GapMind for catabolism of small carbon sources

 

Alignments for a candidate for ytfT in Pseudomonas fluorescens FW300-N1B4

Align Galactofuranose transporter permease protein YtfT (characterized)
to candidate Pf1N1B4_4287 Inositol transport system permease protein

Query= SwissProt::P39328
         (341 letters)



>FitnessBrowser__pseudo1_N1B4:Pf1N1B4_4287
          Length = 340

 Score =  169 bits (429), Expect = 7e-47
 Identities = 110/338 (32%), Positives = 186/338 (55%), Gaps = 24/338 (7%)

Query: 4   QSLPDTTTPKRRFRWPTGMPQLVALLLVLLVDSLVAPHFWQVVLQDGRLFGSP--IDILN 61
           ++ P     K R R+PT +    ++ LVL+   LV   F  +V     L  S   + ++ 
Sbjct: 6   ENKPAAVPVKSRRRFPTEL----SIFLVLIGIGLVFEMFGWIVRDQSFLMNSQRLVLMIL 61

Query: 62  RAAPVALLAIGMTLVIATGGIDLSVGAVMAIAGATTAAM------------TVAGFSLPI 109
           + + + LLAIG+T VI T GIDLS G+V+A++    A++            ++    + I
Sbjct: 62  QVSIIGLLAIGVTQVIITTGIDLSSGSVLALSAMIAASLAQTSDFARAVFPSLTDLPVWI 121

Query: 110 VLLSALGTGILAGLWNGILVAILKIQPFVATLILMVAGRGVAQLITAGQIVTFNSPDLSW 169
            ++  LG G+LAG  NG ++AI  I PF+ATL +MV+ RG+A+  T GQ V+  S   + 
Sbjct: 122 PVIVGLGVGLLAGAINGSIIAITGIPPFIATLGMMVSARGLARYYTEGQPVSMLSDSYTA 181

Query: 170 FGSGSLLFLPTPVIIAVLTLILFWLLTRKTALGMFIEAVGINIRAAKNAGVNTRIIVMLT 229
            G G++     PVII ++  ++F +  R T  G +  A+G N++AA+ +G+N +  +++ 
Sbjct: 182 IGHGAM-----PVIIFLVVAVIFHIALRYTKYGKYTYAIGGNMQAARTSGINVKRHLVIV 236

Query: 230 YVLSGLCAAIAGIIVAADIRGADANNAGLWLELDAILAVVIGGGSLMGGRFNLLLSVVGA 289
           Y ++GL A +AG++ +A      A   G+  ELDAI A VIGG SL GG   +  +V+GA
Sbjct: 237 YSIAGLLAGLAGVVASARAATGQA-GMGMSYELDAIAAAVIGGTSLAGGVGRITGTVIGA 295

Query: 290 LIIQGMNTGILLSGFPPEMNQVVKAVVVLCVLIVQSQR 327
           LI+  M +G    G    +  ++K ++++  +++   R
Sbjct: 296 LILGVMASGFTFVGVDAYIQDIIKGLIIVVAVVIDQYR 333


Lambda     K      H
   0.327    0.142    0.416 

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: 17
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: 341
Length of database: 340
Length adjustment: 28
Effective length of query: 313
Effective length of database: 312
Effective search space:    97656
Effective search space used:    97656
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 (21.7 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