GapMind for catabolism of small carbon sources

 

Alignments for a candidate for glpP in Sinorhizobium fredii NGR234

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

Query= reanno::acidovorax_3H11:Ac3H11_793
         (298 letters)



>NCBI__GCF_000018545.1:WP_015888140.1
          Length = 307

 Score =  145 bits (365), Expect = 1e-39
 Identities = 87/268 (32%), Positives = 146/268 (54%), Gaps = 5/268 (1%)

Query: 13  WFLILPVIICVAFSAILPLMTVVNYSVQDIISPERRV---FVGTEWFAAVMRDEELHAAL 69
           + ++ P ++ +    I P + +  Y+    ISP   +   FVG   FA ++ D + H AL
Sbjct: 29  YLMLAPTVLILLALTIFPSIYMF-YAAVHRISPNPDLPWEFVGVGNFARLLSDPQFHVAL 87

Query: 70  WRQLTFSLAVLAVEIPLGILLALSMPAQGWKSSAVLVVVALSLLIPWNVVGTIWQIYGRA 129
              + F+L  +A+E  LG+ LAL +     + S +  V+ + +++P   V   W++    
Sbjct: 88  RNTVVFTLVAVALEFLLGLGLALLLDRFIRRLSFLKTVLMIPMMLPPIAVAITWKLIYEP 147

Query: 130 DIGLMGRMLQEMGIEY-SYTGNATQAWLTVLLMDVWHWTPLVALLAFAGLRSIPDAYYQA 188
             G++  ++  +G+   ++ G+   A  ++++ DVW WTP V LL  AGL S+P   Y+A
Sbjct: 148 QFGVLNEIMFLLGLPVQAWAGDVNLAMFSIIVADVWQWTPFVFLLMLAGLASLPVEPYEA 207

Query: 189 ARIDGASKFAVFRYIQLPKMRGVLMIAVLLRFMDSFMIYTEPFVLTGGGPGNATTFLSQY 248
           A +DGAS +  F  + LP ++ V+ IA+LLR MD+  ++   F+LTGGGP + T  LS Y
Sbjct: 208 AALDGASSWRQFWDLTLPFLKPVIAIALLLRVMDALRLFDLVFILTGGGPADRTKVLSLY 267

Query: 249 LTTKAVGQFDLGPAAAFSLIYFFIILLL 276
           +   A    D G AAA SL   F+ ++L
Sbjct: 268 IYQVAYRFADPGYAAAISLFVLFVTIVL 295


Lambda     K      H
   0.328    0.140    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: 241
Number of extensions: 13
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 ( 7.1 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.

Links

Downloads

Related tools

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