GapMind for catabolism of small carbon sources

 

Alignments for a candidate for aglF in Sinorhizobium meliloti 1021

Align ABC transporter for D-Maltose and D-Trehalose, permease component 1 (characterized)
to candidate SMc01497 SMc01497 sorbitol/mannitol transport inner membrane transmembrane protein

Query= reanno::Smeli:SMc03062
         (336 letters)



>FitnessBrowser__Smeli:SMc01497
          Length = 290

 Score = 97.4 bits (241), Expect = 4e-25
 Identities = 85/275 (30%), Positives = 136/275 (49%), Gaps = 23/275 (8%)

Query: 57  LFLAPALLALTLYLVYPVVQSVWLSLHGR-----GGQNFVGLSNYSWMINDGEFRQSIFN 111
           L +AP++L L  +++ P+  +++ SL        G + F GL+NY++ + D  F Q+IFN
Sbjct: 12  LMIAPSVLLLLAWMIVPLAMTIYFSLLRYNLLMPGMEEFAGLTNYTYFLTDPAFFQAIFN 71

Query: 112 NFLWLLVVPALSTFFGLIIAALTDRIWWGN-IAKTLIFMPMAISFVGAAVIWKFIYDYRA 170
               +L V  ++   G+ +A L D+  +G  I + L+  P  I    AA++WK ++    
Sbjct: 72  TLAIVLGVLFITVVGGIGLALLLDQPMFGQGIVRILVIAPFLIMPTVAALVWKNMFM--- 128

Query: 171 AGSEQIGLLNAIVVALGGEPQAWITLPFWNNFFLMVILI--WIQTGFAMVILSAALRGIP 228
             +   GL   +   LG +P  ++     N   L +ILI  W    FA +IL  AL+ + 
Sbjct: 129 --NPVNGLFAWLAKLLGLQPFDFLA----NAPLLSIILIVAWQWLPFATLILLTALQSLD 182

Query: 229 EETIEAAVIDGANGWQIFFKIMVPQIWGTIAVVWTTITILVLKVFDIVLAMTNG--QWQS 286
           EE  EAA +DGA     F  +++P +   I +V    TI +L VF  +L  TNG    QS
Sbjct: 183 EEQKEAAQMDGAGAVSRFIYLVLPHLSRAITMVILIQTIFLLSVFAEILVTTNGGPGTQS 242

Query: 287 QVLANLMFD---WMFRGGGDFGRGAAIAVVIMILV 318
             L  L++      F  GG    G  IAV++  +V
Sbjct: 243 TNLTFLVYAQALLQFDVGG-ASAGGIIAVILANIV 276


Lambda     K      H
   0.330    0.142    0.466 

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: 274
Number of extensions: 15
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: 336
Length of database: 290
Length adjustment: 27
Effective length of query: 309
Effective length of database: 263
Effective search space:    81267
Effective search space used:    81267
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 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