GapMind for catabolism of small carbon sources

 

Alignments for a candidate for xylF_Tm in Pseudomonas fluorescens FW300-N1B4

Align ABC-type transporter, integral membrane subunit, component of Xylose porter (Nanavati et al. 2006). Regulated by xylose-responsive regulator XylR (characterized)
to candidate Pf1N1B4_409 L-arabinose transport system permease protein (TC 3.A.1.2.2)

Query= TCDB::Q9WXW7
         (317 letters)



>FitnessBrowser__pseudo1_N1B4:Pf1N1B4_409
          Length = 322

 Score =  193 bits (490), Expect = 5e-54
 Identities = 104/298 (34%), Positives = 171/298 (57%), Gaps = 2/298 (0%)

Query: 16  LVALVSLAVFTAILNPRFLTAFNLQALGRQIAIFGLLAIGETFVIISGGGAIDLSPGSMV 75
           L+A V + V   +L   FL+  N++ LG  I+  G+ A    + + SG    DLS GS++
Sbjct: 27  LLAAVGIFVLCTLLIDNFLSPLNMRGLGLAISTTGIAACTMLYCLASGH--FDLSVGSVI 84

Query: 76  ALTGVMVAWLMTHGVPVWISVILILLFSIGAGAWHGLFVTKLRVPAFIITLGTLTIARGM 135
           A  GV+ A +M     V++ V   L+  +  G  +G+ + KLRV A I TL T+ I RG+
Sbjct: 85  ACAGVVAAVVMRDTDSVFLGVSAALVMGLIVGLINGIVIAKLRVNALITTLATMQIVRGL 144

Query: 136 AAVITKGWPIIGLPSSFLKIGQGEFLKIPIPVWILLAVALVADFFLRKTVYGKHLRASGG 195
           A +   G  +      F   G G+   +P+P+ I +   L   + L  T YG++  A GG
Sbjct: 145 AYIFANGKAVGVSQEQFFVFGNGQLFGVPVPILITIVCFLFFGWLLNYTTYGRNTMAIGG 204

Query: 196 NEVAARFSGVNVDRVRMIAFMVSGFLAGVVGIIIAARLSQGQPGVGSMYELYAIASTVIG 255
           N+ AA  +GVNVDR + + F V G +  + G+I+A+R++ GQP +G  +EL  I++ V+G
Sbjct: 205 NQEAALLAGVNVDRTKTLIFAVHGVIGALAGVILASRMTSGQPMIGQGFELTVISACVLG 264

Query: 256 GTSLTGGEGSVLGAIVGASIISLLWNALVLLNVSTYWHNVVIGIVIVVAVTLDILRRR 313
           G SL+GG G +   I G  I++++ NA+ L N+ T++  V+ G ++++AV +D L++R
Sbjct: 265 GVSLSGGIGMIRHVIAGVLILAIIENAMNLKNIDTFYQYVIRGSILLLAVVIDRLKQR 322


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: 289
Number of extensions: 18
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: 322
Length adjustment: 28
Effective length of query: 289
Effective length of database: 294
Effective search space:    84966
Effective search space used:    84966
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 (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