GapMind for catabolism of small carbon sources

 

Alignments for a candidate for fecD in Pseudomonas stutzeri RCH2

Align iron(III) dicitrate transport system permease protein FecD (characterized)
to candidate GFF992 Psest_1024 ABC-type Fe3+-siderophore transport system, permease component

Query= CharProtDB::CH_004160
         (318 letters)



>FitnessBrowser__psRCH2:GFF992
          Length = 345

 Score =  172 bits (437), Expect = 8e-48
 Identities = 115/297 (38%), Positives = 176/297 (59%), Gaps = 20/297 (6%)

Query: 38  QAGHEHY-YVLMEYRLPRLLLALFVGAALAVAGVLIQGIVRNPLASPDILGVNHAASLAS 96
           QAG E    VL + RLPR LL    GA LA+ GV +QG+ RNPLA P ++GV+  A+L +
Sbjct: 52  QAGLEQAELVLAKIRLPRTLLGCAAGAVLALCGVAMQGLFRNPLADPGLVGVSSGAALGA 111

Query: 97  VGALL---LMPSLPVMVLPLL----AFAGGMAGLILLKMLAK----THQPMKLALTGVAL 145
             A++    +P+LP+   P L    AF GG+   +L+  L +    TH    L L+G+AL
Sbjct: 112 AVAIVGATFVPALPLSWEPYLLSAFAFIGGLGVTLLVYRLGRRDGQTHVATML-LSGIAL 170

Query: 146 SACWASLTD-YLMLSRPQDVNNALLWLTGSLWGRDWSFVKIAIPLMILFLPLSLSF---C 201
           +A   ++   +  L+  + + +   W  GSL G   S+V++  PL+++ + ++       
Sbjct: 171 TALAGAVVGLFTYLADDRTLRSLTFWNLGSLNGA--SYVRLW-PLLLITIAVAFWLPQRA 227

Query: 202 RDLDLLALGDARATTLGVSVPHTRFWALLLAVAMTSTGVAACGPISFIGLVVPHMMRSIT 261
           + L+ L LG++ A  LG +V   +   ++         VAA G I FIGLVVPH+MR + 
Sbjct: 228 KALNALLLGESEARHLGFNVERIKRELVVCTALGVGAAVAAAGLIGFIGLVVPHLMRLLV 287

Query: 262 GGRHRRLLPVSALTGALLLVVADLLARIIHPPLELPVGVLTAIIGAPWFVWLLVRMR 318
           G  HR LLP SAL GA LL++AD+ AR++  P ELP+G++TA++GAP+F++LL+R R
Sbjct: 288 GPDHRLLLPASALAGASLLLLADVAARLVIAPAELPIGIVTALLGAPFFLYLLLRER 344


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: 298
Number of extensions: 12
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: 345
Length adjustment: 28
Effective length of query: 290
Effective length of database: 317
Effective search space:    91930
Effective search space used:    91930
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: 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