GapMind for catabolism of small carbon sources

 

Alignments for a candidate for fecC in Rhizobium subbaraonis JC85

Align Fe(3+) dicitrate transport system permease protein FecC; Iron(III) dicitrate transport system permease protein FecC (characterized)
to candidate WP_097141823.1 CRO48_RS21035 iron ABC transporter permease

Query= SwissProt::P15030
         (332 letters)



>NCBI__GCF_900220975.1:WP_097141823.1
          Length = 343

 Score =  193 bits (490), Expect = 6e-54
 Identities = 122/323 (37%), Positives = 175/323 (54%), Gaps = 3/323 (0%)

Query: 9   LLWGLPVAALIIIFWLSLFCYSAIPVSGADATRALLPGHTPTLPEALVQNLRLPRSLVAV 68
           +LW   VAA++++  +         V+ AD   A+  G   T+ +A V  +R+PR+L+A+
Sbjct: 19  MLWLAVVAAVLVLLCILSVAIGTREVAWADIVAAI-GGREDTIAQAAVA-MRIPRTLLAL 76

Query: 69  LIGASLALAGTLLQTLTHNPMASPSLLGINSGAALAMALTSALSPTPIAGYSLSFIAACG 128
           L GA+L LAG ++Q +T NP+A P +LG+N GA+LA+ +  A      A   + F A  G
Sbjct: 77  LAGAALGLAGAIMQGVTRNPLADPGILGVNMGASLAVVVGVAWFNIASADAYI-FAAVLG 135

Query: 129 GGVSWLLVMTAGGGFRHTHDRNKLILAGIALSAFCMGLTRITLLLAEDHAYGIFYWLAGG 188
            G S + V   G   R      KL LAG A S     L    +L   D A GI  W  GG
Sbjct: 136 AGASAVFVYAIGSLGRGGATPLKLALAGAATSVAFSSLVIALVLPRNDIAGGIRAWQIGG 195

Query: 189 VSHARWQDVWQLLPVVVTAVPVVLLLANQLNLLNLSDSTAHTLGVNLTRLRLVINMLVLL 248
           V  A ++ +  +LP +V    + LL A +LN L L D  A  LG  +   R       +L
Sbjct: 196 VGGATFERMSHVLPFLVAGFIISLLSARKLNSLALGDDLAAGLGERVALARAFAAFGAIL 255

Query: 249 LVGACVSVAGPVAFIGLLVPHLARFWAGFDQRNVLPVSMLLGATLMLLADVLARALAFPG 308
           L GA  +V GP+ F+GL+VPHL R   G D R +LP S + GA L+L AD++ R +A P 
Sbjct: 256 LCGATTAVCGPIGFLGLVVPHLCRLLVGVDHRWLLPFSAVAGACLLLGADIVGRIIARPA 315

Query: 309 DLPAGAVLALIGSPCFVWLVRRR 331
           +L  G V A +G+P F+W+VRR+
Sbjct: 316 ELDVGIVTAFVGAPFFIWVVRRQ 338


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: 335
Number of extensions: 21
Number of successful extensions: 2
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: 343
Length adjustment: 28
Effective length of query: 304
Effective length of database: 315
Effective search space:    95760
Effective search space used:    95760
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 24 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