GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gtsC in Phaeobacter inhibens BS107

Align ABC transporter for D-Glucose-6-Phosphate, permease component 1 (characterized)
to candidate GFF774 PGA1_c07880 alpha-glucoside transport system permease protein AglG

Query= reanno::WCS417:GFF4322
         (281 letters)



>FitnessBrowser__Phaeo:GFF774
          Length = 382

 Score =  117 bits (293), Expect = 4e-31
 Identities = 69/210 (32%), Positives = 109/210 (51%), Gaps = 5/210 (2%)

Query: 74  FWNSIKITVPAVLISTAIGALNGYVLSFWRFKGSQLFFGLLLFGCFLPFQTVLLPASFTL 133
           F+N++ +T+PA +I   + A   Y L++  F G  L    ++    +P Q  L+P     
Sbjct: 175 FFNTLTVTIPATIIPILVAAFAAYALAWMEFPGRALLVAAIVGLLVVPLQLALIPLLKFH 234

Query: 134 GKMGLASTTTGLVFVHVVYGLAFTTLFFRNYYVSIPDALIKAARLDGAGFFTIFRQIILP 193
            ++G+     G+   H  +GL       RNY V IP  +I+ AR+DGA  F IF +IILP
Sbjct: 235 NEIGIGKGYIGVWMAHTGFGLPLAIYLLRNYMVGIPRDIIENARVDGATDFLIFVRIILP 294

Query: 194 MSTPIIMVCLIWQFTQIWNDFLFGVVF---SSGDSQPITVALNNLVNTSTGAKEYNVDMA 250
           +S P +    I+QF   WND L  +VF   ++G++  +T  +  L+ T  G   + +   
Sbjct: 295 LSFPALASFAIFQFLWTWNDLLVAMVFLIDATGETTVMTKQIVELLGTRGG--NWEILAT 352

Query: 251 AAMIAGLPTLLVYVIAGKYFVRGLTAGAVK 280
           +A ++    L V+    KY VRGL AG+VK
Sbjct: 353 SAFVSIAVPLAVFFAMQKYLVRGLLAGSVK 382


Lambda     K      H
   0.328    0.141    0.435 

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: 264
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: 281
Length of database: 382
Length adjustment: 28
Effective length of query: 253
Effective length of database: 354
Effective search space:    89562
Effective search space used:    89562
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