GapMind for catabolism of small carbon sources

 

Alignments for a candidate for mglC in Burkholderia phytofirmans PsJN

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 BPHYT_RS20745 BPHYT_RS20745 ribose ABC transporter permease

Query= TCDB::G4FGN4
         (313 letters)



>FitnessBrowser__BFirm:BPHYT_RS20745
          Length = 341

 Score =  209 bits (532), Expect = 7e-59
 Identities = 115/303 (37%), Positives = 178/303 (58%), Gaps = 8/303 (2%)

Query: 17  LIAIVVFLGVTTREFLTVENIFTVILNVSFIAIMSFGMTMVIITSGIDLSVGSILGAASV 76
           LI ++VF    +  F+ ++N+  ++   +   +++   T VIIT GIDLSVG+++   +V
Sbjct: 38  LILLLVFFSFASPAFMQMDNMLGILQATAVNGVLAIACTFVIITGGIDLSVGTLMTFTAV 97

Query: 77  VMGLLMDEKGLSPFLSVVIGLAVGVGFGLANGLLITKARLAPFISTLGMLSVGRGLAYVM 136
           + G+ +    L  +  V+  +  G   G  +G L  K ++ PFI+TLGM+ + +GL+ V+
Sbjct: 98  ICGVFLTYWHLPMWTGVLAAIGTGAICGTVSGTLTAKMKIPPFIATLGMMMLLKGLSLVV 157

Query: 137 SGGWPI--SPFPESFTVHGQGMVG------PVPVPVIYMAVIGVIAHIFLKYTVTGRRIY 188
           S   PI  +     + +    ++G      PVP  V+ +  + V++ I L  T  GR  +
Sbjct: 158 SADKPIYFTDTENFYMISQDSLIGDLLPSLPVPNAVLILFFLAVVSSITLNRTALGRYTF 217

Query: 189 AIGGNMEASKLVGIKTDRILILVYTINGFLAAFAGFLLTAWLGVAQPNAGQGYELDVIAA 248
           A+G N EA +L G+  DR  I +Y ++G +   AG L+ + L  AQP  GQGYEL+ IAA
Sbjct: 218 ALGSNEEAVRLSGVNVDRWKIAIYGLSGAICGIAGLLIASRLNSAQPALGQGYELEAIAA 277

Query: 249 TVIGGTSLSGGEGTILGAFLGAVIMGVLRNGMILLGVSSFWQQVVIGIVIIIAIAIDQIR 308
            VIGGTSLSGG GTILG  +GA IM VL NG+ ++ V+  WQ VV G++II+A+  D +R
Sbjct: 278 VVIGGTSLSGGAGTILGTIIGAFIMSVLTNGLRIMSVAQEWQIVVTGLIIILAVYGDILR 337

Query: 309 RAK 311
           R K
Sbjct: 338 RKK 340


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: 286
Number of extensions: 19
Number of successful extensions: 3
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: 341
Length adjustment: 28
Effective length of query: 285
Effective length of database: 313
Effective search space:    89205
Effective search space used:    89205
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