GapMind for catabolism of small carbon sources

 

Alignments for a candidate for SM_b21104 in Sinorhizobium fredii NGR234

Align ABC transporter for L-Fucose, permease component 1 (characterized)
to candidate WP_015888140.1 NGR_RS09950 sugar ABC transporter permease

Query= reanno::Smeli:SM_b21104
         (298 letters)



>NCBI__GCF_000018545.1:WP_015888140.1
          Length = 307

 Score =  188 bits (478), Expect = 1e-52
 Identities = 103/280 (36%), Positives = 161/280 (57%), Gaps = 3/280 (1%)

Query: 11  LLLLPAFIVLAVFIVLPLIFSLYSSFTPFRLTKPDSLWVFIGFRNYVNVLTNAEFWVAFG 70
           L+L P  ++L    + P I+  Y++        PD  W F+G  N+  +L++ +F VA  
Sbjct: 30  LMLAPTVLILLALTIFPSIYMFYAAVHRIS-PNPDLPWEFVGVGNFARLLSDPQFHVALR 88

Query: 71  RTVLLLTVALNAEMFLGLGLALLVNKATYGQRALRTAMMFPMMFSPVLVGFQFKFLFNDN 130
            TV+   VA+  E  LGLGLALL+++       L+T +M PMM  P+ V   +K ++   
Sbjct: 89  NTVVFTLVAVALEFLLGLGLALLLDRFIRRLSFLKTVLMIPMMLPPIAVAITWKLIYEPQ 148

Query: 131 IGFVNNALQSLGLTDRAIPWLIDGNLALFSIIVAEVWSSTAVFAILILAGLLAMPKDPVE 190
            G +N  +  LGL  +A  W  D NLA+FSIIVA+VW  T    +L+LAGL ++P +P E
Sbjct: 149 FGVLNEIMFLLGLPVQA--WAGDVNLAMFSIIVADVWQWTPFVFLLMLAGLASLPVEPYE 206

Query: 191 AAHVDGCTPWQTFRYVTWPYLMPFAFIAMTIRSLDVARAYDIVKIMTDGGPAKRTELLWT 250
           AA +DG + W+ F  +T P+L P   IA+ +R +D  R +D+V I+T GGPA RT++L  
Sbjct: 207 AAALDGASSWRQFWDLTLPFLKPVIAIALLLRVMDALRLFDLVFILTGGGPADRTKVLSL 266

Query: 251 LIGRTAYGDARMGMANAMAYVAILLSIFFTVYFFRKLAAA 290
            I + AY  A  G A A++   + ++I  + +F +++  A
Sbjct: 267 YIYQVAYRFADPGYAAAISLFVLFVTIVLSTWFMKRMRLA 306


Lambda     K      H
   0.331    0.142    0.441 

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: 248
Number of extensions: 12
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: 298
Length of database: 307
Length adjustment: 27
Effective length of query: 271
Effective length of database: 280
Effective search space:    75880
Effective search space used:    75880
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: 48 (23.1 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