GapMind for catabolism of small carbon sources

 

Alignments for a candidate for livF in Dinoroseobacter shibae DFL-12

Align High-affinity branched-chain amino acid transport ATP-binding protein BraG, component of Branched chain amino acid uptake transporter. Transports alanine (characterized)
to candidate 3608115 Dshi_1520 ABC transporter related (RefSeq)

Query= TCDB::P21630
         (233 letters)



>FitnessBrowser__Dino:3608115
          Length = 277

 Score =  208 bits (530), Expect = 8e-59
 Identities = 100/217 (46%), Positives = 153/217 (70%), Gaps = 1/217 (0%)

Query: 17  LHDVSVEVKKGEIVTLIGANGAGKSTLLMTLCGSPQAASGSIRYEGEELVGLPSSTIMRK 76
           LHD ++ V +GEI  ++G NGAGKST +  + G     +GS+R +GE++ GL     + K
Sbjct: 62  LHDCTLAVDRGEIAVIVGPNGAGKSTAMKAVFGMLNIHTGSVRLDGEDITGLSPQARVAK 121

Query: 77  SIAVVPEGRRVFSRLTVEENLAMGGFFTDKDDYQVQMDKVLELFPRLKERYEQRAGTMSG 136
            +A VP+   +F+ +TVEENL MG F   +DD    M++V ELFP L+E+  Q AG +SG
Sbjct: 122 GMAFVPQVNNIFTTMTVEENLEMGAFLR-RDDISETMEQVYELFPILREKRRQAAGELSG 180

Query: 137 GEQQMLAIGRALMSKPKLLLLDEPSLGLAPIIIQQIFEIIEQLRREGVTVFLVEQNANQA 196
           G++Q +A+GRALM++P++L+LDEP+ G++PI++ ++F+ I ++ R G+++ +VEQNA QA
Sbjct: 181 GQRQQVAVGRALMTRPQVLMLDEPTAGVSPIVMDELFDRIIEVARTGISILMVEQNARQA 240

Query: 197 LKLADRAYVLENGRIVMHDTGAALLTNPKVRDAYLGG 233
           L++AD+ YVL  GR    DTG ALL +P VR ++LGG
Sbjct: 241 LEIADKGYVLVQGRNRYTDTGQALLADPDVRKSFLGG 277


Lambda     K      H
   0.318    0.136    0.374 

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: 193
Number of extensions: 7
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: 233
Length of database: 277
Length adjustment: 24
Effective length of query: 209
Effective length of database: 253
Effective search space:    52877
Effective search space used:    52877
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