GapMind for catabolism of small carbon sources

 

Alignments for a candidate for fruF in Shewanella sp. ANA-3

Align Fructose import permease protein FruF (characterized)
to candidate 7024902 Shewana3_2076 inner membrane ABC transporter permease protein YjfF (RefSeq)

Query= SwissProt::Q8G846
         (356 letters)



>FitnessBrowser__ANA3:7024902
          Length = 320

 Score =  124 bits (310), Expect = 4e-33
 Identities = 87/294 (29%), Positives = 150/294 (51%), Gaps = 31/294 (10%)

Query: 23  WSIVAFILLVIICTIFQHDFLALSWNSNTGGLAGPLIT-MLQESARYLMIATGMTLVIST 81
           W   + +L + +   FQ D          G  +G ++T +L+++A  L+ A GMTLVI +
Sbjct: 10  WITASLLLTMFLVGTFQFD----------GFASGRVVTNLLRDNAFLLITALGMTLVIIS 59

Query: 82  AGIDLSVGSVMAVAGAAAMQTLSNGM-NVWLSILIALAVGLAIGCVNGALVSFLGLQPFI 140
            GIDLSVG+V+A++G      ++    +  L+ ++ L +G   G + G ++    LQPFI
Sbjct: 60  GGIDLSVGAVIALSGVVTSLLITEYQWHPLLAFVVILPLGTLFGALMGTIIHVYKLQPFI 119

Query: 141 TTLIMMLAGRGMAKVITSGENTDASAVAGNEPLKWFANGFILGIPAN------FVIAVII 194
            TL  M   RG+A  ++        ++A + P         + +P N       +I ++ 
Sbjct: 120 VTLAGMFLARGLATTLSE------ESIAIDHPFYDAVAEMSIALPGNGALDLSSLIFILF 173

Query: 195 VILVGLLCRKTAMGMMIEAVGINQEASRMTGIKPKKILFLVYAISGFLAAIAGL---FAT 251
            +++ ++   T  G  + A+G NQ ++ + GI   K    +YAIS FLA +AG+   F T
Sbjct: 174 FVIIAVVMHYTRFGTNVYAIGGNQHSAELMGISIAKTTISIYAISSFLATLAGIVFTFYT 233

Query: 252 ASVMRVDVVKTGQDLEMYAILAVVIGGTSLLGGKFSLAGSAVGAVIIAMIRKTI 305
            S   +  +     +E+ AI AVVIGGT L GG   + G+ +G +++ +I+  I
Sbjct: 234 FSGYALGAI----GVELDAIAAVVIGGTLLTGGSGFVLGTVLGVILMGVIQTYI 283


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: 323
Number of extensions: 24
Number of successful extensions: 4
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: 320
Length adjustment: 28
Effective length of query: 328
Effective length of database: 292
Effective search space:    95776
Effective search space used:    95776
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.

Links

Downloads

Related tools

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