GapMind for catabolism of small carbon sources

 

Alignments for a candidate for PS417_11885 in Klebsiella michiganensis M5al

Align Inositol transport system sugar-binding protein (characterized)
to candidate BWI76_RS00285 BWI76_RS00285 D-ribose ABC transporter substrate-binding protein

Query= reanno::WCS417:GFF2331
         (309 letters)



>FitnessBrowser__Koxy:BWI76_RS00285
          Length = 296

 Score =  141 bits (356), Expect = 2e-38
 Identities = 89/293 (30%), Positives = 157/293 (53%), Gaps = 10/293 (3%)

Query: 8   TALALSMLLASGVASAADLKIGVSMSAFDDTFLTYLREDMDKQAKSYPKGDGVQLQFEDA 67
           +A+ALS  +++  A A D  I + +S  ++ F   L+E   K+A       G  L   D+
Sbjct: 11  SAVALSATVSAN-AMAKDT-IALVISTLNNPFFVSLKEGAQKEADKL----GYNLVVLDS 64

Query: 68  RADVVKQLSQVENFISQKVDAIIVNPVDTASTANIIKAATAAKIPLVFVNRRPDSQTLAP 127
           + +  K+L+ V++   +    +++NP D+ +  N +K A  AKIP++ ++R+     +  
Sbjct: 65  QNNPAKELANVQDLTVRGTKLLLINPTDSDAVGNAVKLANQAKIPVITLDRQASKGDV-- 122

Query: 128 GVAAVTSDDVEAGKLQMQYIAEKLGGKGNIVILLGDLANNSTTNRTKGVKEVLTKYPGIK 187
            V+ + SD+V  GK+   YIA+K+G    I+ L G    ++   R +G ++ +  +    
Sbjct: 123 -VSHIASDNVLGGKMAGDYIAKKVGENAKIIELQGIAGTSAARERGEGFQQAVAAHK-FN 180

Query: 188 IEQEQTGIWLRDRGMTLVNDWLTQGRDFQAVLSNNDEMAIGAAMALKSAGKKGVLIAGVD 247
           +   Q   + R +G+ ++ + LT   D QAV + NDEMA+GA  AL++AGK  V++ G D
Sbjct: 181 VLASQPADFDRTKGLNVMQNLLTAHPDVQAVFAQNDEMALGALRALQTAGKSDVMVVGFD 240

Query: 248 GTPDGLNAITKGDMTVSAFQDAKGQADKSVETARKMAKNEPIEQNVVIPFQLI 300
           GTPDG  A+  G +  +  Q  +    K VETA K+ K E +E +  +  +L+
Sbjct: 241 GTPDGEKAVNSGKLAATIAQLPEQIGVKGVETADKVLKGEKVETSYPLELKLV 293


Lambda     K      H
   0.314    0.131    0.357 

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: 238
Number of extensions: 15
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: 309
Length of database: 296
Length adjustment: 27
Effective length of query: 282
Effective length of database: 269
Effective search space:    75858
Effective search space used:    75858
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: 42 (22.0 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