GapMind for catabolism of small carbon sources

 

Alignments for a candidate for mtlF in Luteipulveratus mongoliensis MN07-A0370

Align ABC transporter for D-Mannitol, D-Mannose, and D-Sorbitol, permease component 2 (characterized)
to candidate WP_052597074.1 VV02_RS15280 sugar ABC transporter permease

Query= reanno::WCS417:GFF2492
         (297 letters)



>NCBI__GCF_001190945.1:WP_052597074.1
          Length = 302

 Score =  125 bits (315), Expect = 9e-34
 Identities = 90/290 (31%), Positives = 146/290 (50%), Gaps = 10/290 (3%)

Query: 4   TTPKNRLANPGWFLVSPSVALLLLWMIVPLGMTLYFSLIRYNLLYPGENEFVGLENFTYF 63
           +T + R A  G   V P+V +  ++  +P+      SL  Y L   G+  FVG +N++  
Sbjct: 13  STERRREAITGILFVLPTVVIFGIFKFLPILGAGAMSLTDYQL--NGDYTFVGADNYSRI 70

Query: 64  ITDSGFLPGATNTLLLVGSVLLISVVFGVLISALLEASEFLGRGLVRVLLISPFFIMPTV 123
           + D  F      T L V   + + VV  +  + LL   +    GL R LL  P+     +
Sbjct: 71  LQDDAFWQSLKVTGLYVVIFVPLIVVVSLAGAVLLHQMQRY-TGLFRSLLFVPYLCSFVL 129

Query: 124 GALIWKNLIFHPVSGILAAVWKFFGAEPVDWLAHYPLL---SIIIIVSWQWLPFAILLLM 180
             ++W  +      G L A     G   V +++   LL   S+ ++  W+   +++L+ +
Sbjct: 130 AGIVWTWIF--ATDGPLNAALGGLGFGSVPFISGSQLLVLGSLAMVSVWKGFGYSMLIFL 187

Query: 181 TAMQSLDQEQKEAARLDGAGAIAIFWHLTLPHLARPIAV-VVMIETIFLLSVFAEIFTTT 239
             +++L  E  EAAR+DGAGA   FWH+TLP L RPI + V++IETI    VF  I+  T
Sbjct: 188 AGLKALPAEVHEAARIDGAGAWRTFWHITLP-LLRPITLFVLIIETIVGFQVFDTIYVMT 246

Query: 240 NGGPGYASTNLAYLIYNQALVQFDVGMASAGGLIAVVIANIAAIILVRMI 289
            GGP  AS +L Y +Y++    FD G A+A G++  VI  + +++  R +
Sbjct: 247 GGGPNRASHSLIYFLYDEGFKFFDFGYAAAAGVVLFVIVLLLSLVQQRTV 296


Lambda     K      H
   0.328    0.143    0.437 

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: 241
Number of extensions: 16
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: 297
Length of database: 302
Length adjustment: 27
Effective length of query: 270
Effective length of database: 275
Effective search space:    74250
Effective search space used:    74250
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: 48 (23.1 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