TLRPTAMMF----RNLAAMDVEESIRGNPVDGVVLLGGCDKTTPSLLMGAASV 141 + + + M F R + A +E +P D +V + CDK+ P +LM + Sbjct: 74 IAVCDGLAMNHEGMHFSLPSREIIADSIEIMATAHPFDALVFIPNCDKSVPGMLMAMLRM 133 Query: 142 DIPAIVVSGGPMLNGKWRGKDVGSGTAIWQFSEM--VKSGEMSLEEFMDAEQGMARSAGS 199 DIP+I+VSGGPML G G G I F + V+ G+M++ E + + GS Sbjct: 134 DIPSIMVSGGPMLAG---GTLAGRTDLISVFEAVGRVQRGDMTMAELDEMTETACPGCGS 190 Query: 200 CMTMGTASTMASMAEALGMTLSGNAAIPAVDARRRVISQLTGRRIVEMVKEDLKPSDILT 259 C M TA+TM MAE +G+ L GN IPAV A R +++ G +++E++++++ P I+T Sbjct: 191 CAGMFTANTMNCMAETMGLALPGNGTIPAVTAARVRLAKHAGMKVMELLEKNITPRSIVT 250 Query: 260 KEAFENAIRVNGAVGGSTNAVLHLLALAGRVGVDLSLDDWDRLGRDVPTIVNLQPSGKYL 319 A NA+ V+ A+GGSTN VLHL A+ G G+DL+LD +D + R P + L P+G + Sbjct: 251 PRAVANAVAVDMALGGSTNTVLHLPAVFGEAGLDLTLDIFDEVSRKTPNLCKLSPAGHHH 310 Query: 320 MEEFYYAGGLPVVIKAVAEMGLLHNDAITVSGDTIWNDVK--GVVNYNEDVILPREKALT 377 +++ + AGG+P V+ + GL+ +TV+G T+ ++ N DVI + + Sbjct: 311 IQDLHAAGGIPAVMAELTRKGLVDTSVMTVTGKTLAENLAELNARVLNPDVIRSADAPYS 370 Query: 378 KSGGIAVLRGNLAPRGAVLKPSAASPHLMQHKGRAVVFESIEDYHARINREDLDIDETCI 437 GGIA+L+G+LAP+GAV+K SA +P +M + A VF+S + HA I ++ + Sbjct: 371 AQGGIAILKGSLAPQGAVVKQSAVAPEMMVREAVARVFDSEGEAHAAIMGGKINKGDA-- 428 Query: 438 MVLKYCGPKGYPGMAEVGNMGLPPKVLKKGI---TDMIRISDARMSGTAYGTVILHTAPE 494 ++++Y GP+G PGM E+ L P G+ D+ I+D R SG G I H +PE Sbjct: 429 IIIRYEGPRGGPGMREM----LSPTAAIAGMGLGADVALITDGRFSGGTRGAAIGHVSPE 484 Query: 495 AAEGGPLALVENGDLIEVDIPNRTLHLHVSDEELARRRAAWVSPVKPLTGGYGGLYIKTV 554 AA+GG + LV GD I +DIP R L L V + ELA RR +V KP+T Y + V Sbjct: 485 AADGGNIGLVREGDHILIDIPARRLDLLVDEAELAARRETFVPLEKPVTSPLLRRYARQV 544 Query: 555 MQADAGA 561 A GA Sbjct: 545 TSAATGA 551 Lambda K H 0.318 0.135 0.402 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: 876 Number of extensions: 41 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