GapMind for catabolism of small carbon sources

 

Alignments for a candidate for livF in Crocosphaera subtropica ATCC 51142

Align High-affinity branched-chain amino acid transport ATP-binding protein (characterized, see rationale)
to candidate WP_009545830.1 CCE_RS09615 LPS export ABC transporter ATP-binding protein

Query= uniprot:A0A159ZWL6
         (233 letters)



>NCBI__GCF_000017845.1:WP_009545830.1
          Length = 238

 Score =  113 bits (283), Expect = 3e-30
 Identities = 73/236 (30%), Positives = 124/236 (52%), Gaps = 6/236 (2%)

Query: 2   LQFENVSTFYGKIQALHSVNVEVRQGEIVTLIGANGAGKSTLLMTLCGSPQAHSGSIRYM 61
           L  EN+   YGK   ++ VN++V  GEIV L+G NGAGK+T      G  + + G +   
Sbjct: 3   LILENIHKTYGKRDIVNRVNLKVAPGEIVGLLGPNGAGKTTTFYIATGLIKPNKGRVWLN 62

Query: 62  GEELVGQDSSHIMRKSIAVVPEGRRVFARLTVEENLAMGGFFTDKGDYQ--EQMDKVLHL 119
            +E+     +   R  I  + +   +F  L+V EN+ +    T+    Q  +++  +L  
Sbjct: 63  QQEVTRLPLNKRARLGIGYMTQQPSIFRHLSVAENIQVALEQTNVPFRQRPQRLHTLLKE 122

Query: 120 FPRLKERFTQRGGTMSGGEQQMLAIGRAL---MSKPKLLLLDEPSLGLAPIIIQQIFDII 176
           F RL++    +G  +SGGE++   + R+L      P  LLLDEP  G+ PI + +I  +I
Sbjct: 123 F-RLEKIAHTKGSQVSGGERRRTELARSLAVGQQGPDFLLLDEPFAGVDPIAVSEIQTMI 181

Query: 177 EQLRKDGVTVFLVEQNANQALKIADRAYVLENGRVVMQGTGEALLTDPKVREAYLG 232
            QL    + + + + N    L I +RAY++ +G+++  G+ E +  +P VR+ YLG
Sbjct: 182 AQLCDRQMGILITDHNVQATLAITNRAYIMRDGQILAAGSAEEIYNNPLVRQYYLG 237


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: 132
Number of extensions: 7
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: 233
Length of database: 238
Length adjustment: 23
Effective length of query: 210
Effective length of database: 215
Effective search space:    45150
Effective search space used:    45150
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 Apr 09 2024. 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