GapMind for catabolism of small carbon sources

 

Alignments for a candidate for BPHYT_RS24005 in Cupriavidus basilensis 4G11

Align Polar amino acid ABC transporter, inner membrane subunit; Flags: Precursor (characterized, see rationale)
to candidate RR42_RS34310 RR42_RS34310 amino acid ABC transporter permease

Query= uniprot:B2TBJ7
         (240 letters)



>FitnessBrowser__Cup4G11:RR42_RS34310
          Length = 222

 Score =  116 bits (291), Expect = 3e-31
 Identities = 68/199 (34%), Positives = 111/199 (55%), Gaps = 12/199 (6%)

Query: 17  VLLLAALMTVALTLAALAVGAVFGALVAAAKLSRFRTLRVIGDIYTTVFRGVPELLVIYL 76
           +LL  A++TV +T+ A  + ++ G  +A  KLS  RTL         V RG+P ++ ++ 
Sbjct: 15  ILLQGAVVTVEVTVLAFVLSSLLGLALALMKLSPARTLSWGASGAINVIRGLPIIVQLFY 74

Query: 77  FYFGGSTLVTSVGQLFGAEGFVGVPPFVVGALAVGMISGAYQAEVYRSAVLAVSRGELEA 136
            YF    ++   G        + +  F  G + +G+   AYQAE +R+ + AV  G+ EA
Sbjct: 75  IYF----VLPDAG--------IHLTAFQAGVIGLGIAYSAYQAENFRAGIEAVDPGQREA 122

Query: 137 ARSIGMPTLTMARRILIPQVLRFALPGIGNVWQLSLKDSALISVTGLAELLRTSQVAAGS 196
           A+++GM    + RR+++PQ LR +LP  GN   + LKDS+L+S   +AE+ R  Q+ A S
Sbjct: 123 AQAMGMRPALVMRRVILPQALRISLPPYGNTLVMMLKDSSLVSTITVAEMTRAGQLIASS 182

Query: 197 THQYFTFFVVGGALYLIMT 215
           T Q  T + +   LYL+M+
Sbjct: 183 TFQNMTVYTLVALLYLLMS 201


Lambda     K      H
   0.327    0.141    0.403 

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: 102
Number of extensions: 4
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: 240
Length of database: 222
Length adjustment: 23
Effective length of query: 217
Effective length of database: 199
Effective search space:    43183
Effective search space used:    43183
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: 46 (22.3 bits)

This GapMind analysis is from Sep 17 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