GapMind for catabolism of small carbon sources

 

Aligments for a candidate for xylF_Tm in Pseudomonas simiae WCS417

Align ABC-type transporter, integral membrane subunit, component of Xylose porter (Nanavati et al. 2006). Regulated by xylose-responsive regulator XylR (characterized)
to candidate GFF2365 PS417_12060 sugar ABC transporter permease

Query= TCDB::Q9WXW7
         (317 letters)



>lcl|FitnessBrowser__WCS417:GFF2365 PS417_12060 sugar ABC
           transporter permease
          Length = 325

 Score =  220 bits (560), Expect = 4e-62
 Identities = 124/299 (41%), Positives = 185/299 (61%), Gaps = 3/299 (1%)

Query: 15  PLVALVSLAVFTAILNPRFLTAFNLQALGRQIAIFGLLAIGETFVIISGGGAIDLSPGSM 74
           PLV ++ L V  A  +  F+T  N   + RQ +I G+LA+G T+VI++ G  IDLS GS+
Sbjct: 28  PLVFIL-LCVVMAFSSEYFMTWRNWMDILRQTSINGILAVGMTYVILTKG--IDLSVGSI 84

Query: 75  VALTGVMVAWLMTHGVPVWISVILILLFSIGAGAWHGLFVTKLRVPAFIITLGTLTIARG 134
           +A  G+  A + T G  +  +V   +      G  +G  V  L +P F+ TLG L+IARG
Sbjct: 85  LAFAGLCSAMVATQGYGLLAAVSAGMFAGAMLGVVNGFMVANLSIPPFVATLGMLSIARG 144

Query: 135 MAAVITKGWPIIGLPSSFLKIGQGEFLKIPIPVWILLAVALVADFFLRKTVYGKHLRASG 194
           M  ++  G PI  LP ++L +G G+   I +P+ I   VAL+    LR T YG+++ A G
Sbjct: 145 MTFILNDGSPITDLPDAYLALGIGKIGPIGVPIIIFAVVALIFWMVLRYTTYGRYVYAVG 204

Query: 195 GNEVAARFSGVNVDRVRMIAFMVSGFLAGVVGIIIAARLSQGQPGVGSMYELYAIASTVI 254
           GNE +AR SG+ V +V    ++VSG LAG+ G++++AR +   P  G  YEL AIA+ VI
Sbjct: 205 GNEKSARTSGIGVRKVMFSVYVVSGLLAGLAGVVLSARTTSALPQAGVSYELDAIAAVVI 264

Query: 255 GGTSLTGGEGSVLGAIVGASIISLLWNALVLLNVSTYWHNVVIGIVIVVAVTLDILRRR 313
           GGTSL+GG GS++G + GA +I ++ N L LL VS+Y+  V  G++IV AV +D+ R++
Sbjct: 265 GGTSLSGGTGSIVGTLFGALLIGVINNGLNLLGVSSYYQQVAKGLIIVFAVLIDVWRKK 323


Lambda     K      H
   0.328    0.143    0.424 

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: 320
Number of extensions: 16
Number of successful extensions: 2
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: 317
Length of database: 325
Length adjustment: 28
Effective length of query: 289
Effective length of database: 297
Effective search space:    85833
Effective search space used:    85833
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 (21.7 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