GapMind for catabolism of small carbon sources

 

Aligments 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)



>lcl|FitnessBrowser__ANA3:7024902 Shewana3_2076 inner membrane ABC
           transporter permease protein YjfF (RefSeq)
          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.

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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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint on GapMind for carbon sources, or view the source code.

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