GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gtsB in Klebsiella michiganensis M5al

Align ABC transporter for D-Glucose-6-Phosphate, permease component 2 (characterized)
to candidate BWI76_RS23380 BWI76_RS23380 sugar ABC transporter permease

Query= reanno::WCS417:GFF4323
         (302 letters)



>FitnessBrowser__Koxy:BWI76_RS23380
          Length = 296

 Score =  100 bits (250), Expect = 3e-26
 Identities = 77/252 (30%), Positives = 122/252 (48%), Gaps = 11/252 (4%)

Query: 43  TFVLSFTNSTFLPTYKWAGLAQYARLFDNDR-WWVASKNLAVFGGMFIGITLVIGVTLAI 101
           +F LSFT    +    + G+  Y  +   D  +W +      +  + I + L   + +A 
Sbjct: 30  SFFLSFTEYDLMSPPVFNGIENYRYMLTEDGLFWKSMGVTFAYVFLTIPLKLAFALGIAF 89

Query: 102 FLDQKIRREGFIRTIYLYPMAL-SMIVTGTAWKWLLNPGMGLDKLLRDW-GWEGFR-LDW 158
            L+ K+R  GF RT Y  P  L S +     W+ L      +D LL  + G  GF  ++W
Sbjct: 90  VLNFKLRGIGFFRTAYYIPSILGSSVAIAVLWRALF----AIDGLLNSFIGVLGFDPVNW 145

Query: 159 LIDPDRVVYCLVIAAVWQASGFIMAMFLAGLRGVDQSIVRAAQIDGASMPRIYWSVVLPS 218
           L +P   +  + +  VWQ  G  M +FLA L+ V QS   AA IDGAS  +++  V +P 
Sbjct: 146 LGEPSLALMSVTLLRVWQF-GSAMVIFLAALQNVPQSQYEAAMIDGASKWQMFMKVTVPL 204

Query: 219 LRPVFFSAVMILAHIAIKSFDLVAAMTAGGPGYSSDLPAMFMYSFTFSRGQMGMGSASA- 277
           + PV F   ++    A + F     +T GGP YS+ L ++++Y   F    MG G+A A 
Sbjct: 205 ITPVIFFNFIMQTTQAFQEFTGPYVITGGGPTYSTYLFSLYIYDTAFKYFDMGYGAALAW 264

Query: 278 -ILMLGAILAII 288
            + ++ A+ A I
Sbjct: 265 VLFLVVAVFAAI 276


Lambda     K      H
   0.330    0.141    0.455 

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: 306
Number of extensions: 14
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: 302
Length of database: 296
Length adjustment: 27
Effective length of query: 275
Effective length of database: 269
Effective search space:    73975
Effective search space used:    73975
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.8 bits)
S2: 48 (23.1 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