GapMind for catabolism of small carbon sources

 

Alignments for a candidate for hisM in Desulfovibrio vulgaris Miyazaki F

Align ABC transporter for L-Lysine, permease component 2 (characterized)
to candidate 8500827 DvMF_1568 polar amino acid ABC transporter, inner membrane subunit (RefSeq)

Query= reanno::pseudo5_N2C3_1:AO356_09910
         (229 letters)



>FitnessBrowser__Miya:8500827
          Length = 224

 Score =  128 bits (321), Expect = 1e-34
 Identities = 70/196 (35%), Positives = 116/196 (59%), Gaps = 9/196 (4%)

Query: 11  PKLAQGATLTLELVAIAVIAGLLLAIPLGIARSSRLWQVRALPYAYIFFFRGTPLLVQLF 70
           P L  G  ++++L+  + + GLL  + +GI R      ++ +  AY   FRG PLLVQLF
Sbjct: 13  PSLNAGLWMSVKLIVPSAVFGLLFGVIIGIVRVFGKPWMQRIANAYTALFRGVPLLVQLF 72

Query: 71  LVYYGLAQFDAVRSSALWPYLRDPFWCATVTMTLHTAAYIAEILRGAIQAIPKGEIEAAR 130
           ++Y+GL             YL +P+  + +   L +AAY +E +RGA+ +I +G++ AA+
Sbjct: 73  ILYFGLPNIGI--------YL-EPYAASVLGFILCSAAYNSEYVRGALLSIRQGQLRAAQ 123

Query: 131 ALGMSRPKALFYIMLPRAARIGLPAYSNEVILMLKASALASTVTLLELTGMARTIIARTY 190
           ALG S  + L  I++P+A R  LP   NE++ ++K S+LA  +T +ELTG A+ + +RT+
Sbjct: 124 ALGFSTMQTLVSIVVPQAVRRALPGCGNEIVYLIKYSSLAYVITCIELTGEAKVLASRTF 183

Query: 191 LPVEIFFAAGMFYLLM 206
              E+F   G +YL +
Sbjct: 184 RFTEVFLVVGAYYLFL 199


Lambda     K      H
   0.331    0.141    0.434 

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: 144
Number of extensions: 2
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: 229
Length of database: 224
Length adjustment: 22
Effective length of query: 207
Effective length of database: 202
Effective search space:    41814
Effective search space used:    41814
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.9 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