GapMind for catabolism of small carbon sources

 

Alignments for a candidate for malG_Aa 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:C8WUQ9
         (301 letters)



>NCBI__GCF_003217355.1:WP_110804034.1
          Length = 382

 Score =  102 bits (254), Expect = 1e-26
 Identities = 73/234 (31%), Positives = 120/234 (51%), Gaps = 11/234 (4%)

Query: 74  PSNASLANYKALFQGGQFWTWVRNSLVVGVVVAMAQSFITAMSAFAFSKLRFYGRKYGLM 133
           P   +  NY  +           N++ V +   +    I A +A+A + +RF GR   + 
Sbjct: 153 PPRLTTGNYARVITAEGIGRAFLNTMTVTIPATVIPILIAAFAAYALAWMRFPGRALLVA 212

Query: 134 TLLLLQMFPNILAIAAFYTALAKL-NMIDMLGSYILVMLGTSAFN----IWLLKGYMDSV 188
           T++ L + P  LA+      L KL N I +  SY+ + L  + F     I+LL+ YM  +
Sbjct: 213 TIVGLLVVPLQLALIP----LLKLHNQIGLNQSYLGIWLAHTGFGLPLAIYLLRNYMVGL 268

Query: 189 PKELDEAAVIDGATTWQRFIHVTLPLSTPMMVVIFFLTLVGIFSEYMFAGTILQSPWNYT 248
           P+E+ E+A +DGAT +Q F  + LPLS P +        + ++++ + A   L +  +  
Sbjct: 269 PREIIESARVDGATEFQIFRRIVLPLSFPALASFAIFQFLWVWNDLLVATVFLGNATDTQ 328

Query: 249 LGVGMYNLISGQFAKNWGEFAAAALLS-AVPLAIVFAVAQRYLTKGLVAGSVKG 301
           +  G    + G    +W   AA+A +S AVPL + FA+ Q+YL +GL+AGSVKG
Sbjct: 329 VMTGALRALLGSRGGDWEILAASAFVSIAVPLIVFFAL-QKYLVRGLLAGSVKG 381


Lambda     K      H
   0.328    0.136    0.417 

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: 298
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: 301
Length of database: 382
Length adjustment: 28
Effective length of query: 273
Effective length of database: 354
Effective search space:    96642
Effective search space used:    96642
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: 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