GapMind for catabolism of small carbon sources

 

Alignments for a candidate for xylF_Tm in Azospirillum brasilense Sp245

Align ABC-type transporter, integral membrane subunit, component of Xylose porter (Nanavati et al. 2006). Regulated by xylose-responsive regulator XylR (characterized)
to candidate AZOBR_RS27940 AZOBR_RS27940 ABC transporter permease

Query= TCDB::Q9WXW7
         (317 letters)



>FitnessBrowser__azobra:AZOBR_RS27940
          Length = 329

 Score =  182 bits (461), Expect = 1e-50
 Identities = 113/306 (36%), Positives = 175/306 (57%), Gaps = 14/306 (4%)

Query: 14  GPLVALVSLAVFTAILNPRFLTAFNLQALGRQIAIFGLLAIGETFVIISGGGAIDLSPGS 73
           GP +AL +L V   I+NP FL+  N+  +  + A  G++A+G TFVI +GG  IDLS GS
Sbjct: 18  GPFLALAALIVLGTIVNPVFLSPGNIGNVLTRTAFIGIIAVGATFVITAGG--IDLSVGS 75

Query: 74  MVAL-TGVMVAWL------MTHGVPV-WISVILILLFSIGAGAWHGLFVTKLRVPAFIIT 125
           + A  +GVM+  +      M  G+PV  I V++ L   + AG  +GL VTK R+ AFI+T
Sbjct: 76  LAAFASGVMIVVMNALVGSMGAGLPVILIGVLVALGLGLVAGLVNGLLVTKGRMEAFIVT 135

Query: 126 LGTLTIARGMAAVITKGWPII---GLPSSFLKIGQGEFLKIPIPVWILLAVALVADFFLR 182
           LGT+ I R +   I  G  +     + + +  +  G    I  P+     VAL+    + 
Sbjct: 136 LGTMGIFRSLVTYIADGGTLSLNSEIRTIYRPVYYGGVFGISYPILAFAVVALIGALIMY 195

Query: 183 KTVYGKHLRASGGNEVAARFSGVNVDRVRMIAFMVSGFLAGVVGIIIAARLSQGQPGVGS 242
           +T +G++  A G +E  AR+S +NVDRV+++AF++ G    +  +I   RL       G 
Sbjct: 196 RTRFGRYCAAIGSSEDVARYSAINVDRVKLLAFVLQGICVAIAVVIYVPRLGSASATTGL 255

Query: 243 MYELYAIASTVIGGTSLTGGEGSVLGAIVGASIISLLWNALVLLN-VSTYWHNVVIGIVI 301
           ++EL AIA+ +IGGT L GG G + G +VGA +++L+ N L L   +S Y +  + G++I
Sbjct: 256 LWELEAIAAVIIGGTMLKGGYGRIWGTVVGAVMLTLIDNILNLTGAISVYLNGTIQGVII 315

Query: 302 VVAVTL 307
           +VAV L
Sbjct: 316 IVAVLL 321


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: 346
Number of extensions: 23
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: 329
Length adjustment: 28
Effective length of query: 289
Effective length of database: 301
Effective search space:    86989
Effective search space used:    86989
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