GapMind for catabolism of small carbon sources

 

Alignments for a candidate for aglG' in Phaeobacter inhibens BS107

Align Inner membrane ABC transporter permease protein (characterized, see rationale)
to candidate GFF3854 PGA1_78p00180 putative sn-glycerol-3-phosphate transport system permease protein UgpE

Query= uniprot:A8LLL4
         (385 letters)



>FitnessBrowser__Phaeo:GFF3854
          Length = 309

 Score =  117 bits (294), Expect = 3e-31
 Identities = 66/217 (30%), Positives = 112/217 (51%), Gaps = 3/217 (1%)

Query: 170 NSEGMARAFFNTLTVTIPATIIPILVAAFAAYALAWMEFPGRALLIALIVGLLVVPLQLA 229
           N +G++R F N++ + +P+  + I +A+   YALA   F G      +++    +P Q  
Sbjct: 94  NCDGLSRGFGNSIKILVPSVALSIAIASVNGYALANWRFKGSETFFTILIIGAFIPYQTM 153

Query: 230 LIPLLTLHNAIGIGKGYLGTWLAHTGFGMPLAIYLLRNYMVGLPRDIIENAKVDGATDFQ 289
           L P++ +   + +     G  L H+ FGMP+   L RNY   LP ++ + A+VDGA  + 
Sbjct: 154 LYPIVIILRELKLMGSLWGLVLVHSIFGMPILTLLFRNYFSSLPEELFKAARVDGAGFWG 213

Query: 290 IFTKIVLPLSFPALASFAIFQFLWTWNDLLVAKVFLIDATGQTTVMTNQIV-ELLGTRGG 348
           I+ ++++P+S P      I Q    WND L   ++    T   TV  N IV  + G +  
Sbjct: 214 IYLRVMVPMSIPIFVVAMILQVTGIWNDFLFGVIYTKPETYPMTVQLNNIVNSVQGVKEY 273

Query: 349 NWEILATAAFVSIAVPLLVFFSMQRFLVRGLLAGSVK 385
           N  + AT   ++  VPL+++    +  VRG+ AG+VK
Sbjct: 274 NVNMAAT--LLTGLVPLVIYLVSGKLFVRGIAAGAVK 308


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: 278
Number of extensions: 9
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: 309
Length adjustment: 29
Effective length of query: 356
Effective length of database: 280
Effective search space:    99680
Effective search space used:    99680
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