GapMind for catabolism of small carbon sources

 

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

Align TreT, component of Trehalose porter (characterized)
to candidate WP_049988752.1 LT39_RS01710 sugar ABC transporter permease

Query= TCDB::Q97ZC2
         (275 letters)



>NCBI__GCF_000784335.1:WP_049988752.1
          Length = 312

 Score =  112 bits (279), Expect = 1e-29
 Identities = 82/269 (30%), Positives = 140/269 (52%), Gaps = 15/269 (5%)

Query: 10  LLVLPALAYV--ISFAFFPTIEAVYLSFQDPHGGFSLYNYKELSYFNLSSAIINTIVVTI 67
           +LVL  L+ V  I+  +   +E  +L   +P     L NY+ +    ++++   T+   +
Sbjct: 37  VLVLGILSIVPLIALLWLSAMEVNFLPGHEPTF-VGLENYQAMFNSTVANSWKVTVFYIV 95

Query: 68  GALAIQLALGFLVASVLSREFFGKRALSTITIIPMGIATVVAAVTFSFVFQTSGGYANTI 127
           GAL++Q+ LG  +A +L R   G+  L+ I I+PM IA VV  + + F+   S G    +
Sbjct: 96  GALSLQITLGTAIALLLDRVSRGENVLTGIIIMPMMIAPVVVGLLWQFLLDPSFGLYTWL 155

Query: 128 LHSLFGLNVNW--YQSSISSLLVVMIADSWKNTPIVALILLAGMSSIPKELYYASAIDGA 185
           L+ + GL        S  S+L+ V++ D+W+ TP+V LI+LAG+ ++P++LY A+ +DGA
Sbjct: 156 LNQI-GLFTESPILGSQPSALIAVIVMDTWQWTPLVVLIVLAGLKAVPRQLYEAARVDGA 214

Query: 186 GPIRRFFYITLPNLRSFIGISLILRGVQEFNIFALPLILIGEHPPLLTTLI-YDLYTTTF 244
                F Y+TLP L+  + I+L+LR +     F    I  G  P   T +I + +Y  + 
Sbjct: 215 TFWTEFRYVTLPMLKPALAIALLLRSMDLIRYFTKIFITTGGGPASSTKIIGFLVYEESL 274

Query: 245 --------PEVGLALASATILLGFILVFS 265
                     +G+ +   T+LLG     S
Sbjct: 275 RFYNLGYGAAMGIGMLIVTVLLGIFFTES 303


Lambda     K      H
   0.328    0.143    0.414 

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: 209
Number of extensions: 8
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: 275
Length of database: 312
Length adjustment: 26
Effective length of query: 249
Effective length of database: 286
Effective search space:    71214
Effective search space used:    71214
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 (21.7 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