GapMind for catabolism of small carbon sources

 

Aligments for a candidate for PS417_12060 in Pseudomonas simiae WCS417

Align ABC transporter permease; SubName: Full=Monosaccharide ABC transporter membrane protein, CUT2 family; SubName: Full=Sugar ABC transporter permease (characterized, see rationale)
to candidate GFF3462 PS417_17725 ribose ABC transporter permease

Query= uniprot:A0A1N7UKA9
         (325 letters)



>lcl|FitnessBrowser__WCS417:GFF3462 PS417_17725 ribose ABC
           transporter permease
          Length = 330

 Score =  275 bits (704), Expect = 9e-79
 Identities = 149/324 (45%), Positives = 207/324 (63%), Gaps = 6/324 (1%)

Query: 6   ITAPVTAAPRNRLRLSLDRFGLPLVF------ILLCVVMAFSSEYFMTWRNWMDILRQTS 59
           +   ++    +RLRL+L R      F      +++ +VM  +S+ F+T  N  +I RQ S
Sbjct: 7   VNTSISTGDSSRLRLNLARLVRSPAFYPFVGLVVVTLVMILASDTFLTASNLSNIARQVS 66

Query: 60  INGILAVGMTYVILTKGIDLSVGSILAFAGLCSAMVATQGYGLLAAVSAGMFAGAMLGVV 119
           IN I+AVGMT VILT GIDLSVG ++A +G  +A +   G     A+ AGM  G   G+ 
Sbjct: 67  INAIIAVGMTCVILTGGIDLSVGPVMALSGTLTAGLMVAGLPPGLAIGAGMLIGVAFGIG 126

Query: 120 NGFMVANLSIPPFVATLGMLSIARGMTFILNDGSPITDLPDAYLALGIGKIGPIGVPIII 179
           NG  VA L +PP + TL  + IARG+  +  DG PI+ LPD +   G   +  I VPI+I
Sbjct: 127 NGLFVAYLHMPPIIVTLATMGIARGLGLMYTDGYPISGLPDWFAFFGRESLFGIQVPILI 186

Query: 180 FAVVALIFWMVLRYTTYGRYVYAVGGNEKSARTSGIGVRKVMFSVYVVSGLLAGLAGVVL 239
             +  L+ +++L++T  GRY+YA+GGNE++ R SG+   +    VY +SGL A +AG+VL
Sbjct: 187 MLLTYLVAYVLLQHTRIGRYIYAIGGNEEAVRLSGVRAARFKLLVYGISGLTAAIAGLVL 246

Query: 240 SARTTSALPQAGVSYELDAIAAVVIGGTSLSGGTGSIVGTLFGALLIGVINNGLNLLGVS 299
           ++R  S  P AGVS+ELDAIAAVV+GG S++GG G IVGTL GA+L+GV+NNGLN+LGVS
Sbjct: 247 TSRLMSGQPNAGVSFELDAIAAVVLGGASIAGGRGVIVGTLLGAMLLGVLNNGLNMLGVS 306

Query: 300 SYYQQVAKGLIIVFAVLIDVWRKK 323
            Y Q V KG II+ A+ I   R K
Sbjct: 307 PYVQSVIKGGIILLAIFISRQRHK 330


Lambda     K      H
   0.326    0.141    0.412 

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: 268
Number of extensions: 14
Number of successful extensions: 1
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: 325
Length of database: 330
Length adjustment: 28
Effective length of query: 297
Effective length of database: 302
Effective search space:    89694
Effective search space used:    89694
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.6 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