GapMind for catabolism of small carbon sources

 

Alignments for a candidate for aglG' in Sinorhizobium meliloti 1021

Align Inner membrane ABC transporter permease protein (characterized, see rationale)
to candidate SM_b20632 SM_b20632 sugar uptake ABC transporter permease

Query= uniprot:A8LLL4
         (385 letters)



>FitnessBrowser__Smeli:SM_b20632
          Length = 287

 Score =  127 bits (319), Expect = 4e-34
 Identities = 65/213 (30%), Positives = 110/213 (51%)

Query: 173 GMARAFFNTLTVTIPATIIPILVAAFAAYALAWMEFPGRALLIALIVGLLVVPLQLALIP 232
           G+ +  FN+L V+I   ++ + V+  A Y  +   FP +  L  LI+  L++P Q  L P
Sbjct: 75  GIWQHMFNSLIVSIGTVVLTVAVSVLAGYGFSRYRFPFKNALFVLIIATLMIPFQSILTP 134

Query: 233 LLTLHNAIGIGKGYLGTWLAHTGFGMPLAIYLLRNYMVGLPRDIIENAKVDGATDFQIFT 292
           L  +    G+    +G  L +    +P +++++RN    +P++I E A++DGA D ++  
Sbjct: 135 LFIILARFGLNNSLVGLMLVYVTLQLPFSVFMMRNAFDAVPKEIEEAARIDGARDLKLLV 194

Query: 293 KIVLPLSFPALASFAIFQFLWTWNDLLVAKVFLIDATGQTTVMTNQIVELLGTRGGNWEI 352
           +++LPL  P +A+ +IF FL  WN+   A V L      T  +    V        NW  
Sbjct: 195 RVLLPLVMPGIATVSIFAFLNAWNEFFAALVLLSSNDNYTLPVLMTAVRAGRLGAINWGA 254

Query: 353 LATAAFVSIAVPLLVFFSMQRFLVRGLLAGSVK 385
           +     V +   L VF  +QR+ +RGL+AG+VK
Sbjct: 255 VQAGVAVMVVPCLFVFLLLQRYYMRGLMAGAVK 287


Lambda     K      H
   0.323    0.138    0.419 

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: 245
Number of extensions: 8
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: 385
Length of database: 287
Length adjustment: 28
Effective length of query: 357
Effective length of database: 259
Effective search space:    92463
Effective search space used:    92463
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.5 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (22.0 bits)
S2: 49 (23.5 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