GapMind for catabolism of small carbon sources

 

Alignments for a candidate for HSERO_RS00895 in Nocardioides daejeonensis MJ31

Align ABC-type branched-chain amino acid transport system, ATPase component protein (characterized, see rationale)
to candidate WP_110208105.1 DNK54_RS16590 ABC transporter ATP-binding protein

Query= uniprot:D8J1T6
         (255 letters)



>NCBI__GCF_003194585.1:WP_110208105.1
          Length = 263

 Score =  202 bits (513), Expect = 7e-57
 Identities = 111/249 (44%), Positives = 156/249 (62%), Gaps = 12/249 (4%)

Query: 5   LLKIRDVSKRFGGLQALNGVGITIERGQIYGLIGPNGAGKTTFFNVITGLYQPDTGTFEL 64
           LL++ DV  RFGG+ A+N    T +  +I GLIGPNGAGKTT FNVITGL +P +G+   
Sbjct: 3   LLEVNDVVVRFGGVTAVNQARFTADERRITGLIGPNGAGKTTCFNVITGLQRPTSGSVRF 62

Query: 65  DGKPYSPSAPHEVAKAGIARTFQNIRLFGEMTVLENVMVGCHVRTKQNVFGAVFRHKAAR 124
            G+  + +A H  A+ G+ARTFQ +  FG +TV +NV V   +      FG + R  +AR
Sbjct: 63  GGRDVTRTAVHRRARRGMARTFQRLEAFGSLTVRDNVRVALDIA---GGFGGLMRSSSAR 119

Query: 125 EEEAAIREKSQKLLDFVGIGQFAKRTARHLSYGDQRRLEIARALATDPQLLALDEPAAGM 184
            +EA         LD VGI ++A   A  +  G  R LE+AR L  DP+LL LDEP++G+
Sbjct: 120 VDEA---------LDRVGISEYAAERADSIPTGTARLLELARCLVGDPKLLLLDEPSSGL 170

Query: 185 NATEKLGLRELLVKIQAEGKTILLIEHDVKLMMGLCNRITVLDYGKPIAEGVPADVQKNP 244
           + +E     ELL+ + +EGK IL++EHD+ L+M +C+ I VLD+G+ I  G PA+V+ + 
Sbjct: 171 DESETDAFGELLIALASEGKAILMVEHDMDLVMTVCDDIHVLDFGEIICSGSPAEVRADA 230

Query: 245 AVIEAYLGA 253
            V  AYLGA
Sbjct: 231 RVQAAYLGA 239


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: 167
Number of extensions: 3
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: 263
Length adjustment: 24
Effective length of query: 231
Effective length of database: 239
Effective search space:    55209
Effective search space used:    55209
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 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