GapMind for catabolism of small carbon sources

 

Alignments for a candidate for thuG in Phyllobacterium leguminum ORS 1419

Align ABC-type transporter, integral membrane subunit, component of Trehalose porter. Also binds sucrose (Boucher and Noll, 2011). Induced by glucose and trehalose. Directly regulated by trehalose-responsive regulator TreR (characterized)
to candidate WP_110753066.1 C7477_RS13715 carbohydrate ABC transporter permease

Query= TCDB::G4FGN6
         (278 letters)



>NCBI__GCF_003217235.1:WP_110753066.1
          Length = 274

 Score =  179 bits (454), Expect = 6e-50
 Identities = 101/276 (36%), Positives = 163/276 (59%), Gaps = 6/276 (2%)

Query: 3   RSITQRILLYIAVVLILIWCVFPLYWAFISSIKPDRDLFEKNPSLFPKRITFENYVKVFK 62
           +SI  ++   + V +I+   +F   W    S+K + D     P L P+R  + NY ++F 
Sbjct: 4   KSILSKLGTALLVFVIVSPAIFFFVWMLSLSLKYEIDNGAYPPILIPERFAWSNYTQIFA 63

Query: 63  ERPFHINIKNSIIVAGITTVLALVVGSLAGYAIARLKFRGKVIVMSLILAVSMFPQVSIL 122
           E  F +   NS++V G+ T+LAL+VG  AGY IARLK     +V   I+   M P +S L
Sbjct: 64  ENDFLLYFWNSLLVTGMATLLALLVGVPAGYGIARLKAHKSAVV---IMIARMTPGLSYL 120

Query: 123 GSLFLILRGLKLINTYTGLIIPYTAMNLPLTVWVLQSFFRELPKEVEESAFIDGASKLRT 182
             LFL+ + L L+ T    II +  + +P+ +W++  +F   P E+EE+A IDGA+  + 
Sbjct: 121 IPLFLLFQTLGLLGTLWPQIIIHLVVTVPIVIWIMIGYFEATPMELEEAAQIDGANAWQV 180

Query: 183 LWSIVLPMSAPGLVATGLLTFIAAWNEFLFALTFMQKPSLYTVPVAVALFKGASQYEIPW 242
              + LP++ PG+V + +L  I +WN F+F +    + +  T+PVAV  +   S  ++ W
Sbjct: 181 FRLVALPIAKPGIVVSLILAVIFSWNNFVFGIVLASRET-RTLPVAV--YNMLSFEQVSW 237

Query: 243 GQLMAAAVIVTLPLVILVLVFQNRIIAGLSAGAVKG 278
           G L AAA++VTLP+++L ++ Q +I+AGL+AGAVKG
Sbjct: 238 GPLAAAALVVTLPVLLLTVLAQRQIVAGLTAGAVKG 273


Lambda     K      H
   0.329    0.142    0.424 

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: 213
Number of extensions: 12
Number of successful extensions: 3
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: 278
Length of database: 274
Length adjustment: 25
Effective length of query: 253
Effective length of database: 249
Effective search space:    62997
Effective search space used:    62997
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: 47 (22.7 bits)

This GapMind analysis is from Sep 24 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