GapMind for catabolism of small carbon sources

 

Alignments for a candidate for SMc02871 in Rhodobacter viridis JA737

Align N-Acetyl-D-glucosamine ABC transport system, permease component 2 (characterized)
to candidate WP_110804034.1 C8J30_RS01980 carbohydrate ABC transporter permease

Query= reanno::Phaeo:GFF2752
         (280 letters)



>NCBI__GCF_003217355.1:WP_110804034.1
          Length = 382

 Score =  126 bits (316), Expect = 8e-34
 Identities = 65/207 (31%), Positives = 121/207 (58%), Gaps = 1/207 (0%)

Query: 75  FQNSMIVTVVSLALVLLFGAMAAFALAEYRFKGNMLLGLYLALGIMIPIRIGTVAILELM 134
           F N+M VT+ +  + +L  A AA+ALA  RF G  LL   +   +++P+++  + +L+L 
Sbjct: 174 FLNTMTVTIPATVIPILIAAFAAYALAWMRFPGRALLVATIVGLLVVPLQLALIPLLKLH 233

Query: 135 VDTGLVNTLTALILVYTAQGLPLAVFILSEFMKQVSDDLKNAGRIDGLSEYTIFFRLVLP 194
              GL  +   + L +T  GLPLA+++L  +M  +  ++  + R+DG +E+ IF R+VLP
Sbjct: 234 NQIGLNQSYLGIWLAHTGFGLPLAIYLLRNYMVGLPREIIESARVDGATEFQIFRRIVLP 293

Query: 195 LVRPAMATVAVFNMIPIWNDLWFPLI-LAPAEETKTLTLGSQVFIGQFVTDWNAVLSALS 253
           L  PA+A+ A+F  + +WNDL    + L  A +T+ +T   +  +G    DW  + ++  
Sbjct: 294 LSFPALASFAIFQFLWVWNDLLVATVFLGNATDTQVMTGALRALLGSRGGDWEILAASAF 353

Query: 254 MAILPVMVLYVIFSRQLIRGITSGAVK 280
           ++I   ++++    + L+RG+ +G+VK
Sbjct: 354 VSIAVPLIVFFALQKYLVRGLLAGSVK 380


Lambda     K      H
   0.330    0.143    0.414 

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: 280
Number of extensions: 19
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: 280
Length of database: 382
Length adjustment: 28
Effective length of query: 252
Effective length of database: 354
Effective search space:    89208
Effective search space used:    89208
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 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