GapMind for catabolism of small carbon sources

 

Alignments for a candidate for fecD in Pseudomonas simiae WCS417

Align iron(III) dicitrate transport system permease protein FecD (characterized)
to candidate GFF559 PS417_02845 ABC transporter permease

Query= CharProtDB::CH_004160
         (318 letters)



>FitnessBrowser__WCS417:GFF559
          Length = 336

 Score =  181 bits (459), Expect = 2e-50
 Identities = 116/321 (36%), Positives = 174/321 (54%), Gaps = 20/321 (6%)

Query: 13  LAGCALLSLHMGVIPVP----WRALL--------TDWQAGHEHYYVLMEYRLPRLLLALF 60
           L  C +LSL  G   VP    WR +L         +W AG EH   L+  R+PR+LL   
Sbjct: 18  LVSC-VLSLGFGPARVPVEVVWRIVLYKAFGVGEVNWPAGQEHIVWLI--RVPRMLLGAL 74

Query: 61  VGAALAVAGVLIQGIVRNPLASPDILGVNHAASLASVGALLLMPS-LPVMVLPLLAFAGG 119
           VGA LA+ G ++Q + RNPLA P +LGV   A+L +V  +L +   + ++ LPL AF G 
Sbjct: 75  VGAGLALIGAVLQAVTRNPLADPHLLGVTSGATLGAVIVVLHVGEVIGLLTLPLAAFIGA 134

Query: 120 MAGLILLKMLAKTHQPM---KLALTGVALSACWASLTDYLMLSRPQDVNNALL-WLTGSL 175
           +  ++++  +A  +  +   +L L GVA+S    +  + L+        +A++ W+ G L
Sbjct: 135 LLSMLVVLAVASRNGRLESDRLLLCGVAVSFVMMAAANLLLFMGDHRAASAVMFWMLGGL 194

Query: 176 WGRDWSFVKIAIPLMILFLPLSLSFCRDLDLLALGDARATTLGVSVPHTRFWALLLAVAM 235
               W  + +    ++L L L L   R L+ L  G+  A TLG++  + R    L+A  M
Sbjct: 195 GLARWELLAVPTATVLLGLGLLLGMARPLNALMAGEQTAVTLGLNARNVRLKVFLVASLM 254

Query: 236 TSTGVAACGPISFIGLVVPHMMRSITGGRHRRLLPVSALTGALLLVVADLLARIIHPPLE 295
           T   V+  G I F+GL+VPH+ R + G  HRRLLPV  L G+L LV  D+ AR +  P +
Sbjct: 255 TGVLVSISGSIGFVGLMVPHIARRLVGAEHRRLLPVCVLLGSLFLVWVDVAARTLIAPED 314

Query: 296 LPVGVLTAIIGAPWFVWLLVR 316
           LP+GV TA IG  +F+ L+ R
Sbjct: 315 LPIGVATAAIGGLFFIGLMRR 335


Lambda     K      H
   0.330    0.142    0.447 

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: 290
Number of extensions: 11
Number of successful extensions: 2
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: 318
Length of database: 336
Length adjustment: 28
Effective length of query: 290
Effective length of database: 308
Effective search space:    89320
Effective search space used:    89320
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 (21.8 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