GapMind for catabolism of small carbon sources

 

Alignments for a candidate for fecC in Marinobacter adhaerens HP15

Align Fe(3+) dicitrate transport system permease protein FecC; Iron(III) dicitrate transport system permease protein FecC (characterized)
to candidate GFF4015 HP15_3955 bacterial transport system permease protein

Query= SwissProt::P15030
         (332 letters)



>FitnessBrowser__Marino:GFF4015
          Length = 324

 Score =  169 bits (428), Expect = 9e-47
 Identities = 118/321 (36%), Positives = 175/321 (54%), Gaps = 17/321 (5%)

Query: 19  IIIFWLSLFCYSAIPVS------GADATRALLPGHTPTLPEALVQNLRLPRSLVAVLIGA 72
           ++I  L+ F  + + VS      G   T  ++ G    L + L+  LRLPR+L A   G 
Sbjct: 10  LLILLLAGFLAALLSVSIGSTSIGFGDTLRVITGSGTELQQTLILELRLPRTLSAFATGG 69

Query: 73  SLALAGTLLQTLTHNPMASPSLLGINSGAALAMALTSALSPTPIAGYSLSFIAACGGGVS 132
            LA+AG L+Q L  NP+A P +LG++ GAA+  AL + L+    AG+ +S  A  G  ++
Sbjct: 70  LLAVAGALMQVLLRNPLADPYVLGLSGGAAVG-ALLAMLAGA--AGFLISGSAFAGAMLA 126

Query: 133 WLLVMTAGGGFRHTHDRNKLILAGIALSAFCMGLTRITLLLAEDHAY---GIFYWLAGGV 189
            LLV     G   +   ++L+L G+ ++A    +  ITL+L+   A    G+ YWL G +
Sbjct: 127 TLLVFGLAHG-SGSWTPSRLLLTGVVVAAGWGAM--ITLILSMTPASRLPGMLYWLMGDL 183

Query: 190 SHARWQDVWQLLPVVVTAVPVVLLLANQLNLLNLSDSTAHTLGVNLTRLRLVINMLVLLL 249
           SHA     W  L ++V    +V  L   LN+L      A  LGV++  L   I ++  LL
Sbjct: 184 SHAATP--WPGLIILVLVCLMVFPLGRALNVLARGSLQAAALGVSVRPLEWSIYLMASLL 241

Query: 250 VGACVSVAGPVAFIGLLVPHLARFWAGFDQRNVLPVSMLLGATLMLLADVLARALAFPGD 309
             A V++AG V F+GL++PH+ R   G DQR +LP   L G TL++LAD LAR +  P  
Sbjct: 242 TAAAVTMAGSVGFVGLVIPHMLRLVLGNDQRLILPACALAGGTLLVLADTLARVVIAPEQ 301

Query: 310 LPAGAVLALIGSPCFVWLVRR 330
           LP G + ALIG P F++L+ R
Sbjct: 302 LPVGVITALIGVPTFLYLLYR 322


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: 312
Number of extensions: 21
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: 324
Length adjustment: 28
Effective length of query: 304
Effective length of database: 296
Effective search space:    89984
Effective search space used:    89984
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