GapMind for catabolism of small carbon sources

 

Alignments for a candidate for fruF in Tistlia consotensis USBA 355

Align Fructose import permease protein FruF (characterized)
to candidate WP_085121058.1 B9O00_RS01465 ABC transporter permease

Query= SwissProt::Q8G846
         (356 letters)



>NCBI__GCF_900177295.1:WP_085121058.1
          Length = 335

 Score =  140 bits (353), Expect = 5e-38
 Identities = 101/313 (32%), Positives = 161/313 (51%), Gaps = 27/313 (8%)

Query: 5   AKAEGNNFVKKLLSSNLTWSIVAFILLV-IICTIFQHDFLALSWNSNTGGLAGPLITMLQ 63
           A A G   + K L+++L   ++   L++  + ++    FL  S           +  +L 
Sbjct: 16  AAAAGEGRLLKQLATSLELRMLGLALVIGAVLSLLSPYFLTES----------NIFNILD 65

Query: 64  ESARYLMIATGMTLVISTAGIDLSVGSVMAVAGAAAMQTLSNGMNVWLSILIALAVGLAI 123
           +S    +++ GMT VI T GIDLSVGSV  ++G      L +   + ++IL+ +  G  +
Sbjct: 66  QSVVIGILSIGMTFVILTGGIDLSVGSVAGLSGIVLGLALKD-YPIPVAILLGVLTGAGV 124

Query: 124 GCVNGALVSFLGLQPFITTLIMMLAGRGMAKVIT-----SGENTDASAVAGNEPLKWFAN 178
           G V+G L+ +  L  F+ TL MM  GR +A + +     SG  +D S++   +       
Sbjct: 125 GLVSGILIGYFRLAAFVVTLGMMAIGRSLAYIFSGQTAISGFPSDLSSIVYTD------- 177

Query: 179 GFILGIPANFVIAVIIVILVGLLCRKTAMGMMIEAVGINQEASRMTGIKPKKILFLVYAI 238
             + GIP N +      +L       T  G  I A+G N+EA+R  G+       L Y +
Sbjct: 178 --VFGIPTNVLFLGFAYLLAWGYLTYTKGGRTIYAIGSNKEAARAAGLGVLFYSILPYVV 235

Query: 239 SGFLAAIAGLFATASVMRVDVVKTGQDLEMYAILAVVIGGTSLLGGKFSLAGSAVGAVII 298
           SG LAA+A  F+ A ++ VD + TG  +E+ AI AVVIGG SL GG+ S+ G+ +G +I+
Sbjct: 236 SGALAAVAITFSVAQILSVDPL-TGNGMELDAIAAVVIGGASLYGGRGSIVGTLIGVLIM 294

Query: 299 AMIRKTIITLGVN 311
            MIR  +  LGV+
Sbjct: 295 VMIRNGLNLLGVS 307


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: 304
Number of extensions: 21
Number of successful extensions: 5
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: 335
Length adjustment: 29
Effective length of query: 327
Effective length of database: 306
Effective search space:   100062
Effective search space used:   100062
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 Apr 09 2024. 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