GapMind for catabolism of small carbon sources

 

Alignments for a candidate for PS417_11895 in Pseudomonas fluorescens GW456-L13

Align Inositol transport system permease protein (characterized)
to candidate PfGW456L13_3910 Ribose ABC transport system, permease protein RbsC (TC 3.A.1.2.1)

Query= reanno::WCS417:GFF2333
         (340 letters)



>FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_3910
          Length = 325

 Score =  171 bits (433), Expect = 2e-47
 Identities = 109/284 (38%), Positives = 155/284 (54%), Gaps = 17/284 (5%)

Query: 62  QVSIIGLLAIGVTQVIITTGIDLSSGSVLALSAMIAASLAQTSDFSRAVFPSLTDLPVWI 121
           Q+  + +LA+G+T V+I  GIDLS GSVLAL+A   +       +   V P+        
Sbjct: 53  QIPDLMVLAVGMTFVLIIGGIDLSVGSVLALAASTVS--VAILGWGWGVLPA-------- 102

Query: 122 PVAMGLGVGLLAGAINGSIIAVTGIPPFIATLGMMVSARGLARYYTEGQPVSMLSDSYT- 180
              +G+ V  LAG I GSI     IP FI +LG++  ARG+A Y   G   + + D++  
Sbjct: 103 -ALLGMAVAALAGTITGSITVAWRIPSFIVSLGVLEMARGVA-YQMTGSRTAYIGDAFAW 160

Query: 181 ---AIGHGAMP-VIIFLVVAVIFHIALRYTKYGKYTYAIGGNMQAARTSGINVKRHLIIV 236
               I  G  P  II L++  +    L  T +G+Y   IG N +A R +GIN K + ++V
Sbjct: 161 LSNPIAFGISPSFIIALLIIFVAQAVLTRTVFGRYLIGIGTNEEAVRLAGINPKPYKVLV 220

Query: 237 YSIAGLLAGLAGVVASARAATGQAGMGMSYELDAIAAAVIGGTSLAGGVGRITGTVIGAL 296
           +S+ GLLAG+A +   +R        G   EL  IAA VIGGTSL GG G +  T  G L
Sbjct: 221 FSLMGLLAGVAALFQISRLEAADPNAGSGLELQVIAAVVIGGTSLMGGRGSVISTFFGVL 280

Query: 297 ILGVMASGFTFVGVDAYIQDIIKGLIIVVAVVIDQYRNKRKLKR 340
           I+ V+A+G   +G     + II G +IVVAVV+D YR++R  +R
Sbjct: 281 IISVLAAGLAQIGATEPTKRIITGAVIVVAVVLDTYRSQRASRR 324


Lambda     K      H
   0.325    0.140    0.394 

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: 259
Number of extensions: 15
Number of successful extensions: 2
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: 340
Length of database: 325
Length adjustment: 28
Effective length of query: 312
Effective length of database: 297
Effective search space:    92664
Effective search space used:    92664
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.6 bits)
S2: 49 (23.5 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