GapMind for catabolism of small carbon sources

 

Alignments for a candidate for SMc04257 in Phaeobacter inhibens BS107

Align ABC transporter for D-Cellobiose and D-Salicin, permease component 1 (characterized)
to candidate GFF1916 PGA1_c19480 ABC transporter, inner-membrane protein

Query= reanno::Smeli:SMc04257
         (305 letters)



>FitnessBrowser__Phaeo:GFF1916
          Length = 297

 Score =  374 bits (959), Expect = e-108
 Identities = 175/288 (60%), Positives = 229/288 (79%), Gaps = 1/288 (0%)

Query: 18  GRKPRRTLSRRNIIVYGTLIVVALYYLLPLYVMIVTSLKGMPEIRVGNIFAPPLEITFEP 77
           G KP R  S R I +Y  L V A ++L+P+Y++IVTSLK MPEIR+GN+   P   + + 
Sbjct: 11  GPKPTRR-SMRRIAIYVFLSVAAAFFLMPIYIVIVTSLKTMPEIRLGNVLQWPQTWSVDA 69

Query: 78  WVKAWAEACTGLNCDGLSRGFWNSVRITVPSVIISIAIASVNGYALANWRFKGADLFFTI 137
           W+KAW  ACTGL C+G+  GFWNS+RI +PS+++SI   ++ GY L  W F+GA++FF I
Sbjct: 70  WIKAWDTACTGLQCEGIKVGFWNSMRILLPSLVVSITAGALCGYILTFWTFRGAEIFFAI 129

Query: 138 LIVGAFIPYQVMIYPIVIVLREMGVYGTLTGLIIVHTIFGMPILTLLFRNYFAGLPEELF 197
           L+ GAF+PYQ +I+P++ +    G+YGTL G+++VHTIFG+PI+TL+FRNY++ LP E+F
Sbjct: 130 LLFGAFVPYQALIFPMIRIFSATGLYGTLPGIVLVHTIFGLPIMTLIFRNYYSTLPSEIF 189

Query: 198 KAARVDGAGFWTIYFKIMLPMSLPIFVVAMILQVTGIWNDFLFGVVFTRPEYYPMTVQLN 257
           KAARVDGAGF+++++ ++LP+S PI VVA ILQVTGIWND+L G++F   E  PMTVQLN
Sbjct: 190 KAARVDGAGFFSVFWYVLLPISTPIIVVAAILQVTGIWNDYLLGLIFGGRENMPMTVQLN 249

Query: 258 NIVNSVQGVKEYNVNMAATILTGLVPLTVYFVSGRLFVRGIAAGAVKG 305
           NIVNSV+G KEYNVNMAAT+LT LVPLTVYFVSGR FVRGIAAGAVKG
Sbjct: 250 NIVNSVRGGKEYNVNMAATLLTALVPLTVYFVSGRWFVRGIAAGAVKG 297


Lambda     K      H
   0.329    0.145    0.450 

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: 364
Number of extensions: 14
Number of successful extensions: 1
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: 305
Length of database: 297
Length adjustment: 27
Effective length of query: 278
Effective length of database: 270
Effective search space:    75060
Effective search space used:    75060
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 17 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