GapMind for catabolism of small carbon sources

 

Alignments for a candidate for livF in Echinicola vietnamensis KMM 6221, DSM 17526

Align High-affinity branched-chain amino acid transport ATP-binding protein (characterized, see rationale)
to candidate Echvi_1333 Echvi_1333 ABC-type (unclassified) transport system, ATPase component

Query= uniprot:A0A159ZWL6
         (233 letters)



>FitnessBrowser__Cola:Echvi_1333
          Length = 243

 Score =  139 bits (349), Expect = 6e-38
 Identities = 81/234 (34%), Positives = 132/234 (56%), Gaps = 3/234 (1%)

Query: 1   MLQFENVSTFYGKIQALHSVNVEVRQGEIVTLIGANGAGKSTLLMTLCGSPQAHSGSIRY 60
           +L+ EN+   Y   + +++++VEV QGEIV L+G NGAGK+T    + G  + +SG +  
Sbjct: 2   ILRGENLIKIYKGRKVVNNISVEVEQGEIVGLLGPNGAGKTTSFYMIVGLIKPNSGKVFL 61

Query: 61  MGEELVGQDSSHIMRKSIAVVPEGRRVFARLTVEENLAMGGFFTD--KGDYQEQMDKVLH 118
             EE+         +  I  + +   VF +L+VEEN+      T+  K   +E+M+++L 
Sbjct: 62  DKEEITPLPMYRRAKLGIGYLAQEASVFRKLSVEENIMAVLEMTNLPKAAQKEKMEELLE 121

Query: 119 LFPRLKERFTQRGGTMSGGEQQMLAIGRALMSKPKLLLLDEPSLGLAPIIIQQIFDIIEQ 178
            F     R    G  +SGGE++   I RAL   PK +LLDEP  G+ PI +++I  I+ +
Sbjct: 122 EFSLTHVR-KNLGMVLSGGERRRTEIARALAVDPKFVLLDEPFAGVDPIAVEEIQTIVAK 180

Query: 179 LRKDGVTVFLVEQNANQALKIADRAYVLENGRVVMQGTGEALLTDPKVREAYLG 232
           L+   + + + + N N+ L I DRAY++  G+++  GT E L  D +VR+ YLG
Sbjct: 181 LKNKNIGILITDHNVNETLSITDRAYLMFEGKLLKAGTAEELAADEQVRKVYLG 234


Lambda     K      H
   0.320    0.137    0.381 

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: 152
Number of extensions: 6
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: 243
Length adjustment: 23
Effective length of query: 210
Effective length of database: 220
Effective search space:    46200
Effective search space used:    46200
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: 46 (22.3 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