GapMind for catabolism of small carbon sources

 

Aligments for a candidate for HSERO_RS03645 in Shewanella sp. ANA-3

Align ABC-type sugar transport system, permease component protein (characterized, see rationale)
to candidate 7024902 Shewana3_2076 inner membrane ABC transporter permease protein YjfF (RefSeq)

Query= uniprot:D8IZC8
         (344 letters)



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

 Score =  150 bits (380), Expect = 3e-41
 Identities = 106/312 (33%), Positives = 167/312 (53%), Gaps = 20/312 (6%)

Query: 35  LPVLVVLYLLFYGLTLYLSGDGT-SNFASAENTMNILRQVAINLVLAAGMTFVILTAGID 93
           +P+ +   LL   LT++L G      FAS     N+LR  A  L+ A GMT VI++ GID
Sbjct: 7   IPLWITASLL---LTMFLVGTFQFDGFASGRVVTNLLRDNAFLLITALGMTLVIISGGID 63

Query: 94  LSVGSVLAVSAVLG--MQVSLGAAPGWAIPMFIFSGLVMGMVNGAMVALLNINAFVVTLG 151
           LSVG+V+A+S V+   +       P  A  + +  G + G + G ++ +  +  F+VTL 
Sbjct: 64  LSVGAVIALSGVVTSLLITEYQWHPLLAFVVILPLGTLFGALMGTIIHVYKLQPFIVTLA 123

Query: 152 TMTAFRGAAYLLADGTTVLNNDIPSFEWI--------GNGDFLHVPWLIWVAVAVVLLSW 203
            M   RG A  L++ +  +  D P ++ +        GNG  L +  LI++   V++   
Sbjct: 124 GMFLARGLATTLSEESIAI--DHPFYDAVAEMSIALPGNGA-LDLSSLIFILFFVIIA-- 178

Query: 204 VILRKTVLGMHIYAIGGNLQAARLTGIRVGLVLLFVYSISGLFSGLAGAMSASRLYGANG 263
           V++  T  G ++YAIGGN  +A L GI +    + +Y+IS   + LAG +     +    
Sbjct: 179 VVMHYTRFGTNVYAIGGNQHSAELMGISIAKTTISIYAISSFLATLAGIVFTFYTFSGYA 238

Query: 264 NWGSGYELDAIAAVVLGGTSLMGGVGSIWGTVVGALIIGVMNNGLTILG-LSSFWQYVAK 322
               G ELDAIAAVV+GGT L GG G + GTV+G +++GV+   +T  G LSS+W  +  
Sbjct: 239 LGAIGVELDAIAAVVIGGTLLTGGSGFVLGTVLGVILMGVIQTYITFDGSLSSWWTKIVI 298

Query: 323 GAVIVLAVILDK 334
           G ++   ++L K
Sbjct: 299 GLLLFFFILLQK 310


Lambda     K      H
   0.324    0.138    0.417 

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: 330
Number of extensions: 21
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: 344
Length of database: 320
Length adjustment: 28
Effective length of query: 316
Effective length of database: 292
Effective search space:    92272
Effective search space used:    92272
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, 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