GapMind for catabolism of small carbon sources

 

Alignments 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)



>FitnessBrowser__pseudo1_N1B4:Pf1N1B4_4386
          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 (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