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 GFF2333 PS417_11895 ABC transporter

Query= TCDB::Q9WXW7
         (317 letters)



>lcl|FitnessBrowser__WCS417:GFF2333 PS417_11895 ABC transporter
          Length = 340

 Score =  198 bits (504), Expect = 1e-55
 Identities = 117/281 (41%), Positives = 167/281 (59%), Gaps = 19/281 (6%)

Query: 45  QIAIFGLLAIGETFVIISGGGAIDLSPGSMVALTGVMVAWLMTHG------------VPV 92
           Q++I GLLAIG T VII+ G  IDLS GS++AL+ ++ A L                +PV
Sbjct: 62  QVSIIGLLAIGVTQVIITTG--IDLSSGSVLALSAMIAASLAQTSDFSRAVFPSLTDLPV 119

Query: 93  WISVILILLFSIGAGAWHGLFVTKLRVPAFIITLGTLTIARGMAAVITKGWPIIGLPSSF 152
           WI V + L   + AGA +G  +    +P FI TLG +  ARG+A   T+G P+  L  S+
Sbjct: 120 WIPVAMGLGVGLLAGAINGSIIAVTGIPPFIATLGMMVSARGLARYYTEGQPVSMLSDSY 179

Query: 153 LKIGQGEFLKIPIPVWILLAVALVADFFLRKTVYGKHLRASGGNEVAARFSGVNVDRVRM 212
             IG G      +PV I L VA++    LR T YGK+  A GGN  AAR SG+NV R  +
Sbjct: 180 TAIGHGA-----MPVIIFLVVAVIFHIALRYTKYGKYTYAIGGNMQAARTSGINVKRHLI 234

Query: 213 IAFMVSGFLAGVVGIIIAARLSQGQPGVGSMYELYAIASTVIGGTSLTGGEGSVLGAIVG 272
           I + ++G LAG+ G++ +AR + GQ G+G  YEL AIA+ VIGGTSL GG G + G ++G
Sbjct: 235 IVYSIAGLLAGLAGVVASARAATGQAGMGMSYELDAIAAAVIGGTSLAGGVGRITGTVIG 294

Query: 273 ASIISLLWNALVLLNVSTYWHNVVIGIVIVVAVTLDILRRR 313
           A I+ ++ +    + V  Y  +++ G++IVVAV +D  R +
Sbjct: 295 ALILGVMASGFTFVGVDAYIQDIIKGLIIVVAVVIDQYRNK 335


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: 305
Number of extensions: 21
Number of successful extensions: 4
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: 340
Length adjustment: 28
Effective length of query: 289
Effective length of database: 312
Effective search space:    90168
Effective search space used:    90168
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: 49 (23.5 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, 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