GapMind for catabolism of small carbon sources

 

Alignments for a candidate for PGA1_c12640 in Marinobacter adhaerens HP15

Align D-lactate transporter, ATP-binding component (characterized)
to candidate GFF1119 HP15_1097 branched-chain amino acid ABC transporter, ATP-binding protein

Query= reanno::Phaeo:GFF1248
         (251 letters)



>FitnessBrowser__Marino:GFF1119
          Length = 255

 Score =  184 bits (466), Expect = 2e-51
 Identities = 94/247 (38%), Positives = 153/247 (61%), Gaps = 4/247 (1%)

Query: 3   ILEVKNVGKRFGGLQALSDVNLSVRENTVHAIIGPNGAGKSTLLNCLVGKLIPDTGSVMF 62
           ILE +++ K +GG++AL D++L  ++  +H ++GPNGAGKSTLLN L G L P +G +  
Sbjct: 6   ILETESLSKHWGGIKALDDISLQFQDKHLHGVVGPNGAGKSTLLNMLCGTLKPTSGCIFH 65

Query: 63  DGKSVLGRAPYEINQMGISRVFQTPEIFGDLSVLENMMIPCFAKRDGAFEMNAISAVSGQ 122
            G  + G  P+E    GI R FQ   I+ D++ LEN  I    +  G+F  N  ++    
Sbjct: 66  KGDQIEGMKPWEFVHRGIGRSFQKTNIYVDVTCLENCAIAAQRRFTGSF--NLFASRHSN 123

Query: 123 RDILEKAEHMLEEMNMADKRHMNAASMSRGDKRRLEIGMCLSQEPRLLLLDEPTAGMARA 182
           + + E AE  L ++ + ++ H  AA +S G++R+LE+ M L+ +P +LLLDEP AGM   
Sbjct: 124 KLVREGAEKALCQVGLENRVHTVAAEISYGEQRQLELAMVLATDPCILLLDEPMAGMGHE 183

Query: 183 DTNNTIDLLKQIKSERDITIAIIEHDMHVVFSLADRITVLAQGTPLVEDDPQNIKGNPKV 242
           ++   I+L+ Q+K  +  +I ++EHDM  +F L+D++TVL  GT L+      ++ + +V
Sbjct: 184 ESQRIIELMNQLK--QTYSIVLVEHDMDAIFELSDQLTVLDNGTHLITGTVDEVRNDTRV 241

Query: 243 REAYLGE 249
           +EAYLG+
Sbjct: 242 KEAYLGK 248


Lambda     K      H
   0.318    0.135    0.379 

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: 169
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: 251
Length of database: 255
Length adjustment: 24
Effective length of query: 227
Effective length of database: 231
Effective search space:    52437
Effective search space used:    52437
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: 46 (22.3 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