GapMind for catabolism of small carbon sources

 

Alignments for a candidate for fecC in Rhizobium etli CFN 42

Align Fe(3+) dicitrate transport system permease protein FecC; Iron(III) dicitrate transport system permease protein FecC (characterized)
to candidate WP_011425931.1 RHE_RS13725 iron ABC transporter permease

Query= SwissProt::P15030
         (332 letters)



>NCBI__GCF_000092045.1:WP_011425931.1
          Length = 334

 Score =  167 bits (424), Expect = 3e-46
 Identities = 113/321 (35%), Positives = 162/321 (50%), Gaps = 9/321 (2%)

Query: 12  GLPVAALIIIFWLSLFCYSAIPVSGADATRALLPGHTPTLPEALVQNLRLPRSLVAVLIG 71
           GL V A ++   L L    A  +S   A R LL      L   L+  LRLPRSL A   G
Sbjct: 11  GLIVVAAMLAAMLGLLV-GAKTLSVETAIRVLL-APDGKLESVLIWTLRLPRSLAAAAGG 68

Query: 72  ASLALAGTLLQTLTHNPMASPSLLGINSGAALAMALTSALSPTPIAGYSLSFIAACGG-- 129
           A LA++G +LQTLT NP+A P + G+ +G+   +       P     Y   FI   GG  
Sbjct: 69  AGLAVSGYVLQTLTRNPLADPGITGVTAGSVAPIVCCFVFVPWLSPAY-YPFIGLAGGLA 127

Query: 130 GVSWLLVMTAGGGFRHTHDRNKLILAGIALSAFCMGLTRITLLLAEDHAYGIFYWLAGGV 189
             S    ++ GG  R      +L L G+++S F   +T   LLL    +  + +WLAGG 
Sbjct: 128 AASVTFWVSRGGQGRPL----QLALGGVSVSLFLGAITTYVLLLTGPQSASLLFWLAGGF 183

Query: 190 SHARWQDVWQLLPVVVTAVPVVLLLANQLNLLNLSDSTAHTLGVNLTRLRLVINMLVLLL 249
               W  +  +LP  +  V   LLL   + +  LSD  A  +G+ L   + +I +L ++ 
Sbjct: 184 QGRTWSHLLYMLPWTIAGVVGALLLRRVIGMFMLSDHAAAGMGLQLGLWKPLILILAVIP 243

Query: 250 VGACVSVAGPVAFIGLLVPHLARFWAGFDQRNVLPVSMLLGATLMLLADVLARALAFPGD 309
           V     +AGPVAF+GL  PH+AR          + +S  LGA ++ +ADV AR++A P +
Sbjct: 244 VAGVAPIAGPVAFVGLAAPHIARLLKPRGTGWEIGLSAALGALIVTVADVFARSIAIPRE 303

Query: 310 LPAGAVLALIGSPCFVWLVRR 330
           LP G V AL G P F++LV+R
Sbjct: 304 LPVGIVTALFGGPIFIYLVQR 324


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: 341
Number of extensions: 18
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 Apr 09 2024. 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