GapMind for catabolism of small carbon sources

 

Aligments for a candidate for rbsB in Pseudomonas fluorescens FW300-N1B4

Align D-ribose-binding periplasmic protein; EC 3.6.3.17 (characterized)
to candidate Pf1N1B4_4386 Inositol transport system sugar-binding protein

Query= CharProtDB::CH_003593
         (296 letters)



>lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_4386 Inositol transport
           system sugar-binding protein
          Length = 308

 Score =  129 bits (325), Expect = 6e-35
 Identities = 79/277 (28%), Positives = 145/277 (52%), Gaps = 6/277 (2%)

Query: 23  AMAKDTIALVVSTLNNPFFVSLKDGAQKEADKLGYNLVVLDSQNNPAKELANVQDLTVRG 82
           A A   I + ++ +++ F   ++ G +  A K    +   D+Q +  ++L  VQ    + 
Sbjct: 19  AAASYRIGVSIARVDDNFMTYVRSGLEDAARKENVQIQFEDAQGDVVRQLNQVQGFLGQK 78

Query: 83  TKILLINPTDSDAVGNAVKMANQANIPVITLDRQATKGEV---VSHIASDNVLGGKIAGD 139
              +++ P D+ A  N  + A +A IP++ ++R   +  +   V  +AS++V  G++   
Sbjct: 79  VDAVIVLPVDTAATANMTRAAVEAKIPLVYVNRHPDERVLPKGVVTVASNDVEAGQLQMR 138

Query: 140 YIAKKAGEGAKVIELQGIAGTSAARERGEGFQQAVAAHK-FNVLASQPADFDRIKGLNVM 198
           Y+A+K      +  ++G    ++ ++R EG  Q +  +    ++  Q A++ R KG+++ 
Sbjct: 139 YLAEKMAGKGNIAIIKGDLAQNSTQDRTEGVNQVLKDYPGIKIVEQQSAEWQRNKGMDLT 198

Query: 199 QNLLTAHPDVQAVFAQNDEMALGALRALQTAGKS--DVMVVGFDGTPDGEKAVNDGKLAA 256
            N L A  D  A+ A NDEMA+GA  ALQ AGK+  ++ +VG DG PDG  A+  G L A
Sbjct: 199 SNWLLAGADFDAIVANNDEMAIGAAMALQQAGKAKGEIAIVGIDGLPDGLAAIKRGMLVA 258

Query: 257 TIAQLPDQIGAKGVETADKVLKGEKVQAKYPVDLKLV 293
           ++ Q P       ++ A K++KGE V+    V  +L+
Sbjct: 259 SVFQDPKAQATSALQAAIKMIKGEPVETDVWVPFQLI 295


Lambda     K      H
   0.313    0.129    0.344 

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: 222
Number of extensions: 23
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: 296
Length of database: 308
Length adjustment: 27
Effective length of query: 269
Effective length of database: 281
Effective search space:    75589
Effective search space used:    75589
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (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.

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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 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