GapMind for catabolism of small carbon sources

 

Alignments for a candidate for PS417_11885 in Pseudomonas fluorescens FW300-N2E2

Align Rhizopine-binding protein (characterized, see rationale)
to candidate Pf6N2E2_1005 Ribose ABC transport system, periplasmic ribose-binding protein RbsB (TC 3.A.1.2.1)

Query= uniprot:A0A0N9WNI6
         (308 letters)



>FitnessBrowser__pseudo6_N2E2:Pf6N2E2_1005
          Length = 317

 Score =  133 bits (335), Expect = 5e-36
 Identities = 98/313 (31%), Positives = 158/313 (50%), Gaps = 15/313 (4%)

Query: 4   KIRFASLALSLMLASG-------AALADLRIGVSMSQFDDTWLTYLRESMDKQAKSMPDG 56
           K +   L  S +LA+G       A  A  +I ++       +  Y+ E   ++AK +   
Sbjct: 2   KAQKGGLLCSAVLAAGLTFQLSPAFAAGEKILINFQTLSIPYFIYMHEQASQEAKVL--N 59

Query: 57  VKLQFEDARSDVVKQLSQVESFISQKVDAIVVNPVDTAATRKITEAAVKAGIPLVYVNRR 116
           V+L  +DA+S   KQ S VE+ ++Q VDA+VV P D  A        +   +PLV V+RR
Sbjct: 60  VELLVQDAQSSSTKQSSDVENALTQGVDAMVVAPNDVTALAPALNEVLSEKVPLVTVDRR 119

Query: 117 PDDLKLPKGVITVASNDLEAGQMQMQYLAEKMKGKGDIVILLGDLANNSTTNRTKGVKEV 176
            +    P  V  V ++ +  G++  + +   MK    +  + G   +++  +R KGV E 
Sbjct: 120 VEGTDTP--VPYVTADSVAGGRLMAELVTSNMKNGARVAFIGGTPGSSTAIDRAKGVHEG 177

Query: 177 LAKYPG-IKIDQEQTGTWSRDKGMTLVNDWLT--QGRKFDAIVSNNDEMAIGAAMALKQA 233
           L    G  ++  EQ+G W R K M++  + LT       DAI+  + +MA+GAA A++  
Sbjct: 178 LKAGGGKFQLVAEQSGEWERAKAMSVAENILTSLSANPPDAIICASGDMALGAAEAVRAT 237

Query: 234 GVEKGSVLIAGVDGTPDGLRAVKKGDLAVSVFQDANGQAVDSIDAAVKMAKNEPVEQAVW 293
           G+ KG V + G D  P+ LRA++ GD+A  V Q  + Q   ++  AVK  + E   + V 
Sbjct: 238 GL-KGKVKVIGFDAYPEVLRAIRDGDIAGIVEQSPSKQIRTALRMAVKKVRGEGELETVI 296

Query: 294 VPYRLITPENVDQ 306
           V   +ITPEN+ Q
Sbjct: 297 VQPFMITPENLSQ 309


Lambda     K      H
   0.315    0.130    0.360 

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: 206
Number of extensions: 6
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: 308
Length of database: 317
Length adjustment: 27
Effective length of query: 281
Effective length of database: 290
Effective search space:    81490
Effective search space used:    81490
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.5 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