GapMind for catabolism of small carbon sources

 

Alignments for a candidate for livG in Dechlorosoma suillum PS

Align ABC transporter ATP-binding protein (characterized, see rationale)
to candidate Dsui_0842 Dsui_0842 ABC-type branched-chain amino acid transport systems, ATPase component

Query= uniprot:A0A165KC86
         (260 letters)



>FitnessBrowser__PS:Dsui_0842
          Length = 593

 Score =  226 bits (575), Expect = 1e-63
 Identities = 115/249 (46%), Positives = 164/249 (65%), Gaps = 2/249 (0%)

Query: 8   VVLKVAGISKRFGGLQALSDVGITIKRGQVYGLIGPNGAGKTTFFNVITGLYTPDAGTFE 67
           V+L+  G++KRFGGL A  D+ +T++ G+V  LIGPNGAGK+T FN I+G+  P  G   
Sbjct: 344 VLLQAEGVTKRFGGLVANKDMALTVQAGEVMALIGPNGAGKSTMFNCISGVNPPSEGRIS 403

Query: 68  LAGKPYEPTAVHEVAKAGIARTFQNIRLFAEMTALENVMVGRHIRTGSGLFGAVFRTKGF 127
             G+P       ++A+ G++RTFQ++RL + MT LENV +G H+R       A  R +  
Sbjct: 404 FLGQPVAGLEARDIARLGLSRTFQHVRLLSGMTVLENVAIGAHLRGRHNYLAAGLRLE-- 461

Query: 128 KAEEAAIAKRAQELLDYVGIGKFADYKARTLSYGDQRRLEIARALATDPQLIALDEPAAG 187
           +AEEA +   A   ++ VG+ +     A +L+ G QR +EIARALA DP L+ LDEPAAG
Sbjct: 462 RAEEARLLAEAARQIERVGLAEHMFDAAGSLALGKQRIIEIARALAADPCLLLLDEPAAG 521

Query: 188 MNATEKVQLRELIDRIRNDNRTILLIEHDVKLVMGLCDRVTVLDYGKQIAEGNPAEVQKN 247
           +   EK  L EL+ ++R +   ILL+EHD+  VMGL DRV V+++G+++AEG P E+QKN
Sbjct: 522 LRYLEKQALAELLRKLRGEGMGILLVEHDMDFVMGLADRVVVMEFGEKLAEGLPEEIQKN 581

Query: 248 EKVIEAYLG 256
             V+EAYLG
Sbjct: 582 PAVLEAYLG 590


Lambda     K      H
   0.319    0.137    0.384 

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: 422
Number of extensions: 22
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: 260
Length of database: 593
Length adjustment: 30
Effective length of query: 230
Effective length of database: 563
Effective search space:   129490
Effective search space used:   129490
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 (21.7 bits)
S2: 50 (23.9 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