GapMind for catabolism of small carbon sources

 

Alignments for a candidate for fecC in Pseudomonas fluorescens GW456-L13

Align Fe(3+) dicitrate transport system permease protein FecC; Iron(III) dicitrate transport system permease protein FecC (characterized)
to candidate PfGW456L13_3769 Hemin ABC transporter, permease protein

Query= SwissProt::P15030
         (332 letters)



>FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_3769
          Length = 345

 Score =  180 bits (456), Expect = 5e-50
 Identities = 129/346 (37%), Positives = 184/346 (53%), Gaps = 20/346 (5%)

Query: 1   MTAIKHPVLLWGLPVAALIIIFWLSLFCYSAIPVS---------GADATRALLPGHTPTL 51
           MTAI  P       +  L+++FWLSL   +  PVS         G       L G     
Sbjct: 1   MTAIFRPRPTLIFLLLLLVLVFWLSL---ALGPVSLPLGDTLLGGMRLLGLPLDGGDTQQ 57

Query: 52  PEALVQNLRLPRSLVAVLIGASLALAGTLLQTLTHNPMASPSLLGINSGAALAMALT--- 108
            E ++  +RLPRSL+ + +G+ LAL+G  +Q L  NP+A P L+G++ GAAL  AL    
Sbjct: 58  AELILGQIRLPRSLLGIAVGSVLALSGVAMQGLFRNPLADPGLVGVSGGAALGAALAIVG 117

Query: 109 -SALSPTP--IAGYSLSFIAACGGGVSWLLVMTAGGGFRHTHDRNKLILAGIALSAFCMG 165
            S L   P  I  Y LS  A  GG +   +V   G     T D   ++LAG+A++A    
Sbjct: 118 GSLLGGLPPVIEPYLLSVCAFAGGLIVTAVVYRFGRRNGQT-DVATMLLAGVAMTAMAGA 176

Query: 166 LTRITLLLAEDHAYG-IFYWLAGGVSHARWQDVWQLLPVVVTAVPVVLLLANQLNLLNLS 224
              +   LA+D     + +W  G ++ A +  +W LL V +     +   A  LN L L 
Sbjct: 177 GVGLFTYLADDATLRTLTFWNLGSLNGASYPRLWPLLIVTLGVALWLPRRAAALNALLLG 236

Query: 225 DSTAHTLGVNLTRLRLVINMLVLLLVGACVSVAGPVAFIGLLVPHLARFWAGFDQRNVLP 284
           +S A  LG ++ R++L + +   L VGA V+ AG + FIGL+VPHL R   G D R +LP
Sbjct: 237 ESEARHLGFDIERIKLELVLCTALGVGAAVAAAGLIGFIGLVVPHLMRLLVGPDHRVLLP 296

Query: 285 VSMLLGATLMLLADVLARALAFPGDLPAGAVLALIGSPCFVWLVRR 330
            S+L GA+L+LLAD+ AR L  P +LP G V ALIG+P F++L+ R
Sbjct: 297 ASLLAGASLLLLADLAARLLLAPAELPIGIVTALIGAPFFLYLLVR 342


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: 370
Number of extensions: 27
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: 345
Length adjustment: 28
Effective length of query: 304
Effective length of database: 317
Effective search space:    96368
Effective search space used:    96368
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