GapMind for catabolism of small carbon sources

 

Alignments for a candidate for msdB2 in Rhodobacter viridis JA737

Align Binding-protein-dependent transport systems inner membrane component (characterized, see rationale)
to candidate WP_110804034.1 C8J30_RS01980 carbohydrate ABC transporter permease

Query= uniprot:A3DE71
         (289 letters)



>NCBI__GCF_003217355.1:WP_110804034.1
          Length = 382

 Score =  128 bits (321), Expect = 2e-34
 Identities = 74/237 (31%), Positives = 127/237 (53%), Gaps = 9/237 (3%)

Query: 56  IAPTRFS--NYVEVFQKLPFGIYFRNSLIVCSIVMVVALVIATLAGYSLAKYKFPGSGFF 113
           +AP R +  NY  V      G  F N++ V     V+ ++IA  A Y+LA  +FPG    
Sbjct: 151 VAPPRLTTGNYARVITAEGIGRAFLNTMTVTIPATVIPILIAAFAAYALAWMRFPGRALL 210

Query: 114 GILILATQLLPGMMFLLPLYLDFVKIKQATGIQLINSIPGLVIVYSAFFVPFSIWIIRGF 173
              I+   ++P  + L+PL      +K    I L  S  G+ + ++ F +P +I+++R +
Sbjct: 211 VATIVGLLVVPLQLALIPL------LKLHNQIGLNQSYLGIWLAHTGFGLPLAIYLLRNY 264

Query: 174 FASIPGELEEAARIDGCNKFTAFLRVMLPLAVPGIVATAIYIFLTAWDELIFAWVLLKDT 233
              +P E+ E+AR+DG  +F  F R++LPL+ P + + AI+ FL  W++L+ A V L + 
Sbjct: 265 MVGLPREIIESARVDGATEFQIFRRIVLPLSFPALASFAIFQFLWVWNDLLVATVFLGNA 324

Query: 234 KVTTIPAG-IRGFIAYTTARYDLLMAAGTIVTIPVLIMFFTMQKKFISGMTAGAVKG 289
             T +  G +R  +      +++L A+  +     LI+FF +QK  + G+ AG+VKG
Sbjct: 325 TDTQVMTGALRALLGSRGGDWEILAASAFVSIAVPLIVFFALQKYLVRGLLAGSVKG 381


Lambda     K      H
   0.332    0.145    0.434 

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: 295
Number of extensions: 18
Number of successful extensions: 3
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: 289
Length of database: 382
Length adjustment: 28
Effective length of query: 261
Effective length of database: 354
Effective search space:    92394
Effective search space used:    92394
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.9 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