GapMind for catabolism of small carbon sources

 

Alignments for a candidate for HSERO_RS00895 in Methylocystis bryophila S285

Align ABC-type branched-chain amino acid transport system, ATPase component protein (characterized, see rationale)
to candidate WP_085770502.1 B1812_RS04380 ABC transporter ATP-binding protein

Query= uniprot:D8J1T6
         (255 letters)



>NCBI__GCF_002117405.1:WP_085770502.1
          Length = 293

 Score =  211 bits (538), Expect = 1e-59
 Identities = 112/251 (44%), Positives = 161/251 (64%), Gaps = 1/251 (0%)

Query: 6   LKIRDVSKRFGGLQALNGVGITIERGQIYGLIGPNGAGKTTFFNVITGLYQPDTGTFELD 65
           L + ++S  FGG+QAL+ +  ++  G+I  +IGPNGAGK++  NVITGLY+PD G  +LD
Sbjct: 35  LALTNISLSFGGIQALSEIDFSVAAGEICSIIGPNGAGKSSLINVITGLYRPDWGRIQLD 94

Query: 66  GKPYSPSAPHEVAKAGIARTFQNIRLFGEMTVLENVMVGCHVRTKQNVFGAVFRHKAARE 125
              +S      +A  G+ARTFQN+ LF  ++V +N+ VG    T+ +    VF    AR 
Sbjct: 95  KNSFSRMPTERLASLGVARTFQNLALFRGLSVFDNIAVGRVSATRSHWLEQVFGLPRARA 154

Query: 126 EEAAIREKSQKLLDFVGIGQFAKRTARHLSYGDQRRLEIARALATDPQLLALDEPAAGMN 185
           +  A     +++L F+G+GQ   R A  L YG Q+R+E+ARALA  P+LL LDEP AGM 
Sbjct: 155 DRLATEIIVEEMLVFLGLGQVRNRIAGTLPYGMQKRVELARALAIRPRLLLLDEPMAGMT 214

Query: 186 ATEKLGLRELLVKIQAE-GKTILLIEHDVKLMMGLCNRITVLDYGKPIAEGVPADVQKNP 244
           A EK  + E +   +   G +I+LIEHD+ ++M L +R+ VLDYG+ IA+G P+DV  + 
Sbjct: 215 AGEKAEMGEFIQLTRDRFGASIVLIEHDIGVVMELSDRVAVLDYGRKIADGPPSDVMNDE 274

Query: 245 AVIEAYLGAGH 255
           AVI+AYLG  H
Sbjct: 275 AVIDAYLGVAH 285


Lambda     K      H
   0.320    0.138    0.394 

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: 191
Number of extensions: 8
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: 255
Length of database: 293
Length adjustment: 25
Effective length of query: 230
Effective length of database: 268
Effective search space:    61640
Effective search space used:    61640
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 47 (22.7 bits)

This GapMind analysis is from Apr 09 2024. 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