GapMind for catabolism of small carbon sources

 

Alignments for a candidate for livF in Dechlorosoma suillum PS

Align ABC transporter ATP-binding protein-branched chain amino acid transport, component of The branched chain hydrophobic amino acid transporter, LivJFGHM (characterized)
to candidate Dsui_0626 Dsui_0626 ABC-type branched-chain amino acid transport systems, ATPase component

Query= TCDB::Q8DQH7
         (236 letters)



>FitnessBrowser__PS:Dsui_0626
          Length = 238

 Score =  243 bits (621), Expect = 2e-69
 Identities = 122/233 (52%), Positives = 169/233 (72%)

Query: 3   VLKVENLSVHYGMIQAVRDVSFEVNEGEVVSLIGANGAGKTTILRTLSGLVRPSSGKIEF 62
           +L VE L + YG IQAV+ ++F V+ GE V+LIGANGAGKT+ L+ L+  +  + G + +
Sbjct: 5   LLIVEGLRIAYGGIQAVKGITFHVDPGETVALIGANGAGKTSTLKALARQLDAAGGSVRY 64

Query: 63  LGQEIQKMPAQKIVAGGLSQVPEGRHVFPGLTVMENLEMGAFLKKNREENQANLKKVFSR 122
            G+EI  +   ++V  G++ VPEGR VF  LTV ENLEMGA+ + ++ E   +L+++F+ 
Sbjct: 65  QGREISALAPHELVGQGIALVPEGRGVFARLTVTENLEMGAYCRHDKAEIADDLERIFAL 124

Query: 123 FPRLEERKNQDAATLSGGEQQMLAMGRALMSTPKLLLLDEPSMGLAPIFIQEIFDIIQDI 182
            PRL+ER  Q A TLSGGEQQMLAMGRALMS P+LLLLDEPSMGLAPI +Q++F+++Q++
Sbjct: 125 LPRLKERHGQLAGTLSGGEQQMLAMGRALMSRPRLLLLDEPSMGLAPIMVQKVFEVVQEV 184

Query: 183 QKQGTTVLLIEQNANKALAISDRGYVLETGKIVLSGTGKELASSEEVRKAYLG 235
             QG T+LL+EQNA  AL +S RGYV+E+G I L+     L  +  V+ AYLG
Sbjct: 185 ASQGMTILLVEQNARLALQVSRRGYVMESGDITLTDAAGTLLDNPRVKAAYLG 237


Lambda     K      H
   0.315    0.134    0.358 

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: 162
Number of extensions: 3
Number of successful extensions: 1
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: 236
Length of database: 238
Length adjustment: 23
Effective length of query: 213
Effective length of database: 215
Effective search space:    45795
Effective search space used:    45795
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: 42 (22.0 bits)
S2: 46 (22.3 bits)

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

Links

Downloads

Related tools

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