GapMind for catabolism of small carbon sources

 

Alignments for a candidate for glcU in Burkholderia phytofirmans PsJN

Align GlcU, component of Glucose, mannose, galactose porter (characterized)
to candidate BPHYT_RS05035 BPHYT_RS05035 sugar ABC transporter permease

Query= TCDB::Q97UY9
         (287 letters)



>FitnessBrowser__BFirm:BPHYT_RS05035
          Length = 285

 Score =  130 bits (328), Expect = 3e-35
 Identities = 90/296 (30%), Positives = 148/296 (50%), Gaps = 21/296 (7%)

Query: 1   MDKKMRPVIKASLHYLALAIVSVIWLIPVYAMLINGFKSNFEVLSTPVLVPPTKITFEAY 60
           M  KM   I  ++ Y AL + ++ +L P+Y ML   FK   ++ +  +L PPT  T + +
Sbjct: 1   MQPKM--TISRAVIYAALFLFALYFLFPLYVMLSTSFKDIDQLRTGNLLTPPTHWTIDPW 58

Query: 61  VSVLLSLAKPL---------INSLIIVIPTSFISAFLGAMGAYFFYTLSYSFSRASSAIS 111
           +         +         +NS+ +VIP   IS+ +GA   Y      + F  A     
Sbjct: 59  IKAWSGACTGVRCDGMQPFFMNSVRMVIPAVLISSIIGAFNGYVL--THWRFRGA----- 111

Query: 112 DVLFSLISLATFIPQEATLLPLTRLIVSMGLLDSYIGIIFALLIFYIPTGALLMSMFISV 171
           D +F++I +  FIP +A LLP+ R    +GL ++  G++   +I+ I    +    F   
Sbjct: 112 DPIFTMILVGCFIPFQAILLPMARFEGFLGLSNTTTGLVVVHVIYGIAFTTMFFRNFYVS 171

Query: 172 IPRSLIEAAKMDGTGDLKIFMKIVFPLSMPGFISTLIFIIIQAWNNFFIPLVLVTTPGMK 231
           IP  L++AA++DG G   IF KI+ P+S+P F+  LI+   Q WN+F   +V      M 
Sbjct: 172 IPAELVKAARIDGAGFFTIFTKILLPVSLPIFMVCLIWQFTQIWNDFLFGIVFSGVDSMP 231

Query: 232 LT-SIAVLSYSGAYGTLYNDTFAAGMVASIIPLAIFVFLGRYFIRGLMALGGGGKG 286
           +T ++  L  +      YN   A  ++A++  L +++  GRYF+RGL A  G  KG
Sbjct: 232 ITVALNNLVNTSTGVKEYNVDMAGAIIAALPTLLVYIIAGRYFVRGLTA--GAVKG 285


Lambda     K      H
   0.330    0.144    0.417 

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: 234
Number of extensions: 14
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: 287
Length of database: 285
Length adjustment: 26
Effective length of query: 261
Effective length of database: 259
Effective search space:    67599
Effective search space used:    67599
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 (21.8 bits)
S2: 47 (22.7 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