GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gtsC in Marinobacter adhaerens HP15

Align ABC transporter for D-Galactose and D-Glucose, permease component 2 (characterized)
to candidate GFF3012 HP15_2956 sugar ABC transporter, permease protein

Query= reanno::pseudo13_GW456_L13:PfGW456L13_1896
         (281 letters)



>FitnessBrowser__Marino:GFF3012
          Length = 289

 Score =  436 bits (1121), Expect = e-127
 Identities = 215/284 (75%), Positives = 243/284 (85%), Gaps = 9/284 (3%)

Query: 7   KSGISFSRIAIYATLLLAAAVYLIPLVVMLLTSFKSPEDIRTGNLLSWPTVIDGIGWIKA 66
           ++G   SR+AIY  LLLAA VYLIPL +ML+TSFK+P DIRTGNL++ PT    IGW KA
Sbjct: 6   RTGFRPSRVAIYGLLLLAALVYLIPLFIMLVTSFKTPMDIRTGNLMALPTDWTTIGWTKA 65

Query: 67  W---------DVVGGYFWNSVKITVPAVLISTFIGAMNGYVLSMWRFRGSQLFFGLLLFG 117
           W         + + GYFWNS K+TVPAVLIST +GA NGYVLS W+F+GS LFFG+LLFG
Sbjct: 66  WSEACTGVQCEGISGYFWNSFKMTVPAVLISTLLGAFNGYVLSKWKFKGSDLFFGMLLFG 125

Query: 118 CFLPFQTVLLPASFTLGKFGLANTTTGLVLVHVVYGLAFTTLFFRNYYVSIPDALVKAAR 177
           CF+PFQ VLLP + TLGK GLANTT+GLVLVHV+YG+AFTTLFFRNYYV+IPDAL+KAAR
Sbjct: 126 CFVPFQVVLLPMAATLGKLGLANTTSGLVLVHVIYGVAFTTLFFRNYYVAIPDALIKAAR 185

Query: 178 LDGAGFFTIFLKILLPMSIPIVMVCLIWQFTQIWNDFLFGVVFASGDAQPITVALNNLVN 237
           LDGAGFFTIF +ILLPMS PI MV LIWQFTQIWNDFLFGVVFASGD+QPITVALNNLVN
Sbjct: 186 LDGAGFFTIFFRILLPMSTPIFMVSLIWQFTQIWNDFLFGVVFASGDSQPITVALNNLVN 245

Query: 238 TSTGAKEYNVDMAAAMIAGLPTLLVYIFAGKYFLRGLTSGAVKG 281
           TSTG KEYNVDMAAAMIA LPTL+VYI AGKYF+RGLT+G+VKG
Sbjct: 246 TSTGVKEYNVDMAAAMIAALPTLVVYIVAGKYFIRGLTAGSVKG 289


Lambda     K      H
   0.329    0.143    0.447 

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: 333
Number of extensions: 7
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: 289
Length adjustment: 26
Effective length of query: 255
Effective length of database: 263
Effective search space:    67065
Effective search space used:    67065
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 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