GapMind for catabolism of small carbon sources

 

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

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

Query= SwissProt::Q8G846
         (356 letters)



>FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_3910
          Length = 325

 Score =  142 bits (357), Expect = 2e-38
 Identities = 92/304 (30%), Positives = 157/304 (51%), Gaps = 18/304 (5%)

Query: 27  AFILLVIICTIFQHDFLALSWNSNTGGLAGPLITMLQESARYLMIATGMTLVISTAGIDL 86
           A + ++++ ++    FL+    S          T+  +    +++A GMT V+   GIDL
Sbjct: 26  ALLAMIVLFSVLSSHFLSYDTFS----------TLANQIPDLMVLAVGMTFVLIIGGIDL 75

Query: 87  SVGSVMAVAGAA-AMQTLSNGMNVWLSILIALAVGLAIGCVNGALVSFLGLQPFITTLIM 145
           SVGSV+A+A +  ++  L  G  V  + L+ +AV    G + G++     +  FI +L +
Sbjct: 76  SVGSVLALAASTVSVAILGWGWGVLPAALLGMAVAALAGTITGSITVAWRIPSFIVSLGV 135

Query: 146 MLAGRGMAKVITSGENTDASAVAGNEPLKWFANGFILGIPANFVIAVIIVILVGLLCRKT 205
           +   RG+A  +T       +A  G +   W +N    GI  +F+IA++I+ +   +  +T
Sbjct: 136 LEMARGVAYQMTGSR----TAYIG-DAFAWLSNPIAFGISPSFIIALLIIFVAQAVLTRT 190

Query: 206 AMGMMIEAVGINQEASRMTGIKPKKILFLVYAISGFLAAIAGLFATASVMRVDVVKTGQD 265
             G  +  +G N+EA R+ GI PK    LV+++ G LA +A LF  + +   D    G  
Sbjct: 191 VFGRYLIGIGTNEEAVRLAGINPKPYKVLVFSLMGLLAGVAALFQISRLEAAD-PNAGSG 249

Query: 266 LEMYAILAVVIGGTSLLGGKFSLAGSAVGAVIIAMIRKTIITLGVNAEATPAFFAVVVIV 325
           LE+  I AVVIGGTSL+GG+ S+  +  G +II+++   +  +G   E T       VIV
Sbjct: 250 LELQVIAAVVIGGTSLMGGRGSVISTFFGVLIISVLAAGLAQIGA-TEPTKRIITGAVIV 308

Query: 326 ICVM 329
           + V+
Sbjct: 309 VAVV 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: 305
Number of extensions: 19
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