GapMind for catabolism of small carbon sources

 

Alignments for a candidate for livG in Shewanella oneidensis MR-1

Align High-affinity branched-chain amino acid transport ATP-binding protein LivG aka B3455, component of Leucine; leucine/isoleucine/valine porter (characterized)
to candidate 202770 SO_3675 hemin importer ATP-binding subunit (RefSeq)

Query= TCDB::P0A9S7
         (255 letters)



>FitnessBrowser__MR1:202770
          Length = 272

 Score =  100 bits (249), Expect = 3e-26
 Identities = 74/250 (29%), Positives = 122/250 (48%), Gaps = 24/250 (9%)

Query: 6   LSVNGLMMRFGGLLAVNNVNLELYPQEIVSLIGPNGAGKTTVFNCLTGFYKPTGGTILLR 65
           L+V+ L    G    +NN+ ++  P  + +L+GPNGAGK+T+   L        G+I L 
Sbjct: 20  LTVDRLSYAIGDKAVLNNIRVQFQPGSVTALLGPNGAGKSTLLKALCQEIPSAQGSIKLG 79

Query: 66  DQHLEGLPGQQIARMGVVRTFQHVRLFREMTVIENLLVAQHQQLKTGLFSGLLKTPSFRR 125
              L   P  ++A+   V   QH  L    TV E + +        GL+   L       
Sbjct: 80  HCQLVDWPRAELAKSLAVLP-QHASLTFPFTVDEVVAM--------GLYPLTL------- 123

Query: 126 AQSEALDRAATWLERIGLLEHANRQASNLAYGDQRRLEIARCMVTQ------PEILMLDE 179
           +Q E       WL  +G+L  A R    L+ G+++R+++AR ++TQ      P IL+LDE
Sbjct: 124 SQKEGQQLVTKWLAEVGVLHLARRSYPTLSGGEKQRVQLAR-VLTQLSQSPFPPILLLDE 182

Query: 180 PAAGLNPKETKELDELIAELRNHHNTTILLIEHDMKLVMGISDRIYVVNQGTPLANGTPE 239
           P + L+  +  ++  L   L + H  T++++ HD+      SDR+ V+ QG  ++ GTP 
Sbjct: 183 PTSALDLAQQHKVLALAKNLAHKHAYTVIVVLHDLNQAARYSDRVIVLKQGEIVSEGTPN 242

Query: 240 QIRNNPDVIR 249
               + D+IR
Sbjct: 243 DAL-SIDIIR 251


Lambda     K      H
   0.320    0.137    0.395 

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: 159
Number of extensions: 8
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: 255
Length of database: 272
Length adjustment: 25
Effective length of query: 230
Effective length of database: 247
Effective search space:    56810
Effective search space used:    56810
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