GapMind for catabolism of small carbon sources

 

Alignments for a candidate for HSERO_RS17005 in Sinorhizobium fredii NGR234

Align ABC-type sugar transport system, permease component protein (characterized, see rationale)
to candidate WP_015888140.1 NGR_RS09950 sugar ABC transporter permease

Query= uniprot:D8IPH8
         (292 letters)



>NCBI__GCF_000018545.1:WP_015888140.1
          Length = 307

 Score =  155 bits (391), Expect = 1e-42
 Identities = 85/281 (30%), Positives = 163/281 (58%), Gaps = 6/281 (2%)

Query: 9   LPYLFLGPSLLVMLVLGLVPTVAAINLALKNRVLRYPDS--DYVWLRNLERLMSDRRFLN 66
           L YL L P++L++L L + P++     A+ +R+   PD   ++V + N  RL+SD +F  
Sbjct: 27  LRYLMLAPTVLILLALTIFPSIYMFYAAV-HRISPNPDLPWEFVGVGNFARLLSDPQFHV 85

Query: 67  AIEVSAVWEVVTVLGAVIVGIAIAVYLFENVHGKWRQAMCVLLITPVLLPRVSAAFIWKF 126
           A+  + V+ +V V    ++G+ +A+ L   +  +    +  +L+ P++LP ++ A  WK 
Sbjct: 86  ALRNTVVFTLVAVALEFLLGLGLALLLDRFI--RRLSFLKTVLMIPMMLPPIAVAITWKL 143

Query: 127 MYSPLTGILGWLLGLVGIHDTAFLSDPALALYAVALVDIWQWGLFFAVIVLKLLETLPPE 186
           +Y P  G+L  ++ L+G+   A+  D  LA++++ + D+WQW  F  +++L  L +LP E
Sbjct: 144 IYEPQFGVLNEIMFLLGLPVQAWAGDVNLAMFSIIVADVWQWTPFVFLLMLAGLASLPVE 203

Query: 187 PLEAARLDYARTWQVYAYIALPMLKGPLISLVFIKMVESLRSFDLIYVMTKGGPGVATET 246
           P EAA LD A +W+ +  + LP LK  +   + ++++++LR FDL++++T GGP   T+ 
Sbjct: 204 PYEAAALDGASSWRQFWDLTLPFLKPVIAIALLLRVMDALRLFDLVFILTGGGPADRTKV 263

Query: 247 LDMYAYAQGIGLSGKVSYASTMAVLMMIATTLIFTLIWKRV 287
           L +Y Y      +    YA+ +++ ++  T ++ T   KR+
Sbjct: 264 LSLYIYQVAYRFADP-GYAAAISLFVLFVTIVLSTWFMKRM 303


Lambda     K      H
   0.328    0.141    0.439 

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: 269
Number of extensions: 10
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: 292
Length of database: 307
Length adjustment: 27
Effective length of query: 265
Effective length of database: 280
Effective search space:    74200
Effective search space used:    74200
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.7 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