GapMind for catabolism of small carbon sources

 

Alignments for a candidate for fruF in Pseudomonas fluorescens FW300-N2E2

Align Fructose import permease protein FruF (characterized)
to candidate Pf6N2E2_163 Ribose ABC transport system, permease protein RbsC (TC 3.A.1.2.1)

Query= SwissProt::Q8G846
         (356 letters)



>FitnessBrowser__pseudo6_N2E2:Pf6N2E2_163
          Length = 325

 Score =  148 bits (374), Expect = 2e-40
 Identities = 89/271 (32%), Positives = 147/271 (54%), Gaps = 8/271 (2%)

Query: 60  TMLQESARYLMIATGMTLVISTAGIDLSVGSVMAVAGAA-AMQTLSNGMNVWLSILIALA 118
           T+  +    +++A GMT ++   GIDLSVGSV+A+A +  ++  L  G +VW S L+ +A
Sbjct: 49  TLANQIPDLMVLAVGMTFILIIGGIDLSVGSVLALAASTVSVAVLGWGWSVWPSALLGMA 108

Query: 119 VGLAIGCVNGALVSFLGLQPFITTLIMMLAGRGMAKVITSGENTDASAVAGNEPLKWFAN 178
           V    G V G++     +  FI +L ++   RG+A  +T       +A  G+    W +N
Sbjct: 109 VAALAGTVTGSITVAWRIPSFIVSLGVLEMARGLAYQMTGSR----TAYIGDS-FAWLSN 163

Query: 179 GFILGIPANFVIAVIIVILVGLLCRKTAMGMMIEAVGINQEASRMTGIKPKKILFLVYAI 238
               GI  +F+IA++++ +   +  +T  G  +  +G N+EA R+ GI PK    LV+++
Sbjct: 164 PIAFGISPSFIIALLVIFIAQAVLTRTVFGRYLIGIGTNEEAVRLAGINPKPYKILVFSL 223

Query: 239 SGFLAAIAGLFATASVMRVDVVKTGQDLEMYAILAVVIGGTSLLGGKFSLAGSAVGAVII 298
            G LA +A LF  + +   D    G  LE+  I AVVIGGTSL+GG+ S+  +  G +II
Sbjct: 224 MGLLAGVAALFQISRLEAAD-PNAGSGLELQVIAAVVIGGTSLMGGRGSVISTFFGVLII 282

Query: 299 AMIRKTIITLGVNAEATPAFFAVVVIVICVM 329
           +++   +  +G   E T       VIV+ V+
Sbjct: 283 SVLAAGLAQIGA-TEPTKRIITGAVIVVAVV 312


Lambda     K      H
   0.325    0.136    0.384 

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: 316
Number of extensions: 22
Number of successful extensions: 3
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 1
Length of query: 356
Length of database: 325
Length adjustment: 28
Effective length of query: 328
Effective length of database: 297
Effective search space:    97416
Effective search space used:    97416
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