Align L-arabonate dehydratase (EC 4.2.1.25) (characterized)
to candidate RR42_RS33305 RR42_RS33305 dihydroxy-acid dehydratase
Query= reanno::Smeli:SM_b20890 (579 letters) >FitnessBrowser__Cup4G11:RR42_RS33305 Length = 579 Score = 570 bits (1470), Expect = e-167 Identities = 280/567 (49%), Positives = 387/567 (68%), Gaps = 3/567 (0%) Query: 1 MKKKAEWPRKLRSQEWFGGTGKNAIMHRSWMKNQGLPADTFDGRPIIGICNTWSELTPCN 60 M + + P LRS WF + HRS + G D + RPII I NTWS++ PC+ Sbjct: 1 MTSRKKTPETLRSARWFAPDDLRSSGHRSRIMQMGYSPDEWLDRPIIAIINTWSDINPCH 60 Query: 61 AHLRDLAERVKRGVYEAGGFPVEFPVFSTGESTLRPTAMMFRNLAAMDVEESIRGNPVDG 120 +H + + VKRG+ +AGGFP+E P S ES ++PT M++RN+ AM+ EE IR +PVDG Sbjct: 61 SHFKQRVDDVKRGILQAGGFPIELPAISLSESAVKPTTMLYRNMLAMEAEELIRSHPVDG 120 Query: 121 VVLLGGCDKTTPSLLMGAASVDIPAIVVSGGPMLNGKWRGKDVGSGTAIWQFSEMVKSGE 180 VL+GGCDKTTP LLMGA+S +PAI V GPML G W+G +GSG+ W+F + ++G Sbjct: 121 AVLMGGCDKTTPGLLMGASSAGVPAIYVPAGPMLRGNWKGNVLGSGSDAWKFWDERRAGN 180 Query: 181 MSLEEFMDAEQGMARSAGSCMTMGTASTMASMAEALGMTLSGNAAIPAVDARRRVISQLT 240 +S E++ E G+ARS G+CMTMGTASTM ++AEA+GMTL G ++IPA DA + Sbjct: 181 ISKTEWIGIEGGIARSHGTCMTMGTASTMTAIAEAIGMTLPGASSIPAADANHIRMCSEA 240 Query: 241 GRRIVEMVKEDLKPSDILTKEAFENAIRVNGAVGGSTNAVLHLLALAGRVGVDLSLDDWD 300 GRRIV+MV EDL P I T+ +FENAI V A+G STNA++H++A+A R G D+ L+D+D Sbjct: 241 GRRIVDMVWEDLTPQRIQTRASFENAIAVAMAMGCSTNAIIHVIAMARRAGHDIGLEDFD 300 Query: 301 RLGRDVPTIVNLQPSG-KYLMEEFYYAGGLPVVIKAVAEMGLLHNDAITVSGDTIWNDVK 359 + R VP I N++PSG KYLME+F+YAGGLP ++ +++ L+ DA+TV+G T+ ++ Sbjct: 301 KTSRHVPVIANIRPSGDKYLMEDFFYAGGLPALMNRISDK--LNLDALTVTGRTLGENIA 358 Query: 360 GVVNYNEDVILPREKALTKSGGIAVLRGNLAPRGAVLKPSAASPHLMQHKGRAVVFESIE 419 G YN+DVI +E AL + G +AVL+GN+AP G V+KPSA +H G A+VF+ Sbjct: 359 GAEVYNDDVIRTKENALYQEGALAVLKGNIAPDGCVIKPSACEKRFFKHTGPALVFDDYP 418 Query: 420 DYHARINREDLDIDETCIMVLKYCGPKGYPGMAEVGNMGLPPKVLKKGITDMIRISDARM 479 + R+DLD+ I++L+ GP+G PGM E G + +P K++++G+ DM+R+SDARM Sbjct: 419 SMKEAVERDDLDVTADHILILRNAGPQGGPGMPEWGMLPIPKKLVQQGVRDMLRMSDARM 478 Query: 480 SGTAYGTVILHTAPEAAEGGPLALVENGDLIEVDIPNRTLHLHVSDEELARRRAAWVSPV 539 SGT+YG ILH +PE+ GGP ALV GD+I VDI R++HL VSDEELARR+AAW P Sbjct: 479 SGTSYGACILHVSPESYIGGPFALVRTGDMISVDIDRRSIHLEVSDEELARRKAAWTPPP 538 Query: 540 KPLTGGYGGLYIKTVMQADAGADLDFL 566 GYG ++ K + QA+ G D DFL Sbjct: 539 PRFGRGYGWMFSKHIRQANDGCDFDFL 565 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: 1009 Number of extensions: 39 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: 579 Length adjustment: 36 Effective length of query: 543 Effective length of database: 543 Effective search space: 294849 Effective search space used: 294849 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