GapMind for catabolism of small carbon sources

 

Alignments for a candidate for iolJ in Sinorhizobium meliloti 1021

Align 5-dehydro-2-deoxygluconokinase (EC 2.7.1.92); possible 5-dehydro-2-deoxyphosphogluconate aldolase DUF2090 (EC 4.1.2.29) (characterized)
to candidate SMc01165 SMc01165 sugar kinase

Query= reanno::Smeli:SMc01165
         (650 letters)



>FitnessBrowser__Smeli:SMc01165
          Length = 650

 Score = 1292 bits (3343), Expect = 0.0
 Identities = 650/650 (100%), Positives = 650/650 (100%)

Query: 1   MSQIPSAQVPSGAGAKPLDLITIGRASVDLYGQQIGTRLEDVASFAKSVGGCPCNISVGT 60
           MSQIPSAQVPSGAGAKPLDLITIGRASVDLYGQQIGTRLEDVASFAKSVGGCPCNISVGT
Sbjct: 1   MSQIPSAQVPSGAGAKPLDLITIGRASVDLYGQQIGTRLEDVASFAKSVGGCPCNISVGT 60

Query: 61  ARLGLKSALLTRVGDEQMGRFIREQLQREGVETRGIVTDPERLTALAILSVENDKSFPLL 120
           ARLGLKSALLTRVGDEQMGRFIREQLQREGVETRGIVTDPERLTALAILSVENDKSFPLL
Sbjct: 61  ARLGLKSALLTRVGDEQMGRFIREQLQREGVETRGIVTDPERLTALAILSVENDKSFPLL 120

Query: 121 FYRDNCADNALCEDDISEDFIRSARAVLVTGTHFAKPNADAAQRKAIRIAKESGARIVFD 180
           FYRDNCADNALCEDDISEDFIRSARAVLVTGTHFAKPNADAAQRKAIRIAKESGARIVFD
Sbjct: 121 FYRDNCADNALCEDDISEDFIRSARAVLVTGTHFAKPNADAAQRKAIRIAKESGARIVFD 180

Query: 181 IDYRPNLWGLAGHDAGESRYIASDRVSAHLKTVLGDCDLIVGTEEEVLIASGESDLLAAL 240
           IDYRPNLWGLAGHDAGESRYIASDRVSAHLKTVLGDCDLIVGTEEEVLIASGESDLLAAL
Sbjct: 181 IDYRPNLWGLAGHDAGESRYIASDRVSAHLKTVLGDCDLIVGTEEEVLIASGESDLLAAL 240

Query: 241 KTIRSLSKATIVLKRGPMGCIVYDGPISDDLEDGIVGKGFPIEVYNVLGAGDAFMSGFLR 300
           KTIRSLSKATIVLKRGPMGCIVYDGPISDDLEDGIVGKGFPIEVYNVLGAGDAFMSGFLR
Sbjct: 241 KTIRSLSKATIVLKRGPMGCIVYDGPISDDLEDGIVGKGFPIEVYNVLGAGDAFMSGFLR 300

Query: 301 GWLTGEPHATSATWANACGAFAVSRLLCAPEIPTWTELQYFLEHGSKEKALRKDEAINHV 360
           GWLTGEPHATSATWANACGAFAVSRLLCAPEIPTWTELQYFLEHGSKEKALRKDEAINHV
Sbjct: 301 GWLTGEPHATSATWANACGAFAVSRLLCAPEIPTWTELQYFLEHGSKEKALRKDEAINHV 360

Query: 361 HWATTRRRDIPLLMALAVDHRSQLEDIAEGNPELLSRIPAFKVLAVKAAAEVAQGRSGFG 420
           HWATTRRRDIPLLMALAVDHRSQLEDIAEGNPELLSRIPAFKVLAVKAAAEVAQGRSGFG
Sbjct: 361 HWATTRRRDIPLLMALAVDHRSQLEDIAEGNPELLSRIPAFKVLAVKAAAEVAQGRSGFG 420

Query: 421 MLIDDKYGRDALYAAGAHRDFWIGKPIELPGSRPLTFEFSQDLGSRLVDWPVDHCIKVLS 480
           MLIDDKYGRDALYAAGAHRDFWIGKPIELPGSRPLTFEFSQDLGSRLVDWPVDHCIKVLS
Sbjct: 421 MLIDDKYGRDALYAAGAHRDFWIGKPIELPGSRPLTFEFSQDLGSRLVDWPVDHCIKVLS 480

Query: 481 FYHPDDPAELKAAQVAKLRSAFEAARKVGREILIEIIAGKHGKLDDRTIPRALEELYDAG 540
           FYHPDDPAELKAAQVAKLRSAFEAARKVGREILIEIIAGKHGKLDDRTIPRALEELYDAG
Sbjct: 481 FYHPDDPAELKAAQVAKLRSAFEAARKVGREILIEIIAGKHGKLDDRTIPRALEELYDAG 540

Query: 541 LKPDWWKLEPQASRAAWAAIDAVIETRDPLCRGVVLLGLEAPYEVLKDGFAAARTSKTVK 600
           LKPDWWKLEPQASRAAWAAIDAVIETRDPLCRGVVLLGLEAPYEVLKDGFAAARTSKTVK
Sbjct: 541 LKPDWWKLEPQASRAAWAAIDAVIETRDPLCRGVVLLGLEAPYEVLKDGFAAARTSKTVK 600

Query: 601 GFAVGRTIFADAAKAWLAGRMTDEQAVSDMAAKFKALVDLWLQLGETKAA 650
           GFAVGRTIFADAAKAWLAGRMTDEQAVSDMAAKFKALVDLWLQLGETKAA
Sbjct: 601 GFAVGRTIFADAAKAWLAGRMTDEQAVSDMAAKFKALVDLWLQLGETKAA 650


Lambda     K      H
   0.320    0.136    0.407 

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: 1522
Number of extensions: 40
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: 650
Length of database: 650
Length adjustment: 38
Effective length of query: 612
Effective length of database: 612
Effective search space:   374544
Effective search space used:   374544
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 54 (25.4 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:

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