GapMind for catabolism of small carbon sources

 

Aligments for a candidate for frcC in Shewanella sp. ANA-3

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

Query= SwissProt::Q9F9B1
         (360 letters)



>lcl|FitnessBrowser__ANA3:7024902 Shewana3_2076 inner membrane ABC
           transporter permease protein YjfF (RefSeq)
          Length = 320

 Score =  136 bits (342), Expect = 9e-37
 Identities = 92/301 (30%), Positives = 152/301 (50%), Gaps = 7/301 (2%)

Query: 55  LVLSLIAFGVILGGKFFSAFTMTLILQQVAIVGIVGAAQTLVILTAGIDLSVGAIMVLSS 114
           L+L++   G      F S   +T +L+  A + I     TLVI++ GIDLSVGA++ LS 
Sbjct: 15  LLLTMFLVGTFQFDGFASGRVVTNLLRDNAFLLITALGMTLVIISGGIDLSVGAVIALSG 74

Query: 115 VIMGQFTFRYGFPPALSVICGLGVGALCGYINGTLVARMKLPPFIVTL-GMWQIVLASNF 173
           V+       Y + P L+ +  L +G L G + GT++   KL PFIVTL GM+   LA   
Sbjct: 75  VVTSLLITEYQWHPLLAFVVILPLGTLFGALMGTIIHVYKLQPFIVTLAGMF---LARGL 131

Query: 174 LYSANETIRAQDISANASILQFFGQNFRIGNAVFTYGVVVMVLLVCLLWYVLNRTAWGRY 233
             + +E   A D     ++ +        GN       ++ +L   ++  V++ T +G  
Sbjct: 132 ATTLSEESIAIDHPFYDAVAEM--SIALPGNGALDLSSLIFILFFVIIAVVMHYTRFGTN 189

Query: 234 VYAVGDDPEAAKLAGVNVTRMLISIYTLSGLICALAGWALIGRIGSVSPTAGQFANIESI 293
           VYA+G +  +A+L G+++ +  ISIY +S  +  LAG        S          +++I
Sbjct: 190 VYAIGGNQHSAELMGISIAKTTISIYAISSFLATLAGIVFTFYTFSGYALGAIGVELDAI 249

Query: 294 TAVVIGGISLFGGRGSIMGMLFGALIVGVFSLGLRLMGT-DPQWTYLLIGLLIIIAVAID 352
            AVVIGG  L GG G ++G + G +++GV    +   G+    WT ++IGLL+   + + 
Sbjct: 250 AAVVIGGTLLTGGSGFVLGTVLGVILMGVIQTYITFDGSLSSWWTKIVIGLLLFFFILLQ 309

Query: 353 Q 353
           +
Sbjct: 310 K 310


Lambda     K      H
   0.327    0.141    0.420 

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: 355
Number of extensions: 23
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: 360
Length of database: 320
Length adjustment: 28
Effective length of query: 332
Effective length of database: 292
Effective search space:    96944
Effective search space used:    96944
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.7 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, 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