GapMind for catabolism of small carbon sources

 

Alignments for a candidate for xylH in Azospirillum brasilense Sp245

Align Putative beta-xyloside ABC transporter, permease component, component of Glucose porter. Also bind xylose (Boucher and Noll 2011). Induced by glucose (Frock et al. 2012). Directly regulated by glucose-responsive regulator GluR (characterized)
to candidate AZOBR_RS27940 AZOBR_RS27940 ABC transporter permease

Query= TCDB::G4FGN4
         (313 letters)



>FitnessBrowser__azobra:AZOBR_RS27940
          Length = 329

 Score =  164 bits (415), Expect = 3e-45
 Identities = 107/312 (34%), Positives = 167/312 (53%), Gaps = 11/312 (3%)

Query: 6   FKAREAGIFLILIAIVVFLGVTTREFLTVENIFTVILNVSFIAIMSFGMTMVIITSGIDL 65
           F  +  G FL L A++V   +    FL+  NI  V+   +FI I++ G T VI   GIDL
Sbjct: 12  FDLKLYGPFLALAALIVLGTIVNPVFLSPGNIGNVLTRTAFIGIIAVGATFVITAGGIDL 71

Query: 66  SVGSILGAASVVMGLLMDE------KGLSPFL-SVVIGLAVGVGFGLANGLLITKARLAP 118
           SVGS+   AS VM ++M+        GL   L  V++ L +G+  GL NGLL+TK R+  
Sbjct: 72  SVGSLAAFASGVMIVVMNALVGSMGAGLPVILIGVLVALGLGLVAGLVNGLLVTKGRMEA 131

Query: 119 FISTLGMLSVGRGLAYVMSGGWPISPFPESFTVHGQ---GMVGPVPVPVIYMAVIGVIAH 175
           FI TLG + + R L   ++ G  +S   E  T++     G V  +  P++  AV+ +I  
Sbjct: 132 FIVTLGTMGIFRSLVTYIADGGTLSLNSEIRTIYRPVYYGGVFGISYPILAFAVVALIGA 191

Query: 176 IFLKYTVTGRRIYAIGGNMEASKLVGIKTDRILILVYTINGFLAAFAGFLLTAWLGVAQP 235
           + +  T  GR   AIG + + ++   I  DR+ +L + + G   A A  +    LG A  
Sbjct: 192 LIMYRTRFGRYCAAIGSSEDVARYSAINVDRVKLLAFVLQGICVAIAVVIYVPRLGSASA 251

Query: 236 NAGQGYELDVIAATVIGGTSLSGGEGTILGAFLGAVIMGVLRNGMILLG-VSSFWQQVVI 294
             G  +EL+ IAA +IGGT L GG G I G  +GAV++ ++ N + L G +S +    + 
Sbjct: 252 TTGLLWELEAIAAVIIGGTMLKGGYGRIWGTVVGAVMLTLIDNILNLTGAISVYLNGTIQ 311

Query: 295 GIVIIIAIAIDQ 306
           G++II+A+ + +
Sbjct: 312 GVIIIVAVLLQR 323


Lambda     K      H
   0.328    0.145    0.421 

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: 317
Number of extensions: 24
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: 313
Length of database: 329
Length adjustment: 28
Effective length of query: 285
Effective length of database: 301
Effective search space:    85785
Effective search space used:    85785
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