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_1109 Dsui_1109 ABC-type branched-chain amino acid transport systems, ATPase component

Query= TCDB::P21629
         (255 letters)



>FitnessBrowser__PS:Dsui_1109
          Length = 266

 Score =  190 bits (482), Expect = 3e-53
 Identities = 91/251 (36%), Positives = 149/251 (59%)

Query: 5   ILEVSGLTMRFGGLLAVNGVNLKVEEKQVVSMIGPNGAGKTTVFNCLTGFYQPTGGLIRL 64
           IL++  +++RFGG+ A+  ++  V+E ++ ++IGPNGAGK+++ N + G Y P  G I  
Sbjct: 15  ILDLQNISLRFGGVKALTDISFNVKEHEIRAIIGPNGAGKSSMLNVINGVYHPQEGRIVF 74

Query: 65  DGEEIQGLPGHKIARKGVVRTFQNVRLFKEMTAVENLLVAQHRHLNTNFLAGLFKTPAFR 124
            GEE + +  H  A +G+ RTFQN+ LFK M+ ++N++  +   +   FL         +
Sbjct: 75  HGEERKKMEPHMAATQGIARTFQNIALFKGMSVLDNIMTGRITKMKCGFLEQALYLGRAQ 134

Query: 125 RSEREAMEYAAHWLEEVNLTEFANRSAGTLAYGQQRRLEIARCMMTRPRILMLDEPAAGL 184
           + E    E     ++ + +        G L YG Q+R+E+ R +   P +L+LDEP AG+
Sbjct: 135 KEELAHREKVEEVIDFLEIQHIRKTPVGRLPYGLQKRVELGRALAAEPSLLLLDEPMAGM 194

Query: 185 NPKETDDLKALIAKLRSEHNVTVLLIEHDMKLVMSISDHIVVINQGAPLADGTPEQIRDN 244
           N +E  D+   I  +  +   T++LIEHDM +VM ISD +VV++ G  + DGTP+ +R+N
Sbjct: 195 NVEEKQDMCRFILDVNDQFGTTIVLIEHDMGVVMDISDRMVVLDYGKKIGDGTPDDVRNN 254

Query: 245 PDVIKAYLGEA 255
            +VI AYLG A
Sbjct: 255 QEVISAYLGVA 265


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: 158
Number of extensions: 7
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: 255
Length of database: 266
Length adjustment: 24
Effective length of query: 231
Effective length of database: 242
Effective search space:    55902
Effective search space used:    55902
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