Align L-arabonate dehydratase (EC 4.2.1.25) (characterized)
to candidate 208900 DVU3373 dihydroxy-acid dehydratase (TIGR)
Query= reanno::Smeli:SM_b20890 (579 letters) >FitnessBrowser__DvH:208900 Length = 554 Score = 345 bits (886), Expect = 2e-99 Identities = 209/547 (38%), Positives = 311/547 (56%), Gaps = 22/547 (4%) Query: 27 HRSWMKNQGLPADTFDGRPIIGICNTWSELTPCNAHLRDLAERVKRGVYEAGGFPVEFPV 86 HRS + GL + RP++G+ N +E+ P + HL D+AE VK GV AGG P+EFP Sbjct: 15 HRSLLHALGLTREEL-ARPLVGVVNAANEVVPGHIHLDDIAEAVKAGVRAAGGTPLEFPA 73 Query: 87 FSTGES-TLRPTAMMF----RNLAAMDVEESIRGNPVDGVVLLGGCDKTTPSLLMGAASV 141 + + + M F R L A +E +P D +V + CDK+ P +LM + Sbjct: 74 IAVCDGLAMNHEGMRFSLPSRELIADSIEIMATAHPFDALVFIPNCDKSVPGMLMAMLRL 133 Query: 142 DIPAIVVSGGPMLNGKWRGKDVGSGTAIWQFSEM--VKSGEMSLEEFMDAEQGMARSAGS 199 D+P+++VSGGPML G G I F + V+ G+M+ E + +G GS Sbjct: 134 DVPSVMVSGGPMLAGATLA---GRADLITVFEGVGRVQRGDMTEAELDELVEGACPGCGS 190 Query: 200 CMTMGTASTMASMAEALGMTLSGNAAIPAVDARRRVISQLTGRRIVEMVKEDLKPSDILT 259 C M TA++M +AE +G+ L GN PAV A R +++ G +++EM++ +++P DI+T Sbjct: 191 CAGMFTANSMNCLAETIGLALPGNGTTPAVTAARIRLAKHAGMKVMEMLERNIRPRDIVT 250 Query: 260 KEAFENAIRVNGAVGGSTNAVLHLLALAGRVGVDLSLDDWDRLGRDVPTIVNLQPSGKYL 319 ++A NA+ V+ A+G STN VLHL A+ G+DL+LD +D++ R P + L P+G + Sbjct: 251 EKAVANAVAVDMALGCSTNTVLHLPAVFAEAGLDLTLDIFDKVSRKTPNLCKLSPAGHHH 310 Query: 320 MEEFYYAGGLPVVIKAVAEMGLLHNDAITVSGDTIWN--DVKGVVNYNEDVILPREKALT 377 +++ + AGG+P V+ + +GL+ A+TV+G T+ D G + DVI P + + Sbjct: 311 IQDLHAAGGIPAVMAELDRIGLIDRSAMTVTGRTVGENLDALGAKVRDADVIRPVDAPYS 370 Query: 378 KSGGIAVLRGNLAPRGAVLKPSAASPHLMQHKGRAVVFESIEDYHARINREDLDIDETCI 437 GGIA+L+G+LAP GAV+K SA +P +M + A VF+S E I + + Sbjct: 371 PQGGIAILKGSLAPGGAVVKQSAVAPEMMVREAVARVFDSEEAACEAIMGGRIKAGDA-- 428 Query: 438 MVLKYCGPKGYPGMAEVGNMGLPPKVLKKGI---TDMIRISDARMSGTAYGTVILHTAPE 494 +V++Y GPKG PGM E+ L P G+ D+ I+D R SG G I H +PE Sbjct: 429 IVIRYEGPKGGPGMREM----LTPTSAIAGMGLGADVALITDGRFSGGTRGAAIGHVSPE 484 Query: 495 AAEGGPLALVENGDLIEVDIPNRTLHLHVSDEELARRRAAWVSPVKPLTGGYGGLYIKTV 554 AAEGGP+ LV+ GD I +DIP R L L V ++ELARRRAA+V K +T Y + V Sbjct: 485 AAEGGPIGLVQEGDRIRIDIPARALDLLVDEDELARRRAAFVPVEKEITSPLLRRYARMV 544 Query: 555 MQADAGA 561 A GA Sbjct: 545 SSAATGA 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: 888 Number of extensions: 49 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: 554 Length adjustment: 36 Effective length of query: 543 Effective length of database: 518 Effective search space: 281274 Effective search space used: 281274 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 Apr 09 2024. 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