Align L-arabonate dehydratase (EC 4.2.1.25) (characterized)
to candidate SM_b20115 SM_b20115 dihydroxy-acid dehydratase
Query= reanno::Smeli:SM_b20890 (579 letters) >FitnessBrowser__Smeli:SM_b20115 Length = 573 Score = 550 bits (1417), Expect = e-161 Identities = 282/565 (49%), Positives = 381/565 (67%), Gaps = 3/565 (0%) Query: 11 LRSQEWFGGTGKNAIMHRSWMKNQGLPADTFDGRPIIGICNTWSELTPCNAHLRDLAERV 70 LRS WF + HRS + G A + +PII I NTWS+L PC+AH + + V Sbjct: 5 LRSARWFAPDDLRSSGHRSRLMQMGYDAKDWGEKPIIAILNTWSDLNPCHAHFKHRIDDV 64 Query: 71 KRGVYEAGGFPVEFPVFSTGESTLRPTAMMFRNLAAMDVEESIRGNPVDGVVLLGGCDKT 130 KRGV +AGGFPVE PV S ES+L+PT M++RN AM+ EE +RG+P+DG VL+GGCDKT Sbjct: 65 KRGVLQAGGFPVELPVQSLSESSLKPTTMLYRNFLAMEAEELLRGHPIDGAVLMGGCDKT 124 Query: 131 TPSLLMGAASVDIPAIVVSGGPMLNGKWRGKDVGSGTAIWQFSEMVKSGEMSLEEFMDAE 190 TP+L+MGA S +P I + GPML G ++G+ +GSG+ W++ + ++G ++ E+++ E Sbjct: 125 TPALVMGAISAGLPMIFLPSGPMLRGHYKGEHLGSGSDAWKYWDERRAGTITDEQWIGVE 184 Query: 191 QGMARSAGSCMTMGTASTMASMAEALGMTLSGNAAIPAVDARRRVISQLTGRRIVEMVKE 250 +G+ARS G CMT GTASTM ++AE+LG+TL G ++IPA DA +S GRRIVEMV E Sbjct: 185 EGIARSYGHCMTFGTASTMTAIAESLGLTLPGASSIPAADANHIRMSTRCGRRIVEMVHE 244 Query: 251 DLKPSDILTKEAFENAIRVNGAVGGSTNAVLHLLALAGRVGVDLSLDDWDRLGRDVPTIV 310 L P I+T+++ NA V A G STNAV+HL+A+A R GV L+L+D D + R P I Sbjct: 245 KLGPEKIITEKSVANASAVAMATGCSTNAVVHLIAMARRAGVPLTLEDLDGISRTTPVIA 304 Query: 311 NLQPSGK-YLMEEFYYAGGLPVVIKAVAEMGLLHNDAITVSGDTIWNDVKGVVNYNEDVI 369 N++PSGK YLME+FYYAGGL ++ + E LLH DA+TVSG + ++G +N DVI Sbjct: 305 NIRPSGKQYLMEDFYYAGGLRALMAEMKE--LLHLDAMTVSGFPLGATLEGAEVHNSDVI 362 Query: 370 LPREKALTKSGGIAVLRGNLAPRGAVLKPSAASPHLMQHKGRAVVFESIEDYHARINRED 429 P + G +AVL+GNLAP G V+KPSA L H+G A+VF+S + A I+ ED Sbjct: 363 RPLSNPIYHEGSLAVLKGNLAPDGCVVKPSACEERLRVHEGPALVFDSYPEMKAAIDDED 422 Query: 430 LDIDETCIMVLKYCGPKGYPGMAEVGNMGLPPKVLKKGITDMIRISDARMSGTAYGTVIL 489 LD+ +++L+ GPKG PGM E G + +P K+LK+G DM+RISDARMSGT+YG IL Sbjct: 423 LDVTPDHVLILRNAGPKGGPGMPEWGMLPIPKKILKQGYRDMLRISDARMSGTSYGACIL 482 Query: 490 HTAPEAAEGGPLALVENGDLIEVDIPNRTLHLHVSDEELARRRAAWVSPVKPLTGGYGGL 549 H APE+ GGPL+LV GD+I VD+ NRT+ + V +E LA RRAAW P GYG + Sbjct: 483 HVAPESHVGGPLSLVRTGDIIRVDVANRTIDMLVDEEILAMRRAAWTRPADKYERGYGWM 542 Query: 550 YIKTVMQADAGADLDFLVGARGSVV 574 + K + QA+ G D DFL A G+ V Sbjct: 543 FSKHIKQANEGCDFDFLETAFGTAV 567 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: 969 Number of extensions: 52 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: 573 Length adjustment: 36 Effective length of query: 543 Effective length of database: 537 Effective search space: 291591 Effective search space used: 291591 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