GapMind for catabolism of small carbon sources

 

Alignments for a candidate for fecC in Escherichia coli BW25113

Align Fe(3+) dicitrate transport system permease protein FecC; Iron(III) dicitrate transport system permease protein FecC (characterized)
to candidate 14726 b0590 iron-enterobactin transporter subunit (NCBI)

Query= SwissProt::P15030
         (332 letters)



>FitnessBrowser__Keio:14726
          Length = 334

 Score =  177 bits (449), Expect = 3e-49
 Identities = 108/277 (38%), Positives = 160/277 (57%), Gaps = 2/277 (0%)

Query: 55  LVQNLRLPRSLVAVLIGASLALAGTLLQTLTHNPMASPSLLGINSGAALAMALTSALSPT 114
           +V + RLPR+L  +L G +L LAG L+QTLT NP+A P LLG+N+GA+ A+ L +AL   
Sbjct: 55  IVLDARLPRTLAGLLAGGALGLAGALMQTLTRNPLADPGLLGVNAGASFAIVLGAALFGY 114

Query: 115 PIAGYSLSFIAACGGGVSWLLVMTAGGGFRHTHDRNKLILAGIALSAFCMGLTRITLLLA 174
             A   L+ +A  G  V+ L+V   G          +L LAG+AL+A   GLT    LL 
Sbjct: 115 SSAQEQLA-MAFAGALVASLIVAFTGSQGGGQLSPVRLTLAGVALAAVLEGLTSGIALLN 173

Query: 175 EDHAYGIFYWLAGGVSHARWQDVWQLLPVVVTAVPVVLLLANQLNLLNLSDSTAHTLGVN 234
            D    + +W AG +       +  +L  V+ A    LLL+  LN L+L   TA  LG  
Sbjct: 174 PDVYDQLRFWQAGSLDIRNLHTLKVVLIPVLIAGATALLLSRALNSLSLGSDTATALGSR 233

Query: 235 LTRLRLVINMLVLLLVGACVSVAGPVAFIGLLVPHLARFWAGFDQRNVLPVSMLLGATLM 294
           + R +L+  + + +L G+  ++ GP+AFIGL++PH+AR+  G D R  LPV++L    L+
Sbjct: 234 VARTQLIGLLAITVLCGSATAIVGPIAFIGLMMPHMARWLVGADHRWSLPVTLLATPALL 293

Query: 295 LLADVLARALAFPGDLPAGAVLALIGSPCFVWLVRRR 331
           L AD++ R +  PG+L    V A IG+P  ++LVRR+
Sbjct: 294 LFADIIGRVIV-PGELRVSVVSAFIGAPVLIFLVRRK 329


Lambda     K      H
   0.327    0.140    0.436 

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: 327
Number of extensions: 13
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: 332
Length of database: 334
Length adjustment: 28
Effective length of query: 304
Effective length of database: 306
Effective search space:    93024
Effective search space used:    93024
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 (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