GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gtsC in Caldicellulosiruptor hydrothermalis 108

Align ABC transporter for D-Galactose and D-Glucose, permease component 2 (characterized)
to candidate WP_013402055.1 CALHY_RS00400 carbohydrate ABC transporter permease

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



>NCBI__GCF_000166355.1:WP_013402055.1
          Length = 281

 Score =  118 bits (295), Expect = 2e-31
 Identities = 82/277 (29%), Positives = 144/277 (51%), Gaps = 10/277 (3%)

Query: 11  SFSRIAIYATLLLAAAVYLIPLVVMLLTSFKSPEDIRTGNLLSWPTVIDGIGWIKA---- 66
           SF+ +  Y  L+L A   ++PL+ +L  SFK   +I   N +  P+ +    + +     
Sbjct: 9   SFADVIKYLILVLWACTTILPLLWVLNNSFKESNEILL-NPMKLPSKLSFFNYSQLISYG 67

Query: 67  -WDVVGGYFWNSVKITVPAVLISTFIGAMNGYVLSMWRFRGSQLFFGLLLFGCFLPFQTV 125
             ++  G F NS+ I+   VL+    G    YV++ + F+ + +          +P  ++
Sbjct: 68  NMNIFRG-FLNSLIISGSVVLLVLLFGGFAAYVIARFDFKLTGIVKIFFTGAMLVPAFSI 126

Query: 126 LLPASFTLGKFGLANTTTGLVLVHVVYGLAFTTLFFRNYYVSIPDALVKAARLDGAGFFT 185
           ++P+   L K GL  +   L+L      L F TL    +  ++P  L +AA +DGAG   
Sbjct: 127 VIPSLVILRKLGLNGSYLALILPQTAGLLPFATLTLAGFMKTLPVELEEAAIIDGAGVLR 186

Query: 186 IFLKILLPMSIPIVMVCLIWQFTQIWNDFLFGVVFAS-GDAQPITVALNNLVNTSTGAKE 244
           IF +I++P+SIP ++   I+ F   +ND    ++F    + QPI V L +LV++  G   
Sbjct: 187 IFFRIIVPLSIPGLVTAAIFVFLWSYNDLFMSLIFIPIREKQPICVLL-SLVSSIYGT-N 244

Query: 245 YNVDMAAAMIAGLPTLLVYIFAGKYFLRGLTSGAVKG 281
           Y   MAA +I  LP +++Y+F  +Y ++G+T+GA+KG
Sbjct: 245 YGAMMAALIITVLPVIILYVFLQEYVIKGMTAGAIKG 281


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: 228
Number of extensions: 18
Number of successful extensions: 5
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: 281
Length adjustment: 26
Effective length of query: 255
Effective length of database: 255
Effective search space:    65025
Effective search space used:    65025
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.

Links

Downloads

Related tools

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