Align L-arabonate dehydratase (EC 4.2.1.25) (characterized)
to candidate WP_085634854.1 MGEO_RS01140 dihydroxy-acid dehydratase
Query= reanno::Smeli:SM_b20890 (579 letters) >NCBI__GCF_002115805.1:WP_085634854.1 Length = 587 Score = 308 bits (790), Expect = 3e-88 Identities = 188/539 (34%), Positives = 298/539 (55%), Gaps = 31/539 (5%) Query: 21 GKNAIMHRSWMKNQGLPADTFDGRPIIGICNTWSELTPCNAHLRDLAERVKRGVYEAGGF 80 G HRS+ G+ + +P++G+ W+E PCN L A+ VK GV +A G Sbjct: 19 GPERAPHRSYYYAMGMTEEEIH-QPLVGVATCWNEAAPCNIALNRQAQAVKMGVKQAFGT 77 Query: 81 PVEFPVFST------GESTLRPTAMMFRNLAAMDVEESIRGNPVDGVVLLGGCDKTTPSL 134 P EF + G +R +++ R A VE ++RG+ D VV L GCDK+ P + Sbjct: 78 PREFTTITVTDGIAMGHEGMR-SSLASREAIADTVELTMRGHCYDAVVGLAGCDKSLPGM 136 Query: 135 LMGAASVDIPAIVVSGGPMLNGK----------WRGKDVGSGTAIWQFSEMV---KSGEM 181 +M +++P++ + GG +L GK +R +D+ + E V ++ E+ Sbjct: 137 MMAMVRLNVPSVFIYGGSILPGKAPQVAEIPEDFRTRDL----TVQDMFEAVGRHQNNEL 192 Query: 182 SLEEFMDAEQGMARSAGSCMTMGTASTMASMAEALGMTLSGNAAIPAVDARRRVISQLTG 241 S + E+ SAG+C TA+TMA ++EA+G+ L ++ +PA R + +G Sbjct: 193 SDKALDMLERVACPSAGACGGQFTANTMACVSEAIGLALFNSSGMPAPYESRDAYGEASG 252 Query: 242 RRIVEMVKEDLKPSDILTKEAFENAIRVNGAVGGSTNAVLHLLALAGRVGVDLSLDDWDR 301 R +++++++++K DI+T+EA ENA RV GGSTNA LHL A+A G++ L+D Sbjct: 253 RAVMDLIEQNIKARDIVTREALENAARVVACTGGSTNAGLHLPAIAHEAGIEFYLEDVCD 312 Query: 302 LGRDVPTIVNLQPSGKYLMEEFYYAGGLPVVIKAVAEMGLLHNDAITVSGDTIWNDVKGV 361 + +D P V+L+P G Y+ ++ Y AGG+PVV+K + + GL+H D +T S TI ++ + Sbjct: 313 IFKDTPYFVDLKPGGTYVAKDLYDAGGIPVVMKELRKAGLIHEDCVTASTRTIGEELDRI 372 Query: 362 VNYNE-DVILPREKALTKSGGIAVLRGNLAPRGAVLKPSAASPHLMQHKGRAVVFESIED 420 + VI E +TK+GG+ L+GNLAP GA++K + G A VFE ED Sbjct: 373 EREADGKVIYSIETPITKTGGVVGLKGNLAPEGAIVKVAGIKAEDQIFTGPARVFECEED 432 Query: 421 YHARINREDLDIDETCIMVLKYCGPKGYPGMAEVGNMGLPPKVLKKGITDMIR-ISDARM 479 A + D E ++V++ GP G PGM E+ + + +G+ + I+D R Sbjct: 433 AFAAVKARDYKEGE--VIVIRNEGPAGGPGMREM--LATTAALSGQGMGKKVALITDGRF 488 Query: 480 SGTAYGTVILHTAPEAAEGGPLALVENGDLIEVDIPNRTLHLHVSDEELARRRAAWVSP 538 SG G + H PEAA GGP+AL++NGD+I +D N +L + +SDEELA+R+A W P Sbjct: 489 SGATRGFCVGHVGPEAALGGPIALLKNGDMITIDAVNGSLSVDLSDEELAQRKADWTGP 547 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: 882 Number of extensions: 52 Number of successful extensions: 7 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: 587 Length adjustment: 36 Effective length of query: 543 Effective length of database: 551 Effective search space: 299193 Effective search space used: 299193 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 24 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