GapMind for catabolism of small carbon sources

 

Alignments for a candidate for peb1C in Dechlorosoma suillum PS

Align PEB1C, component of Uptake system for glutamate and aspartate (characterized)
to candidate Dsui_2068 Dsui_2068 ABC-type metal ion transport system, ATPase component

Query= TCDB::A3ZI83
         (242 letters)



>FitnessBrowser__PS:Dsui_2068
          Length = 278

 Score =  148 bits (374), Expect = 1e-40
 Identities = 85/198 (42%), Positives = 122/198 (61%), Gaps = 3/198 (1%)

Query: 21  NLSVKEGEKLVIIGPSGSGKSTTIRCMNGLEEVSSGEVVVN--NLVLNHKNKIEICRKYC 78
           +L V  GE   IIG SG+GKST +R  N LE   +G+VVV+  +L+      +   R+  
Sbjct: 34  DLDVAPGEIHGIIGFSGAGKSTLLRLANLLERPDAGQVVVHGQDLMTLSPADLRTARQRI 93

Query: 79  AMVFQHFNLYPHMTVLQNLTLAPMKLQKKSKKEAEETAFKYLKVVGLLDKANVYPATLSG 138
            M+FQHFNL  + TV  N+   P+++    +    E     L+ VGL +KA VYPA LSG
Sbjct: 94  GMIFQHFNLLHNRTVADNVAF-PLRIAGADEARINERVKTCLEFVGLSEKAGVYPAQLSG 152

Query: 139 GQQQRVAIARSLCTKKPYILFDEPTSALDPETIQEVLDVMKEISHQSNTTMVVVTHEMGF 198
           GQ+QRVAIAR+L  +   +L DEPTSALDP T Q +L+V+ +++ +   T+++V+HEMG 
Sbjct: 153 GQKQRVAIARALAPEPHVLLADEPTSALDPRTTQSLLEVLADVNRRLGVTILLVSHEMGV 212

Query: 199 AKEVADRIIFMEDGAIVE 216
            + +  R+  ME G IVE
Sbjct: 213 IRRLCHRVSVMEAGQIVE 230


Lambda     K      H
   0.317    0.133    0.372 

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: 136
Number of extensions: 6
Number of successful extensions: 3
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: 242
Length of database: 278
Length adjustment: 24
Effective length of query: 218
Effective length of database: 254
Effective search space:    55372
Effective search space used:    55372
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 47 (22.7 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