GapMind for catabolism of small carbon sources

 

Alignments for a candidate for HSERO_RS00895 in Phaeobacter inhibens BS107

Align ABC-type branched-chain amino acid transport system, ATPase component protein (characterized, see rationale)
to candidate GFF249 PGA1_c02610 putative high-affinity branched-chain amino acid transport ATP-binding protein LivG

Query= uniprot:D8J1T6
         (255 letters)



>FitnessBrowser__Phaeo:GFF249
          Length = 255

 Score =  206 bits (523), Expect = 5e-58
 Identities = 105/252 (41%), Positives = 160/252 (63%), Gaps = 1/252 (0%)

Query: 4   TLLKIRDVSKRFGGLQALNGVGITIERGQIYGLIGPNGAGKTTFFNVITGLYQPDTGTFE 63
           +LL+I   + +FGG+ A+N +  ++E G++Y ++GPNGAGK+T FN+I+  YQP +G   
Sbjct: 2   SLLEIEHATLKFGGVVAVNDLSFSVEEGEVYAIVGPNGAGKSTVFNLISRFYQPHSGRLS 61

Query: 64  LDGKPYSPSAPHEVAKAGIARTFQNIRLFGEMTVLENVMVGCHVRTKQNVFGAVFRHKAA 123
            DG+    S    VA  GIARTFQNI LF   TVL+N++VG H   +  +   +F     
Sbjct: 62  FDGRDLLQSKADAVADLGIARTFQNIELFDHATVLQNLLVGRHRHRRSTLMEELFFTPRV 121

Query: 124 REEEAAIREKSQKLLDFVGIGQFAKRTARHLSYGDQRRLEIARALATDPQLLALDEPAAG 183
           R EE   R   ++++DF+ +  +  +    L YG ++ +E+ RALA+ P+LL LDEPA+G
Sbjct: 122 RREERRHRAAVEEVIDFLDLQAYRDKMIAGLPYGVRKVVELGRALASGPRLLLLDEPASG 181

Query: 184 MNATEKLGLRELLVKIQAE-GKTILLIEHDVKLMMGLCNRITVLDYGKPIAEGVPADVQK 242
           ++  E   +R  +  I+ + G T+L++EHD+ L+  + +R+  L  G  +AEG PA+VQ 
Sbjct: 182 LSVEETRDMRWWIDDIRKQMGITVLMVEHDMGLVSSVSDRVLALADGAKLAEGTPAEVQA 241

Query: 243 NPAVIEAYLGAG 254
           NPAVIEAYLGAG
Sbjct: 242 NPAVIEAYLGAG 253


Lambda     K      H
   0.320    0.138    0.394 

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: 255
Length adjustment: 24
Effective length of query: 231
Effective length of database: 231
Effective search space:    53361
Effective search space used:    53361
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