GapMind for catabolism of small carbon sources

 

Alignments for a candidate for msdC2 in Nocardiopsis gilva YIM 90087

Align Binding-protein-dependent transport systems inner membrane component (characterized, see rationale)
to candidate WP_026125974.1 CDO52_RS20925 ABC transporter permease subunit

Query= uniprot:A3DHA2
         (303 letters)



>NCBI__GCF_002263495.1:WP_026125974.1
          Length = 311

 Score =  107 bits (268), Expect = 3e-28
 Identities = 64/210 (30%), Positives = 109/210 (51%), Gaps = 7/210 (3%)

Query: 99  FLLMFLNSAIMTIPIVIIQVIVGVFAAYAFAKLRFPLRDKLFFVFIVVMLMPLQVTLVPN 158
           F L  +NSAI+     +  V+    A +A AKLRF  R+ +    ++ M++P+Q+ +VP 
Sbjct: 103 FALGLVNSAIVASVTAVSVVLFCSLAGFALAKLRFTGRNAITLGVVLTMMVPVQMAVVPM 162

Query: 159 YILLRKLDMIGSFLSVILPGGFSAFGVVLLRQY-MRGIPDECCEAAMIDGAGYLKTFTKI 217
            I++   D  G   +VI+P   + FGV ++RQY ++G+P E  EAA IDG    + F  +
Sbjct: 163 LIMMDAFDWRGDLKAVIVPFMVTGFGVFMMRQYALQGVPTELLEAARIDGCSMFRAFWSV 222

Query: 218 ILPQCKSIIASLAILAFIDNWNMVEQPLIFLS-DSAKYPLSVYLAYINEG---DLGLAFA 273
           +LP  +  +  L +L F+ NWN    P+  L  D+    +S++   +N G   D  L F 
Sbjct: 223 VLPALRPPMVVLGLLTFMQNWNEFIWPIAVLGPDNPTVQVSIH--QLNSGYTTDFALMFT 280

Query: 274 SGVLYMIPTVLIYLYGEKYFVEGIQLTGIK 303
                 +P +L+++   +  + GI    +K
Sbjct: 281 GAAFATLPLLLVFVLFGRRLIGGIMEGAVK 310


Lambda     K      H
   0.331    0.147    0.425 

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: 181
Number of extensions: 7
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: 303
Length of database: 311
Length adjustment: 27
Effective length of query: 276
Effective length of database: 284
Effective search space:    78384
Effective search space used:    78384
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: 48 (23.1 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