GapMind for catabolism of small carbon sources

 

Alignments for a candidate for braF in Dechlorosoma suillum PS

Align High-affinity branched-chain amino acid transport ATP-binding protein BraF, component of Branched chain amino acid uptake transporter. Transports alanine (characterized)
to candidate Dsui_2058 Dsui_2058 ABC-type branched-chain amino acid transport systems, ATPase component

Query= TCDB::P21629
         (255 letters)



>FitnessBrowser__PS:Dsui_2058
          Length = 260

 Score =  221 bits (564), Expect = 9e-63
 Identities = 111/250 (44%), Positives = 157/250 (62%), Gaps = 1/250 (0%)

Query: 5   ILEVSGLTMRFGGLLAVNGVNLKVEEKQVVSMIGPNGAGKTTVFNCLTGFYQPTGGLIRL 64
           +L +  +   FGGL  +  V+ +V    +  +IGPNGAGKTTVFN +TG   P+ G I  
Sbjct: 9   LLSIRNVGKHFGGLHVLQDVSFEVPAGSIYGLIGPNGAGKTTVFNLITGLLTPSAGQIDF 68

Query: 65  DGEEIQGLPGHKIARKGVVRTFQNVRLFKEMTAVENLLVAQHRHLNTNFLAGLFKTPAFR 124
            G+ + GL  H+I  +G+ RTFQN+R+FKEM  +EN++V  H HLN         +PA R
Sbjct: 69  QGQTLIGLEPHRITHQGIARTFQNIRIFKEMDLLENVMVGMHDHLNYGGFGIFLNSPACR 128

Query: 125 RSEREAMEYAAHWLEEVNLTEFANRSAGTLAYGQQRRLEIARCMMTRPRILMLDEPAAGL 184
            +E++A E A   L  V L   A+  A  L+YG QR+LE AR + T P++L+LDEP AG+
Sbjct: 129 AAEKKARERALELLSWVGLDHKADMLADNLSYGDQRKLEFARALATEPKLLLLDEPVAGM 188

Query: 185 NPKETDDLKALIAKLRSEHNVTVLLIEHDMKLVMSISDHIVVINQGAPLADGTPEQIRDN 244
           NP E   L   I  +R+     V +IEHDM+ VM + D I V+N G  +A+GTP+++R+N
Sbjct: 189 NPSEKTILMEEINNIRN-RGYGVFMIEHDMRFVMGLCDRIAVLNFGRIIAEGTPDEVRNN 247

Query: 245 PDVIKAYLGE 254
           PDVI+AYLG+
Sbjct: 248 PDVIEAYLGK 257


Lambda     K      H
   0.320    0.137    0.391 

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: 198
Number of extensions: 5
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: 255
Length of database: 260
Length adjustment: 24
Effective length of query: 231
Effective length of database: 236
Effective search space:    54516
Effective search space used:    54516
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 (21.8 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