GapMind for catabolism of small carbon sources

 

Alignments for a candidate for HSERO_RS00890 in Sinorhizobium meliloti 1021

Align ABC-type branched-chain amino acid transport system, permease component protein (characterized, see rationale)
to candidate SMa0217 SMa0217 ABC transporter permease

Query= uniprot:D8IUY5
         (404 letters)



>FitnessBrowser__Smeli:SMa0217
          Length = 359

 Score = 63.9 bits (154), Expect = 7e-15
 Identities = 67/220 (30%), Positives = 95/220 (43%), Gaps = 30/220 (13%)

Query: 123 LSLWLIVPISAFLAALFGALLGAPTLKLRGDYLAIVTLGFGEIIRIFMNNLNAPVNITNG 182
           LS ++  PI+     L G+L G  TL+  G    IVTLG     R  +   N  V +   
Sbjct: 131 LSAFIAAPIAILTGLLIGSLNGHITLRF-GLPSFIVTLGGLLFWRGAVLLYNGAVQVR-- 187

Query: 183 PQGINLIDPIKVFGVSLAGEPGSGSMVKVFGMSMPSVNAYYFLFLLLCIGVIFFSVRLQD 242
                  DP  VF               +F  ++  VNA +   +L   G   F + L  
Sbjct: 188 ------FDPEPVF-------------TSLFSGTLFGVNAAFIWIVLFVTG---FHLLLHR 225

Query: 243 SRLGRAWVAIREDEIAAKAMGINTRNVKLLAFAMGASFGGVAGAMFGAFQGFVSPESFSL 302
            R G    A   +  AA+A+GINT  VKL+AFA+      VAG +  A  G V P   + 
Sbjct: 226 HRFGNHVFATGGNRGAAEAIGINTSRVKLIAFAIAGGMAAVAGILATARVGSVQPGQGAG 285

Query: 303 TESIAVLAMVV-----LGGIGHIPGVVLGGVILAALPEVL 337
            E  A+ A V+      GG G I G+ LG +++  + +VL
Sbjct: 286 LELQAIAACVIGGLSLRGGRGSIIGIFLGVLLIHTITDVL 325


Lambda     K      H
   0.327    0.143    0.430 

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: 344
Number of extensions: 17
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: 404
Length of database: 359
Length adjustment: 30
Effective length of query: 374
Effective length of database: 329
Effective search space:   123046
Effective search space used:   123046
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: 50 (23.9 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