GapMind for catabolism of small carbon sources

 

Alignments for a candidate for livG in Crocosphaera subtropica ATCC 51142

Align High-affinity branched-chain amino acid transport ATP-binding protein LivG aka B3455, component of Leucine; leucine/isoleucine/valine porter (characterized)
to candidate WP_009545830.1 CCE_RS09615 LPS export ABC transporter ATP-binding protein

Query= TCDB::P0A9S7
         (255 letters)



>NCBI__GCF_000017845.1:WP_009545830.1
          Length = 238

 Score =  141 bits (356), Expect = 1e-38
 Identities = 90/251 (35%), Positives = 137/251 (54%), Gaps = 19/251 (7%)

Query: 6   LSVNGLMMRFGGLLAVNNVNLELYPQEIVSLIGPNGAGKTTVFNCLTGFYKPTGGTILLR 65
           L +  +   +G    VN VNL++ P EIV L+GPNGAGKTT F   TG  KP  G + L 
Sbjct: 3   LILENIHKTYGKRDIVNRVNLKVAPGEIVGLLGPNGAGKTTTFYIATGLIKPNKGRVWLN 62

Query: 66  DQHLEGLPGQQIARMGVVRTFQHVRLFREMTVIENLLVAQHQQLKTGLFSGLLKTPSFRR 125
            Q +  LP  + AR+G+    Q   +FR ++V EN+ VA  Q             P  +R
Sbjct: 63  QQEVTRLPLNKRARLGIGYMTQQPSIFRHLSVAENIQVALEQ----------TNVPFRQR 112

Query: 126 AQSEALDRAATWLERIGLLEHANRQASNLAYGDQRRLEIARCMVT---QPEILMLDEPAA 182
            Q     R  T L+   L + A+ + S ++ G++RR E+AR +      P+ L+LDEP A
Sbjct: 113 PQ-----RLHTLLKEFRLEKIAHTKGSQVSGGERRRTELARSLAVGQQGPDFLLLDEPFA 167

Query: 183 GLNPKETKELDELIAELRNHHNTTILLIEHDMKLVMGISDRIYVVNQGTPLANGTPEQIR 242
           G++P    E+  +IA+L +     IL+ +H+++  + I++R Y++  G  LA G+ E+I 
Sbjct: 168 GVDPIAVSEIQTMIAQLCD-RQMGILITDHNVQATLAITNRAYIMRDGQILAAGSAEEIY 226

Query: 243 NNPDVIRAYLG 253
           NNP V + YLG
Sbjct: 227 NNPLVRQYYLG 237


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: 10
Number of successful extensions: 4
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: 238
Length adjustment: 24
Effective length of query: 231
Effective length of database: 214
Effective search space:    49434
Effective search space used:    49434
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