GapMind for catabolism of small carbon sources

 

Alignments for a candidate for thuF in Phaeobacter inhibens BS107

Align ABC transporter permease (characterized, see rationale)
to candidate GFF1304 PGA1_c13200 ABC transporter permease protein

Query= uniprot:A0A166QFV1
         (320 letters)



>FitnessBrowser__Phaeo:GFF1304
          Length = 288

 Score =  137 bits (346), Expect = 2e-37
 Identities = 88/291 (30%), Positives = 150/291 (51%), Gaps = 13/291 (4%)

Query: 28  AAWLFLTPMLLCLALVAAWPLLRTFWFSLTDANLADTGGGTFIGFGNYLFHNGSSWSGIL 87
           AA + + P ++ L      PL  T +FS         G   ++GF NY     SS     
Sbjct: 9   AARIMMAPAVILLLGWMLVPLTMTLYFSFKKYLPLRGGDLGWVGFDNYARFLSSS----- 63

Query: 88  VDPQWWNAVRNTLYFTVVSVGLEVVLGLLVALLLNIKFTGRALVRALILIPWAIPTIVSA 147
               +W +V+ TL      + + V+LG+ +ALLLN    G+ +VR L++ P+ +   VSA
Sbjct: 64  ---AFWPSVQATLVIVGGVLAITVILGVFLALLLNQPMWGQGIVRILVIAPFFVMPTVSA 120

Query: 148 KIWSWMLNDQF-GIINHLMLSLGLIDAPLAWTADADLSMWAVIIVDVWKTVPFVTLLMLA 206
            +W  M  D   G+  HL  + G    P++W ++A L   ++I++  W+ +PF TL++L 
Sbjct: 121 LVWKNMFMDPVNGLFAHLWKAFGA--EPVSWLSEASLQ--SIILIVSWQWLPFATLILLT 176

Query: 207 ALQMLPSDCYEAARVDGIHPLKVFWRVTLPLLMPALLVAAIFRILDSLRVFDVIYVLTSN 266
           A+Q L S+  EAA +DG  P+  F  +TLP L  A+ V  + + +  L +F  I+V T  
Sbjct: 177 AIQSLDSEQLEAAEMDGAPPVARFGYITLPHLSRAITVVVLIQTIFLLSIFAEIFVTTQG 236

Query: 267 SSSTMSMSVYARQHLVEFQDVGYGSAASTLLFLVVAVIALLYLYLGRRQLE 317
           S  T +++    Q ++E Q+VG GSA      ++  ++A+  + +  + L+
Sbjct: 237 SFGTKTLTYLIYQRVLESQNVGLGSAGGVYAIILANIVAIFLMRIVGKNLD 287


Lambda     K      H
   0.329    0.140    0.443 

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: 237
Number of extensions: 18
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: 320
Length of database: 288
Length adjustment: 27
Effective length of query: 293
Effective length of database: 261
Effective search space:    76473
Effective search space used:    76473
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