GapMind for catabolism of small carbon sources

 

Aligments for a candidate for xacD in Sinorhizobium meliloti 1021

Align L-arabonate dehydratase (EC 4.2.1.25) (characterized)
to candidate SM_b20890 SM_b20890 dihydroxy-acid dehydratase

Query= reanno::Smeli:SM_b20890
         (579 letters)



>lcl|FitnessBrowser__Smeli:SM_b20890 SM_b20890 dihydroxy-acid
           dehydratase
          Length = 579

 Score = 1158 bits (2996), Expect = 0.0
 Identities = 579/579 (100%), Positives = 579/579 (100%)

Query: 1   MKKKAEWPRKLRSQEWFGGTGKNAIMHRSWMKNQGLPADTFDGRPIIGICNTWSELTPCN 60
           MKKKAEWPRKLRSQEWFGGTGKNAIMHRSWMKNQGLPADTFDGRPIIGICNTWSELTPCN
Sbjct: 1   MKKKAEWPRKLRSQEWFGGTGKNAIMHRSWMKNQGLPADTFDGRPIIGICNTWSELTPCN 60

Query: 61  AHLRDLAERVKRGVYEAGGFPVEFPVFSTGESTLRPTAMMFRNLAAMDVEESIRGNPVDG 120
           AHLRDLAERVKRGVYEAGGFPVEFPVFSTGESTLRPTAMMFRNLAAMDVEESIRGNPVDG
Sbjct: 61  AHLRDLAERVKRGVYEAGGFPVEFPVFSTGESTLRPTAMMFRNLAAMDVEESIRGNPVDG 120

Query: 121 VVLLGGCDKTTPSLLMGAASVDIPAIVVSGGPMLNGKWRGKDVGSGTAIWQFSEMVKSGE 180
           VVLLGGCDKTTPSLLMGAASVDIPAIVVSGGPMLNGKWRGKDVGSGTAIWQFSEMVKSGE
Sbjct: 121 VVLLGGCDKTTPSLLMGAASVDIPAIVVSGGPMLNGKWRGKDVGSGTAIWQFSEMVKSGE 180

Query: 181 MSLEEFMDAEQGMARSAGSCMTMGTASTMASMAEALGMTLSGNAAIPAVDARRRVISQLT 240
           MSLEEFMDAEQGMARSAGSCMTMGTASTMASMAEALGMTLSGNAAIPAVDARRRVISQLT
Sbjct: 181 MSLEEFMDAEQGMARSAGSCMTMGTASTMASMAEALGMTLSGNAAIPAVDARRRVISQLT 240

Query: 241 GRRIVEMVKEDLKPSDILTKEAFENAIRVNGAVGGSTNAVLHLLALAGRVGVDLSLDDWD 300
           GRRIVEMVKEDLKPSDILTKEAFENAIRVNGAVGGSTNAVLHLLALAGRVGVDLSLDDWD
Sbjct: 241 GRRIVEMVKEDLKPSDILTKEAFENAIRVNGAVGGSTNAVLHLLALAGRVGVDLSLDDWD 300

Query: 301 RLGRDVPTIVNLQPSGKYLMEEFYYAGGLPVVIKAVAEMGLLHNDAITVSGDTIWNDVKG 360
           RLGRDVPTIVNLQPSGKYLMEEFYYAGGLPVVIKAVAEMGLLHNDAITVSGDTIWNDVKG
Sbjct: 301 RLGRDVPTIVNLQPSGKYLMEEFYYAGGLPVVIKAVAEMGLLHNDAITVSGDTIWNDVKG 360

Query: 361 VVNYNEDVILPREKALTKSGGIAVLRGNLAPRGAVLKPSAASPHLMQHKGRAVVFESIED 420
           VVNYNEDVILPREKALTKSGGIAVLRGNLAPRGAVLKPSAASPHLMQHKGRAVVFESIED
Sbjct: 361 VVNYNEDVILPREKALTKSGGIAVLRGNLAPRGAVLKPSAASPHLMQHKGRAVVFESIED 420

Query: 421 YHARINREDLDIDETCIMVLKYCGPKGYPGMAEVGNMGLPPKVLKKGITDMIRISDARMS 480
           YHARINREDLDIDETCIMVLKYCGPKGYPGMAEVGNMGLPPKVLKKGITDMIRISDARMS
Sbjct: 421 YHARINREDLDIDETCIMVLKYCGPKGYPGMAEVGNMGLPPKVLKKGITDMIRISDARMS 480

Query: 481 GTAYGTVILHTAPEAAEGGPLALVENGDLIEVDIPNRTLHLHVSDEELARRRAAWVSPVK 540
           GTAYGTVILHTAPEAAEGGPLALVENGDLIEVDIPNRTLHLHVSDEELARRRAAWVSPVK
Sbjct: 481 GTAYGTVILHTAPEAAEGGPLALVENGDLIEVDIPNRTLHLHVSDEELARRRAAWVSPVK 540

Query: 541 PLTGGYGGLYIKTVMQADAGADLDFLVGARGSVVERDSH 579
           PLTGGYGGLYIKTVMQADAGADLDFLVGARGSVVERDSH
Sbjct: 541 PLTGGYGGLYIKTVMQADAGADLDFLVGARGSVVERDSH 579


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: 1394
Number of extensions: 65
Number of successful extensions: 1
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.

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About GapMind

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:

where "other" refers to the best ublast hit to a sequence that is not annotated as performing this step (and is not "ignored").

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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 on GapMind for carbon sources, or view the source code.

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