GapMind for catabolism of small carbon sources

 

Alignments for a candidate for fruF in Paraburkholderia bryophila 376MFSha3.1

Align Fructose import permease protein FruF (characterized)
to candidate H281DRAFT_02175 H281DRAFT_02175 monosaccharide ABC transporter membrane protein, CUT2 family

Query= SwissProt::Q8G846
         (356 letters)



>FitnessBrowser__Burk376:H281DRAFT_02175
          Length = 353

 Score =  157 bits (397), Expect = 4e-43
 Identities = 96/311 (30%), Positives = 165/311 (53%), Gaps = 21/311 (6%)

Query: 25  IVAFILLVIICTIFQHDFLAL-SWNSNTGGLAGPLITMLQESARYLMIATGMTLVISTAG 83
           ++  + +V+   IF   F +L ++N N           L +    +++  GMTLV++T G
Sbjct: 55  VIVLLAMVLFNLIFTPHFWSLQTFNVN-----------LTQVVTIVIVGIGMTLVVATGG 103

Query: 84  IDLSVGSVMAVAGAAAMQTLSN---GMNVWLSILIALAVGLAIGCVNGALVSFLGLQPFI 140
           IDLSVG+ MA++GA A     N      + L+ ++ +      G  NG LV+ L +QP +
Sbjct: 104 IDLSVGASMAISGALAPMLFLNIPVPGGIALAFVLPVLAAALCGVFNGLLVTRLAVQPIV 163

Query: 141 TTLIMMLAGRGMAKVITSGENTDASAVAGNEP-LKWFANGFILGIPANFVIAVIIVILVG 199
            TL++ +AGRG+A+V+T G     S  A N P  +W A G + G+P   ++ + +V+   
Sbjct: 164 ATLVLFIAGRGIAQVVTDG-----SLQAFNTPAFQWIALGKVAGVPFQVLLMLALVVAFA 218

Query: 200 LLCRKTAMGMMIEAVGINQEASRMTGIKPKKILFLVYAISGFLAAIAGLFATASVMRVDV 259
            + RKT  G  +   G N++A+ ++G+    +  + Y +   LA +AGL + +     D 
Sbjct: 219 WVVRKTLFGQYLLITGGNEKAAYLSGVPTASVKLIAYTLCAALAGLAGLISISVNSSSDA 278

Query: 260 VKTGQDLEMYAILAVVIGGTSLLGGKFSLAGSAVGAVIIAMIRKTIITLGVNAEATPAFF 319
              G  +E+ AI AV +GGT+L GGK  + G+ VGA+II ++R T++  G+   A     
Sbjct: 279 NVVGLGIELDAIAAVAVGGTALTGGKAFIGGTLVGALIIQLLRYTLLAHGIPDAAALVVK 338

Query: 320 AVVVIVICVMQ 330
           A +++    +Q
Sbjct: 339 AGIIVAAVYVQ 349


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: 312
Number of extensions: 19
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: 356
Length of database: 353
Length adjustment: 29
Effective length of query: 327
Effective length of database: 324
Effective search space:   105948
Effective search space used:   105948
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