GapMind for catabolism of small carbon sources

 

Alignments for a candidate for aglG' in Cupriavidus basilensis 4G11

Align Inner membrane ABC transporter permease protein (characterized, see rationale)
to candidate RR42_RS13775 RR42_RS13775 sugar ABC transporter permease

Query= uniprot:A8LLL4
         (385 letters)



>FitnessBrowser__Cup4G11:RR42_RS13775
          Length = 277

 Score =  111 bits (277), Expect = 3e-29
 Identities = 70/232 (30%), Positives = 119/232 (51%), Gaps = 7/232 (3%)

Query: 153 PPEFTFANYENMLLDPNNSEGMARAFFNTLTVTIPATIIPILVAAFAAYALAWMEFPGRA 212
           P +FT  +Y+ +  DP+   G    + N++      T+I I VA  AAYA +   F G  
Sbjct: 53  PNDFTLEHYKTIFTDPSWYSG----YINSMIYVAMNTVISITVALPAAYAFSRYRFIGDK 108

Query: 213 LLIALIVGLLVVPLQLALIPLLTLHNAIGIGKGYLGTWLAHTGFGMPLAIYLLRNYMVGL 272
            +   ++   + P  + L+P   L+  IG+   +LG  LAH  F +PLA+++L  +M G+
Sbjct: 109 HVFFWLLTNRMTPPAVFLLPFFQLYTTIGLMDTHLGVALAHLVFNVPLAVWILEGFMSGV 168

Query: 273 PRDIIENAKVDGATDFQIFTKIVLPLSFPALASFAIFQFLWTWNDLLVAKVFLIDATGQT 332
           PR+I E A VDG +  + F  I LPL    +   A F F+++W +LL+A+  L     + 
Sbjct: 169 PREIDETAYVDGYSFGRFFITIFLPLIKAGVGVAAFFCFMFSWVELLLART-LTSVNAKP 227

Query: 333 TVMTNQIVELLGTRGGNWEILATAAFVSIAVPLLVFFSMQRFLVRGLLAGSV 384
            V T  +   +   G +W +LA A  ++I    +V + ++ ++ +G   G V
Sbjct: 228 IVAT--MTRTVSASGMDWGVLAAAGVLTIVPGGIVIWFVRHYIAKGFAMGRV 277



 Score = 23.1 bits (48), Expect = 0.010
 Identities = 16/57 (28%), Positives = 29/57 (50%), Gaps = 1/57 (1%)

Query: 7  SKSSLTWAVQLSVVGLVVLWLLPTFGLFVSSFRTVEQI-SSSGWWKAMFPSEQNLTL 62
          +K S T+   + +V  +V  +LP + +   SF++ E+I S+   W   F  E   T+
Sbjct: 8  AKQSATYWRAVFLVVYLVFAILPIYWMLNMSFKSNEEIVSTLSLWPNDFTLEHYKTI 64


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: 283
Number of extensions: 20
Number of successful extensions: 3
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 2
Length of query: 385
Length of database: 277
Length adjustment: 28
Effective length of query: 357
Effective length of database: 249
Effective search space:    88893
Effective search space used:    88893
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: 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