GapMind for catabolism of small carbon sources

 

Alignments for a candidate for xylF_Tm in Rhizobium freirei PRF 81

Align ABC-type transporter, integral membrane subunit, component of Xylose porter (Nanavati et al. 2006). Regulated by xylose-responsive regulator XylR (characterized)
to candidate WP_004111334.1 RHSP_RS07045 ABC transporter permease

Query= TCDB::Q9WXW7
         (317 letters)



>NCBI__GCF_000359745.1:WP_004111334.1
          Length = 326

 Score =  219 bits (559), Expect = 5e-62
 Identities = 133/304 (43%), Positives = 185/304 (60%), Gaps = 4/304 (1%)

Query: 14  GPLVALVSLAVFTAILNPRFLTAFNLQALGRQIAIFGLLAIGETFVIISGGGAIDLSPGS 73
           GPLV L++L VF ++    FL+  N   +  QI + G++A+G TFVI+ GG  IDLS GS
Sbjct: 25  GPLVGLLALCVFLSLSTDAFLSLRNGLNILDQITVLGIMAVGMTFVILIGG--IDLSVGS 82

Query: 74  MVALTGVMVAWLMT-HGVPVWISVILILLFSIGAGAWHGLFVTKLRVPAFIITLGTLTIA 132
           ++AL  +++ W     G+P+   V + L+ S  +G   GL VT  RVPAFI TL  ++ A
Sbjct: 83  VLALAMMVMGWTANIAGLPLVAGVAVALVASALSGLIVGLLVTLFRVPAFIATLAMMSAA 142

Query: 133 RGMAAVITKGWPIIGLPSSFLKIG-QGEFLKIPIPVWILLAVALVADFFLRKTVYGKHLR 191
           RG+A +IT G  I+G P  F+ +     F  +   V+++LAV   A  FL     G+ L 
Sbjct: 143 RGVANMITDGQQIVGFPDWFMMLAIDRHFGVLTATVFLMLAVVAAAWVFLHFRSEGRMLY 202

Query: 192 ASGGNEVAARFSGVNVDRVRMIAFMVSGFLAGVVGIIIAARLSQGQPGVGSMYELYAIAS 251
           A GGN   AR +G+NV  V +  ++ S  LAG+ GI++AARL   QP  G  YEL  IA+
Sbjct: 203 AVGGNPEVARLAGINVQLVTIAVYVASAVLAGLAGIVLAARLDSVQPSSGFGYELDTIAA 262

Query: 252 TVIGGTSLTGGEGSVLGAIVGASIISLLWNALVLLNVSTYWHNVVIGIVIVVAVTLDILR 311
            VIGGTSL+GG G + G ++G  II +L N L LLNVS +   V+IGIVIV+AV  + +R
Sbjct: 263 VVIGGTSLSGGSGGIGGTLIGVLIIGVLRNGLNLLNVSPFLQQVIIGIVIVLAVGAETIR 322

Query: 312 RRLA 315
           RR A
Sbjct: 323 RRRA 326


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: 350
Number of extensions: 25
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: 326
Length adjustment: 28
Effective length of query: 289
Effective length of database: 298
Effective search space:    86122
Effective search space used:    86122
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 24 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