GapMind for catabolism of small carbon sources

 

Alignments for a candidate for msdB1 in Sinorhizobium fredii NGR234

Align Binding-protein-dependent transport systems inner membrane component (characterized, see rationale)
to candidate WP_015888140.1 NGR_RS09950 sugar ABC transporter permease

Query= uniprot:A3DE72
         (327 letters)



>NCBI__GCF_000018545.1:WP_015888140.1
          Length = 307

 Score =  149 bits (375), Expect = 1e-40
 Identities = 87/287 (30%), Positives = 162/287 (56%), Gaps = 17/287 (5%)

Query: 32  YAMLIPTFVCMMCIHFIPMLQGIYLSLLDLNQLTMTKFLNAPFIGLKNYYEILFDEKSLI 91
           Y ML PT + ++ +   P    IY+    +++++    L   F+G+ N+  +L D +   
Sbjct: 29  YLMLAPTVLILLALTIFP---SIYMFYAAVHRISPNPDLPWEFVGVGNFARLLSDPQ--- 82

Query: 92  RRGFWFALRNTAIYTVVVTFATFALGIILAMLVNREFKGRGIVRTALLMPWVVPSYVVGM 151
              F  ALRNT ++T+V     F LG+ LA+L++R  +    ++T L++P ++P   V +
Sbjct: 83  ---FHVALRNTVVFTLVAVALEFLLGLGLALLLDRFIRRLSFLKTVLMIPMMLPPIAVAI 139

Query: 152 TWGFLWRQDSGLINIILCDILHILPEKPYWLVGSNQIWAIIIPTIWRGLPLSMILMLAGL 211
           TW  ++    G++N I+   L  LP + +    +  +++II+  +W+  P   +LMLAGL
Sbjct: 140 TWKLIYEPQFGVLNEIM--FLLGLPVQAWAGDVNLAMFSIIVADVWQWTPFVFLLMLAGL 197

Query: 212 QSISPDYYEAADIDGANGWQKFWHITLPLLKPILAINVMFSLISNIYSFNIVSMMFGNGA 271
            S+  + YEAA +DGA+ W++FW +TLP LKP++AI ++  ++  +  F++V ++ G G 
Sbjct: 198 ASLPVEPYEAAALDGASSWRQFWDLTLPFLKPVIAIALLLRVMDALRLFDLVFILTGGG- 256

Query: 272 GIPGEWGDLLMTYIQRNTFQMWRFGPG-AAALMIVMFFVLGIVALWY 317
             P +   +L  YI +  ++     PG AAA+ + + FV  +++ W+
Sbjct: 257 --PADRTKVLSLYIYQVAYRF--ADPGYAAAISLFVLFVTIVLSTWF 299


Lambda     K      H
   0.330    0.145    0.468 

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: 292
Number of extensions: 17
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: 327
Length of database: 307
Length adjustment: 27
Effective length of query: 300
Effective length of database: 280
Effective search space:    84000
Effective search space used:    84000
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 (21.8 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