GapMind for catabolism of small carbon sources

 

Alignments for a candidate for fecC in Pseudomonas fluorescens FW300-N2E2

Align Fe(3+) dicitrate transport system permease protein FecC; Iron(III) dicitrate transport system permease protein FecC (characterized)
to candidate Pf6N2E2_1634 ABC-type Fe3+-siderophore transport system, permease component

Query= SwissProt::P15030
         (332 letters)



>FitnessBrowser__pseudo6_N2E2:Pf6N2E2_1634
          Length = 321

 Score =  172 bits (436), Expect = 1e-47
 Identities = 120/336 (35%), Positives = 182/336 (54%), Gaps = 29/336 (8%)

Query: 7   PVLLWGLPVAALIIIFWLSLFCYSAIPVSGADATRALLPGHTPTLPEALVQNLRLPRSLV 66
           PV L  L   AL  +  L++    A  +   +A +AL+        +++++  RLPR LV
Sbjct: 2   PVWLGLLMAIALTSLLHLAV---GAKDIPWQEAWQALVAYAPGNPDQSVIRGSRLPRLLV 58

Query: 67  AVLIGASLALAGTLLQTLTHNPMASPSLLGINSGAALAMALTSALSP------TPIAGYS 120
           A+L+GASL LAG ++Q +  NP+A P +LGINSGAAL +     + P       P+  ++
Sbjct: 59  AMLVGASLGLAGAIMQAVGDNPLADPGILGINSGAALFVVFGLLVLPGNDMSMIPLFAFA 118

Query: 121 LSFIAACGGGVSWLLVMTAGGGFRHTHDRNKLILAGIALSAFCMGLTRITLLLAEDHAYG 180
            + +A+ G      +++ AG G    H+  +L L+G  ++A    +T I LLL +     
Sbjct: 119 GALVASVG------VLLLAGRG----HNPIRLTLSGAMIAALFSAITSILLLLDQQGLDS 168

Query: 181 IFYWLAGGV-----SHARWQDVWQLLPVVVTAVPVVLLLANQLNLLNLSDSTAHTLGVNL 235
           +  WL G +     S   W  VW   P V+  + + L+    LN   L    A  +GVNL
Sbjct: 169 LRRWLTGSIGVTGGSMQAW--VW---PYVLLGMCLCLVNVRALNAHRLGPQAAAGMGVNL 223

Query: 236 TRLRLVINMLVLLLVGACVSVAGPVAFIGLLVPHLARFWAGFDQRNVLPVSMLLGATLML 295
            ++R++    V+LL G  V++AGP+ F+GL+VPH AR   G D R +L  + LLGA L++
Sbjct: 224 LKMRVLGLASVVLLSGGAVALAGPIGFVGLVVPHAARLLFGDDYRRLLLAAPLLGALLLI 283

Query: 296 LADVLARALAFPGDLPAGAVLALIGSPCFVWLVRRR 331
           LAD+ AR +  P +L  G V ALIG P FV LV R+
Sbjct: 284 LADIAARTVVRPFELNTGIVTALIGGPIFVVLVLRK 319


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: 313
Number of extensions: 16
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: 321
Length adjustment: 28
Effective length of query: 304
Effective length of database: 293
Effective search space:    89072
Effective search space used:    89072
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: 48 (23.1 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