Align L-arabonate dehydratase (EC 4.2.1.25) (characterized)
to candidate HSERO_RS22480 HSERO_RS22480 dihydroxy-acid dehydratase
Query= reanno::Smeli:SM_b20890 (579 letters) >FitnessBrowser__HerbieS:HSERO_RS22480 Length = 594 Score = 456 bits (1173), Expect = e-132 Identities = 250/585 (42%), Positives = 368/585 (62%), Gaps = 15/585 (2%) Query: 1 MKKKAEWPRKLRSQEWFGGTGK--NAIMHRSWMKNQGLPADTF-DGRPIIGICNTWSELT 57 M K PR+ RSQ+WF ++ N G+ A+ GRPIIGI + S+++ Sbjct: 1 MNKPNATPRRFRSQDWFDNPDHIDMTALYLERFMNYGITAEELRSGRPIIGIAQSGSDIS 60 Query: 58 PCNAHLRDLAERVKRGVYEAGGFPVEFPVFSTGESTLRPTAMMFRNLAAMDVEESIRGNP 117 PCN +LA+RV+ G+ +AGG P+EFP+ E+ RPTA + RNLA + + E + G P Sbjct: 61 PCNRIHLELAKRVRDGIRDAGGIPMEFPLHPIFENCRRPTAAIDRNLAYLGLVEILHGYP 120 Query: 118 VDGVVLLGGCDKTTPSLLMGAASVDIPAIVVSGGPMLNGKWRGKDVGSGTAIWQFSEMVK 177 +D VVL GCDKTTPS +M AA+VDIPAIV+SGGPML+G G+ VGSG+AIW+ +++ Sbjct: 121 IDAVVLTTGCDKTTPSQIMAAATVDIPAIVLSGGPMLDGWMDGELVGSGSAIWKGRKLLS 180 Query: 178 SGEMSLEEFMDAEQGMARSAGSCMTMGTASTMASMAEALGMTLSGNAAIPAVDARRRVIS 237 +G + E+F++ A S+G C TMGTASTM +MAEALGM+L+G +AIPA R ++ Sbjct: 181 AGSIDNEKFLEIAAASAPSSGHCNTMGTASTMNAMAEALGMSLTGCSAIPAPYRERGQMA 240 Query: 238 QLTGRRIVEMVKEDLKPSDILTKEAFENAIRVNGAVGGSTNAVLHLLALAGRVGVDLSLD 297 TGRRIV M EDL+PS ILT++AF +AI VN A+GGSTNA H++A+A GV+L + Sbjct: 241 YETGRRIVGMAYEDLRPSAILTRDAFLDAIVVNAAIGGSTNAQPHIMAMARHAGVELQSE 300 Query: 298 DWDRLGRDVPTIVNLQPSGKYLMEEFYYAGGLPVVIKAVAEMGLLHNDAITVSGDTIWND 357 DW + G DVP ++N+QP+GKYL E F+ AGG+P ++ + + G L + IT +G T+ + Sbjct: 301 DWMKYGYDVPLLLNMQPAGKYLGERFHRAGGVPAIMWELQQAGKLRAERITATGKTMAEN 360 Query: 358 VKGVVNYNEDVILPREKALTKSGGIAVLRGNLAPRGAVLKPSAASPHLMQH--------- 408 ++G + + ++I P L + G VL+GNL A++K S S + Sbjct: 361 LQGRASNDREMIYPFAAPLRERAGFLVLKGNLFD-FAIMKTSVISETFRERYLSTPGQEN 419 Query: 409 --KGRAVVFESIEDYHARINREDLDIDETCIMVLKYCGPKGYPGMAEVGNMGLPPKVLKK 466 + RAVVF+ +DYHARIN L IDE ++ ++ GP G+PG AEV NM P ++K+ Sbjct: 420 IFECRAVVFDGSDDYHARINDPALKIDENTLLAIRGAGPVGWPGSAEVVNMQPPDALIKR 479 Query: 467 GITDMIRISDARMSGTAYGTVILHTAPEAAEGGPLALVENGDLIEVDIPNRTLHLHVSDE 526 G++ + + D R SGT+ IL+ +PE+A GG LA + +GD + +D+ ++ VS+E Sbjct: 480 GVSTLPTLGDGRQSGTSDSPSILNASPESAVGGGLAYLRDGDRVRIDLNTGECNMLVSEE 539 Query: 527 ELARRRAAWVSPVKPLTGGYGGLYIKTVMQADAGADLDFLVGARG 571 ELARR++ + PV P + +Y TV Q + GA ++ + +G Sbjct: 540 ELARRKSEGIPPVPPSQTPWQEIYRSTVGQLETGACMELALKYQG 584 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: 933 Number of extensions: 37 Number of successful extensions: 3 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