GapMind for catabolism of small carbon sources

 

Alignments for a candidate for ytfT in Rhodobacter viridis JA737

Align Galactofuranose transporter permease protein YtfT (characterized)
to candidate WP_110806514.1 C8J30_RS14100 ABC transporter permease

Query= SwissProt::P39328
         (341 letters)



>NCBI__GCF_003217355.1:WP_110806514.1
          Length = 339

 Score =  150 bits (378), Expect = 6e-41
 Identities = 113/330 (34%), Positives = 175/330 (53%), Gaps = 34/330 (10%)

Query: 19  PTGMPQLVALLLVLLVDSLVAPHFWQVVLQDGRLFGSPIDILN----RAAPVALLAIGMT 74
           P  +P  V +L VL+  +LV      +    G+ F   ID L     + + + ++++G+T
Sbjct: 15  PRRLPPEVNILFVLVGIALVFEILGWIF--QGQSFLMSIDRLKIMILQVSVIGIISVGVT 72

Query: 75  LVIATGGIDLSVGAV--------MAIAGATTAAMTVAG--FSLPIVLLSALG--TGILAG 122
            VI  GGIDLS G+V        M+ A  +T A  V      LP ++  ALG   G L G
Sbjct: 73  QVIIAGGIDLSSGSVVGAVAMFAMSFAQVSTYARAVYPDLTDLPAIVPIALGLMAGALVG 132

Query: 123 LWNGILVAILKIQPFVATLILMVAGRGVAQLITAGQIVTFNSPDLSWFGSGSLLFLPTPV 182
           L NG L+A  KI PF+ATL  MV  RG A+  T GQ ++F + D ++ G G +     PV
Sbjct: 133 LINGALIAYAKIPPFIATLGTMVTARGFAKWYTKGQPISFPTDDFAFIGKGMM-----PV 187

Query: 183 IIAVLTLILFWLLTRKTALGMFIEAVGINIRAAKNAGVNTRIIVMLTYVLSGLCAAIAGI 242
            I +    +F +  + T  G F  A+G N +AA+ +G+N    ++  YV++   AA+AG+
Sbjct: 188 AIFLAVAAIFHVAMKYTRYGKFTYAIGANQQAARVSGINVEHHLIKVYVVAATLAALAGM 247

Query: 243 IVAADIRGADANNAGLWLELDAILAVVIGGGSLMGGRFNLLLSVVGALIIQGMNTGILLS 302
           +VAA  + A A   GL  ELDAI   VIGG SL GGR ++L +++G +I      G+++S
Sbjct: 248 VVAARGQTAQA-GMGLAYELDAIAMAVIGGVSLTGGRGSILGTMIGMVIF-----GVIIS 301

Query: 303 GF-----PPEMNQVVKAVVVLCVLIVQSQR 327
           GF          +++K V+++  ++    R
Sbjct: 302 GFTFLRLDAYYQEMIKGVIIVAAVVADVYR 331


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: 260
Number of extensions: 21
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: 339
Length adjustment: 28
Effective length of query: 313
Effective length of database: 311
Effective search space:    97343
Effective search space used:    97343
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 24 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