GapMind for catabolism of small carbon sources

 

Alignments for a candidate for fecD in Burkholderia phytofirmans PsJN

Align iron(III) dicitrate transport system permease protein FecD (characterized)
to candidate BPHYT_RS04855 BPHYT_RS04855 iron ABC transporter

Query= CharProtDB::CH_004160
         (318 letters)



>FitnessBrowser__BFirm:BPHYT_RS04855
          Length = 350

 Score =  167 bits (424), Expect = 3e-46
 Identities = 116/333 (34%), Positives = 173/333 (51%), Gaps = 29/333 (8%)

Query: 9   ITLALAGCALL----SLHMGVIPVPWRALLTDWQAGHEHYY--------VLMEYRLPRLL 56
           I LALAG AL     SL +G + +    +L      H            ++   RLPR +
Sbjct: 23  IWLALAGIALAVLMASLALGSVTLAPMRVLAALMPSHAPASGSSDLAAEIVRTLRLPRAV 82

Query: 57  LALFVGAALAVAGVLIQGIVRNPLASPDILGVNHAASLASVGALLLMPSLPVMVLPLLAF 116
                GA LA+AG L+Q ++RNPLA P +LGV+  A  AS   + ++      ++   AF
Sbjct: 83  AGFACGALLALAGALLQVLLRNPLAEPYVLGVSGGA--ASFALIAMIAGCAWWIVDASAF 140

Query: 117 AGGMAGLILLKMLAKTH----QPM----KLALTGVALSACWASLTDYLMLSRPQD-VNNA 167
           AG    ++L+  LA+      +P     +L LTG  ++A W +L   L+   P + +   
Sbjct: 141 AGAFVSILLVLGLARRELWRGEPQDTSPRLLLTGAVIAAGWGALITLLLNLAPDNRLRGM 200

Query: 168 LLWLTGSLWG--RDWSFVKIAIPLMILFLPLSLSFCRDLDLLALGDARATTLGVSVPHTR 225
           L WLTG L G    W+ +   + +++  +P +      L++L  GDA A  LGV+V   R
Sbjct: 201 LFWLTGDLNGGAMPWTALAALVIVLVAIVPAAPR----LNVLLRGDAAAQALGVAVMPLR 256

Query: 226 FWALLLAVAMTSTGVAACGPISFIGLVVPHMMRSITGGRHRRLLPVSALTGALLLVVADL 285
               L+A    +  V   G I F+GLVVPHM+R   G   R LLP +AL G + ++ ADL
Sbjct: 257 LRVYLVASLAAAAAVTTAGTIGFVGLVVPHMLRLAFGNDQRMLLPAAALGGGVAVMGADL 316

Query: 286 LARIIHPPLELPVGVLTAIIGAPWFVWLLVRMR 318
           +AR +  P +LPVGV+T+IIG P F+W+L+  R
Sbjct: 317 IARTVIAPAQLPVGVITSIIGVPVFLWMLLHRR 349


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: 310
Number of extensions: 18
Number of successful extensions: 5
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 1
Length of query: 318
Length of database: 350
Length adjustment: 28
Effective length of query: 290
Effective length of database: 322
Effective search space:    93380
Effective search space used:    93380
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