GapMind for catabolism of small carbon sources

 

Alignments for a candidate for fecD in Cupriavidus basilensis 4G11

Align iron(III) dicitrate transport system permease protein FecD (characterized)
to candidate RR42_RS16135 RR42_RS16135 ABC transporter permease

Query= CharProtDB::CH_004160
         (318 letters)



>FitnessBrowser__Cup4G11:RR42_RS16135
          Length = 335

 Score =  182 bits (461), Expect = 1e-50
 Identities = 123/337 (36%), Positives = 186/337 (55%), Gaps = 29/337 (8%)

Query: 1   MKIALVIFITLALAGCA--LLSLHMGVIPVP----WRALL--TDWQAGHEHYYVLMEYRL 52
           M+ AL I++ LA AG A  LLSL +G +P+     W AL    D  AG     ++ E RL
Sbjct: 4   MRRALAIWLMLAAAGVAVFLLSLAVGSVPLSGAQVWHALCGGADDTAGA----IVRELRL 59

Query: 53  PRLLLALFVGAALAVAGVLIQGIVRNPLASPDILGVNHAASLASVGALLLMPSLPVMVLP 112
           PR   A   G  LA+ G L+Q ++RNPLA P +LGV+  A+  ++ A+L+M   P+  + 
Sbjct: 60  PRAAAAFACGGLLALTGALMQVLLRNPLAEPYVLGVSGGAATGALTAMLMM--WPLWTVQ 117

Query: 113 LLAFAGGMAGLILLKMLAKT-----------HQP-MKLALTGVALSACWASLTDYLMLSR 160
             A  G +  ++L+  LA+            H+   +L LTGV L+A W +L   ++   
Sbjct: 118 AGAAGGALFSMVLVATLARRDLLHPQVQGGHHEAGSRLLLTGVILAAGWGALITLILSVA 177

Query: 161 PQD-VNNALLWLTGSLWGRDWSFVKIAIPLMILFLPLSLSFCRDLDLLALGDARATTLGV 219
           P+  +   L WLTG L G   +   +A+  + L + L++   R L+ + +G+  A  LGV
Sbjct: 178 PEARLRGMLFWLTGDLGGT--ASYGLALGALALAVLLAMPMARSLNAMLMGETVAQALGV 235

Query: 220 SVPHTRFWALLLAVAMTSTGVAACGPISFIGLVVPHMMRSITGGRHRRLLPVSALTGALL 279
            V   R    +LA    +  + + G I F+GLVVPH++R   G   R +LP SAL G  L
Sbjct: 236 RVGAVRLSVFVLASLAIAVAITSAGSIGFVGLVVPHLVRLAWGNDQRLMLPASALLGGTL 295

Query: 280 LVVADLLARIIHPPLELPVGVLTAIIGAPWFVWLLVR 316
           L+ ADL+AR +  P +LPVGV+TA++G P F++LL+R
Sbjct: 296 LMAADLVARTVIAPAQLPVGVITALLGVPTFLFLLLR 332


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: 321
Number of extensions: 20
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: 318
Length of database: 335
Length adjustment: 28
Effective length of query: 290
Effective length of database: 307
Effective search space:    89030
Effective search space used:    89030
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