GapMind for catabolism of small carbon sources

 

Alignments for a candidate for fecC in Bacteroides thetaiotaomicron VPI-5482

Align Fe(3+) dicitrate transport system permease protein FecC; Iron(III) dicitrate transport system permease protein FecC (characterized)
to candidate 351479 BT1951 Fe3+ ABC transporter, permease protein (NCBI ptt file)

Query= SwissProt::P15030
         (332 letters)



>FitnessBrowser__Btheta:351479
          Length = 326

 Score =  149 bits (375), Expect = 1e-40
 Identities = 104/327 (31%), Positives = 173/327 (52%), Gaps = 18/327 (5%)

Query: 9   LLWGLPVAALIIIFWLSLFCYSAIPVSGADATRALLPGHTPTLPEALVQNLRLPRSLVAV 68
           +L+ + +   + +F L L    A+ +   D   AL  G+     E +V N+RL +++VA+
Sbjct: 7   ILFSILITLTVGLFLLDL-AVGAVNIPIRDVWAALTGGNCSRATEKIVLNIRLIKAIVAL 65

Query: 69  LIGASLALAGTLLQTLTHNPMASPSLLGINSGAALAMALTSAL---SPTPIAGYSLSFIA 125
           L GA+L+++G  +QTL  NP+A P +LGI+SGA+L +AL       S   IAG      A
Sbjct: 66  LAGAALSVSGLQMQTLFRNPLAGPYVLGISSGASLGVALVVLAGIGSSIGIAG------A 119

Query: 126 ACGGGVSWLLVMTAGGGFRHTHDRNKLILAGIALSAFCMGLTRITLLLAEDHAYGIF-YW 184
           A  G    LLV+TA G  +   D   +++ G+  S+    + +I   L+++ +   F  W
Sbjct: 120 AWVGAAVVLLVITAVG--QRIKDIMVILILGMMFSSGVGAVVQILQYLSKEESLKAFVIW 177

Query: 185 LAGGVSHARWQDVWQLLPVVVTAVPVVLLLANQLNLLNLSDSTAHTLGVNLTRLRLVINM 244
             G +       +  L+P V   + + +L    LNLL   +  A T+G+N+ R R ++ +
Sbjct: 178 TMGALGDVTSGQLLILVPSVFAGLLLAVLTIKPLNLLLFGEEYAVTMGLNIRRSRSLLFL 237

Query: 245 LVLLLVGACVSVAGPVAFIGLLVPHLAR-FWAGFDQRNVLPVSMLLGATLMLLADVLARA 303
              LL G   +  GP+ FIGL +PH+ R  +   D   +LP ++L GA+++LL D++++ 
Sbjct: 238 STTLLAGTITAFCGPIGFIGLAMPHVTRMLFQNSDHHVLLPGTILSGASILLLCDIISKI 297

Query: 304 LAFPGDLPAGAVLALIGSPCFVWLVRR 330
                 LP  A+ AL+G P  VW+V R
Sbjct: 298 FT----LPINAITALLGIPIVVWVVLR 320


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: 264
Number of extensions: 18
Number of successful extensions: 4
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: 326
Length adjustment: 28
Effective length of query: 304
Effective length of database: 298
Effective search space:    90592
Effective search space used:    90592
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