GapMind for catabolism of small carbon sources

 

Alignments for a candidate for treV in Erythrobacter marinus HWDM-33

Align TreV, component of Trehalose porter (characterized)
to candidate WP_047092042.1 AAV99_RS00435 ABC transporter ATP-binding protein

Query= TCDB::Q97ZC0
         (324 letters)



>NCBI__GCF_001013305.1:WP_047092042.1
          Length = 233

 Score =  115 bits (289), Expect = 8e-31
 Identities = 68/199 (34%), Positives = 103/199 (51%), Gaps = 9/199 (4%)

Query: 17  VINGITEKIETGEFFVILGPSGEGKSTLLKILAGIEKLDKGKIIADGADITDKPPE---- 72
           ++ GI   +  GE   +LGPSG GKS+L+ +L+G+E+   GK+   G D T    +    
Sbjct: 29  ILRGIDLDVARGETLALLGPSGSGKSSLMSVLSGLERATSGKLTVAGEDFTALNEDALAM 88

Query: 73  --KRNVAMVFQNYALYPNMSVRDNIAFPLKMRGMKKEEIIERVEKAAKLLGISEILDKKV 130
             +  + +V Q + L P M+  +N+A PL++ G  ++   ER     + +G+   L    
Sbjct: 89  ARRGRIGIVLQAFHLLPTMTAVENVATPLELAG--EDGAWERATAELEAVGLGHRLTHYP 146

Query: 131 TQISGGQQQRVALARAIVRNPSYFLLDEPLSNLDARVRTTARGELKRIQKELKGTFIYVT 190
            Q+SGG+QQRVA+ARAIV  P     DEP  NLD     +    L   + E   T I +T
Sbjct: 147 AQLSGGEQQRVAIARAIVSRPPLIFADEPTGNLDTNTGASVEDALFERRAETGATLIIIT 206

Query: 191 HDQKEALSLADRIAILHKG 209
           HD+K A    +R+  L  G
Sbjct: 207 HDRKLA-ERCNRVVTLGDG 224


Lambda     K      H
   0.318    0.137    0.385 

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: 163
Number of extensions: 7
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: 324
Length of database: 233
Length adjustment: 25
Effective length of query: 299
Effective length of database: 208
Effective search space:    62192
Effective search space used:    62192
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 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