GapMind for catabolism of small carbon sources

 

Alignments for a candidate for glpP in Halopiger salifodinae KCY07-B2

Align GlpP, component of Glycerol uptake porter, GlpSTPQV (characterized)
to candidate WP_049988752.1 LT39_RS01710 sugar ABC transporter permease

Query= TCDB::G3LHZ0
         (288 letters)



>NCBI__GCF_000784335.1:WP_049988752.1
          Length = 312

 Score =  147 bits (371), Expect = 3e-40
 Identities = 93/275 (33%), Positives = 151/275 (54%), Gaps = 12/275 (4%)

Query: 12  LVLPVLLLVAFSAVIPLMTVVNYSVQDT--FGNNEFFWAGTDWFVQTLHSDRFWESLQRN 69
           L+ P +L++   +++PL+ ++  S  +      +E  + G + + Q + +     S +  
Sbjct: 32  LLAPSVLVLGILSIVPLIALLWLSAMEVNFLPGHEPTFVGLENY-QAMFNSTVANSWKVT 90

Query: 70  LLFSFIILALEIPLGIFIALNMPKSGPGVPVCLVLMALPLLIPWNVVGTIWQVFGRVDIG 129
           + +    L+L+I LG  IAL + +   G  V   ++ +P++I   VVG +WQ       G
Sbjct: 91  VFYIVGALSLQITLGTAIALLLDRVSRGENVLTGIIIMPMMIAPVVVGLLWQFLLDPSFG 150

Query: 130 LLGHTLEAIGLDYNYVRDPI-----DAWVTVIVMDVWHWTSLVVLLCYAGLVSIPDAYYQ 184
           L    L  IGL   +   PI      A + VIVMD W WT LVVL+  AGL ++P   Y+
Sbjct: 151 LYTWLLNQIGL---FTESPILGSQPSALIAVIVMDTWQWTPLVVLIVLAGLKAVPRQLYE 207

Query: 185 AAKIDGASRWSVFRYIQLPKMKRVLLIAVLLRFMDSFMIYTEPFVVTGGGPGNSTTFLSI 244
           AA++DGA+ W+ FRY+ LP +K  L IA+LLR MD    +T+ F+ TGGGP +ST  +  
Sbjct: 208 AARVDGATFWTEFRYVTLPMLKPALAIALLLRSMDLIRYFTKIFITTGGGPASSTKIIGF 267

Query: 245 DLVKMAVGQFDLGPAAAMSIIYFLIILLLSWVFYT 279
            + + ++  ++LG  AAM  I  LI+ +L  +F+T
Sbjct: 268 LVYEESLRFYNLGYGAAMG-IGMLIVTVLLGIFFT 301


Lambda     K      H
   0.329    0.143    0.464 

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: 262
Number of extensions: 18
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: 288
Length of database: 312
Length adjustment: 27
Effective length of query: 261
Effective length of database: 285
Effective search space:    74385
Effective search space used:    74385
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 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