GapMind for catabolism of small carbon sources

 

Aligments for a candidate for rbsC in Pseudomonas simiae WCS417

Align Ribose import permease protein RbsC (characterized)
to candidate GFF2333 PS417_11895 ABC transporter

Query= SwissProt::P0AGI1
         (321 letters)



>lcl|FitnessBrowser__WCS417:GFF2333 PS417_11895 ABC transporter
          Length = 340

 Score =  213 bits (542), Expect = 5e-60
 Identities = 137/335 (40%), Positives = 194/335 (57%), Gaps = 34/335 (10%)

Query: 2   TTQTVSGRRYFTKAWLMEQKSLIALLVLIAIVSTL-----SPNFFTINN--LFNILQQTS 54
           T  T S RR      L  + S+  +L+ I +V  L         F +N+  L  ++ Q S
Sbjct: 11  TVPTKSRRR------LPTELSIFLVLIGIGLVFELFGWIVRDQSFLMNSQRLVLMILQVS 64

Query: 55  VNAIMAVGMTLVILTSGIDLSVGSLLALTGAVAASIVGI------------EVNALVAVA 102
           +  ++A+G+T VI+T+GIDLS GS+LAL+  +AAS+               ++   + VA
Sbjct: 65  IIGLLAIGVTQVIITTGIDLSSGSVLALSAMIAASLAQTSDFSRAVFPSLTDLPVWIPVA 124

Query: 103 AALALGAAIGAVTGVIVAKGRVQAFIATLVMMLLLRGVTMVYTNGSPVNTGFTENADLFG 162
             L +G   GA+ G I+A   +  FIATL MM+  RG+   YT G PV+      +D + 
Sbjct: 125 MGLGVGLLAGAINGSIIAVTGIPPFIATLGMMVSARGLARYYTEGQPVSM----LSDSYT 180

Query: 163 WFGIGRPLGVPTPVWIMGIVFLAAWYMLHHTRLGRYIYALGGNEAATRLSGINVNKIKII 222
             G G       PV I  +V +     L +T+ G+Y YA+GGN  A R SGINV +  II
Sbjct: 181 AIGHGA-----MPVIIFLVVAVIFHIALRYTKYGKYTYAIGGNMQAARTSGINVKRHLII 235

Query: 223 VYSLCGLLASLAGIIEVARLSSAQPTAGTGYELDAIAAVVLGGTSLAGGKGRIVGTLIGA 282
           VYS+ GLLA LAG++  AR ++ Q   G  YELDAIAA V+GGTSLAGG GRI GT+IGA
Sbjct: 236 VYSIAGLLAGLAGVVASARAATGQAGMGMSYELDAIAAAVIGGTSLAGGVGRITGTVIGA 295

Query: 283 LILGFLNNGLNLLGVSSYYQMIVKAVVILLAVLVD 317
           LILG + +G   +GV +Y Q I+K ++I++AV++D
Sbjct: 296 LILGVMASGFTFVGVDAYIQDIIKGLIIVVAVVID 330


Lambda     K      H
   0.324    0.139    0.393 

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: 293
Number of extensions: 15
Number of successful extensions: 3
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: 321
Length of database: 340
Length adjustment: 28
Effective length of query: 293
Effective length of database: 312
Effective search space:    91416
Effective search space used:    91416
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.6 bits)
S2: 49 (23.5 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, the preprint on GapMind for carbon sources, 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