GapMind for catabolism of small carbon sources

 

Aligments for a candidate for xylF_Tm in Pseudomonas fluorescens FW300-N2C3

Align ABC-type transporter, integral membrane subunit, component of Xylose porter (Nanavati et al. 2006). Regulated by xylose-responsive regulator XylR (characterized)
to candidate AO356_20255 AO356_20255 arabinose ABC transporter permease

Query= TCDB::Q9WXW7
         (317 letters)



>lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_20255 AO356_20255
           arabinose ABC transporter permease
          Length = 322

 Score =  196 bits (498), Expect = 6e-55
 Identities = 105/298 (35%), Positives = 173/298 (58%), Gaps = 2/298 (0%)

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

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

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

Query: 196 NEVAARFSGVNVDRVRMIAFMVSGFLAGVVGIIIAARLSQGQPGVGSMYELYAIASTVIG 255
           N+ AA  +GVNVDR ++I F V G +  + G+I+A+R++ GQP +G  +EL  I++ V+G
Sbjct: 205 NQEAALLAGVNVDRTKIIIFAVHGLIGALAGVILASRMTSGQPMIGQGFELTVISACVLG 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: 286
Number of extensions: 20
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 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