GapMind for catabolism of small carbon sources

 

Alignments for a candidate for xylF_Tm in Pseudomonas putida KT2440

Align ABC-type transporter, integral membrane subunit, component of Xylose porter (Nanavati et al. 2006). Regulated by xylose-responsive regulator XylR (characterized)
to candidate PP_2456 PP_2456 D-ribose ABC transporter - permease subunit

Query= TCDB::Q9WXW7
         (317 letters)



>FitnessBrowser__Putida:PP_2456
          Length = 331

 Score =  153 bits (387), Expect = 5e-42
 Identities = 106/306 (34%), Positives = 158/306 (51%), Gaps = 4/306 (1%)

Query: 13  LGPLVALVSLAVFTAILNPRFLTAFNLQALGRQIAIFGLLAIGETFVIISGGGAIDLSPG 72
           LG   AL+++ V  + L+  F +      L  QI    +LA+G TFV+I GG  IDLS G
Sbjct: 27  LGLAGALLAMIVLFSFLSSHFWSYGTFSTLANQIPDLMVLAVGMTFVLIIGG--IDLSVG 84

Query: 73  SMVALTGVMVAW-LMTHGVPVWISVILILLFSIGAGAWHGLFVTKLRVPAFIITLGTLTI 131
           S++AL    V+  ++  G  V  S +L +  +  AG+  G      R+P+FI++LG L +
Sbjct: 85  SVLALAASTVSVAILGWGWGVLPSALLGMAVAALAGSITGGVTVAWRIPSFIVSLGVLEM 144

Query: 132 ARGMAAVITKGWPIIGLPSSFLKIGQGEFLKIPIPVWILLAVALVADFFLRKTVYGKHLR 191
           ARG+A   T       +  ++          +     I L V ++A   L +TV+G++L 
Sbjct: 145 ARGLAYQFTDSRTAY-IGDAYAWFSNPVAFGVSPAFIIALLVIVLAQLVLTRTVFGRYLI 203

Query: 192 ASGGNEVAARFSGVNVDRVRMIAFMVSGFLAGVVGIIIAARLSQGQPGVGSMYELYAIAS 251
             G NE A R +G++    +++ F + G LAG+  +   +RL    P  GS  EL  IA+
Sbjct: 204 GIGTNEEAVRLAGIDPRPYKVLVFALMGLLAGLAALFQISRLEAADPNAGSGLELQVIAA 263

Query: 252 TVIGGTSLTGGEGSVLGAIVGASIISLLWNALVLLNVSTYWHNVVIGIVIVVAVTLDILR 311
            VIGGTSL GG GSV+    G  IIS+L   L  +  S     ++ G VIV+AV LD  R
Sbjct: 264 VVIGGTSLMGGRGSVISTFFGVLIISVLAAGLAQIGASEPTKRIITGAVIVIAVVLDTYR 323

Query: 312 RRLASK 317
            R A +
Sbjct: 324 SRRAGR 329


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: 296
Number of extensions: 20
Number of successful extensions: 5
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: 331
Length adjustment: 28
Effective length of query: 289
Effective length of database: 303
Effective search space:    87567
Effective search space used:    87567
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.

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