GapMind for catabolism of small carbon sources

 

Aligments for a candidate for SMc02872 in Phaeobacter inhibens BS107

Align ABC transporter for N-Acetyl-D-glucosamine, permease protein 1 (characterized)
to candidate GFF773 PGA1_c07870 alpha-glucoside transport system permease protein AglF

Query= reanno::Smeli:SMc02872
         (315 letters)



>lcl|FitnessBrowser__Phaeo:GFF773 PGA1_c07870 alpha-glucoside
           transport system permease protein AglF
          Length = 335

 Score =  126 bits (316), Expect = 8e-34
 Identities = 94/309 (30%), Positives = 153/309 (49%), Gaps = 28/309 (9%)

Query: 13  IKRPRRWHILVFLLPALVVYTAVMILPLFETLRQSFYNTVDGQLT-FVGLGNFKVLFGDP 71
           I+R       +FL PAL+     +  P+ ETLR S    V G  + FVGL N++ +  + 
Sbjct: 45  IRRANMIRPWLFLFPALLALGLYLAYPVVETLRLSVTERVPGGGSEFVGLANYQQMLAE- 103

Query: 72  RWAADFWNALKNNFVFFLIHMAVQNPIGIALAAMLSVPKLRFGAFYRTAIFLPTLLSFVI 131
              A FW AL+NNF++ L+  A     G+ LAA L+  +L +G   ++ IF+P  +SFV 
Sbjct: 104 ---AKFWEALQNNFLWLLVVPAASTAFGL-LAAQLT-DRLAWGNIAKSLIFMPMAISFVG 158

Query: 132 VGFIWKLILSPIWGVAPYLLDTVG-LRSLF------GP--WLGKPDTALIAVSLISVWQY 182
              IWKL+    +   P   D +G L +L+      GP  WL  P      + ++ +W  
Sbjct: 159 AAVIWKLV----YDARPEGTDQIGVLNALYIYFGGDGPMQWLTIPFWNSFFLMMVLIWIQ 214

Query: 183 IGIPMMLIYAALLNIPDEVTEAAELDGVTGWSQFWKIKLPLILPAIGIVSILTFVGNFNA 242
            G  M+++ AAL  IP+E  EAA +DG   +  F+KIK+P I+  I +V     +     
Sbjct: 215 TGFAMVILSAALRGIPEETVEAAIVDGAGPFQIFFKIKVPQIMDTIVVVWTTITIVVLKV 274

Query: 243 FDLIYTVQGALAGPDKSTDILGTLLYRTFFGFQLQLGDRSMGATIAAIMFLIILAGVALY 302
           FD+++    A+      T +L   +Y   F    +  D  +G+  A ++ L++L  +   
Sbjct: 275 FDIVF----AMTNGQWETQVLANYMYDKLF----RANDWGVGSASAMVIMLLVLPILVWN 326

Query: 303 LFGIQRRMR 311
           ++  +R MR
Sbjct: 327 VYNARREMR 335


Lambda     K      H
   0.331    0.146    0.461 

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: 340
Number of extensions: 18
Number of successful extensions: 4
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: 315
Length of database: 335
Length adjustment: 28
Effective length of query: 287
Effective length of database: 307
Effective search space:    88109
Effective search space used:    88109
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.9 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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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 the paper from 2019 on GapMind for amino acid biosynthesis, or view the source code.

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