GapMind for catabolism of small carbon sources

 

Alignments for a candidate for fecC in Klebsiella michiganensis M5al

Align Fe(3+) dicitrate transport system permease protein FecC; Iron(III) dicitrate transport system permease protein FecC (characterized)
to candidate BWI76_RS22470 BWI76_RS22470 transporter permease

Query= SwissProt::P15030
         (332 letters)



>FitnessBrowser__Koxy:BWI76_RS22470
          Length = 331

 Score =  191 bits (484), Expect = 3e-53
 Identities = 118/334 (35%), Positives = 189/334 (56%), Gaps = 20/334 (5%)

Query: 6   HPVL-LWGLPVAALIIIFWLSLFCYSAIPVSGADATRALLPGHTPTLPEALVQNLRLPRS 64
           HP   LW + +  +++    +      +P++      +LLP     L    +  +RLPR 
Sbjct: 4   HPARHLWLMTLLLIVLTLLATTLGAMRLPLT------SLLPAGDEILRNIWL-TIRLPRV 56

Query: 65  LVAVLIGASLALAGTLLQTLTHNPMASPSLLGINSGAALAMALTSALS---PTPIAGYS- 120
           L+A+L+GA+LAL+G ++Q L  NP+A P LLGI+ GAALA+A    L    P  +A Y+ 
Sbjct: 57  LLALLVGAALALSGCVMQGLFRNPLADPGLLGISGGAALAVACWLVLPLSLPALVALYAP 116

Query: 121 --LSFIAACGGGVSWLLVMTAGGGFRHTHDRNKLILAGIALSAFCMGLTRITLLLAED-H 177
              +FI +    V   ++  AG         ++L+L GIA++A C  L  +   ++ D  
Sbjct: 117 MLAAFIGSTAVMVVIFILSQAGDA-----SLSRLLLVGIAINALCGALVGVLAWISNDTQ 171

Query: 178 AYGIFYWLAGGVSHARWQDVWQLLPVVVTAVPVVLLLANQLNLLNLSDSTAHTLGVNLTR 237
              +  W  G +  A W  +     +++ A  VV  +A++LNLL L D  AH LGVN+  
Sbjct: 172 LRQLSLWGMGSLGQAEWSTLLVAATLMIPASLVVWAMASRLNLLQLGDEEAHYLGVNVRA 231

Query: 238 LRLVINMLVLLLVGACVSVAGPVAFIGLLVPHLARFWAGFDQRNVLPVSMLLGATLMLLA 297
           L+ ++ +   LLV + V+++G + FIGL+VPHL R W G D R ++P S+L GA L+LLA
Sbjct: 232 LQRLLLLCSALLVASAVAISGIIGFIGLVVPHLMRMWLGPDHRGLVPGSLLCGAILLLLA 291

Query: 298 DVLARALAFPGDLPAGAVLALIGSPCFVWLVRRR 331
           D LAR +A P ++P G + +++G+P F+WL+ R+
Sbjct: 292 DTLARTVAAPAEMPVGLLTSVLGAPWFLWLIFRQ 325


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: 374
Number of extensions: 25
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: 331
Length adjustment: 28
Effective length of query: 304
Effective length of database: 303
Effective search space:    92112
Effective search space used:    92112
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