GapMind for catabolism of small carbon sources

 

Aligments for a candidate for gtsB in Phaeobacter inhibens BS107

Align GtsB (GLcF), component of Glucose porter, GtsABCD (characterized)
to candidate GFF3853 PGA1_78p00170 putative sn-glycerol-3-phosphate transport system permease protein UgpA

Query= TCDB::Q88P37
         (302 letters)



>lcl|FitnessBrowser__Phaeo:GFF3853 PGA1_78p00170 putative
           sn-glycerol-3-phosphate transport system permease
           protein UgpA
          Length = 310

 Score =  270 bits (690), Expect = 3e-77
 Identities = 128/292 (43%), Positives = 192/292 (65%)

Query: 9   RASPLDALQRWLPKLVLAPSMFIVLVGFYGYILWTFVLSFTTSTFLPTYKWAGLAQYARL 68
           R  P   L+    K+   P +   LV F G   WT   SFT S  LP +K+ G  QY RL
Sbjct: 17  RPRPPRVLRNLNAKIASVPMILTALVVFMGGTAWTVAHSFTKSRLLPKWKFVGFDQYERL 76

Query: 69  FDNDRWWVASKNLLLFGGLFIAISLAIGVLLAVLLDQRIRREGFIRTIYLYPMALSMIVT 128
           + ++RW ++ +NLL++G   + +++AIG  LA LLD++IR EG  RTI+LYP ALS +VT
Sbjct: 77  WSSNRWLISVENLLIYGLCSLVLTMAIGFTLAALLDRKIRFEGAFRTIFLYPFALSFVVT 136

Query: 129 GTAWKWLLNPGMGLDKLLRDWGWEGFRLDWLIDPDRVVYCLVIAAVWQASGFIMAMFLAG 188
           G AW+W+LNP  G+  ++R WGWE F  D L +P+ V++ ++IA +WQ SGF+M + LAG
Sbjct: 137 GLAWQWILNPDFGIQNVVRSWGWESFAFDPLNNPETVIFGVLIAGLWQGSGFVMVIMLAG 196

Query: 189 LRGVDPSIIRAAQMDGASLPRIYWTVVLPSLRPVFFSALMILSHIAIKSFDLVAAMTAGG 248
           LRG+D  I +AA++DG  + + Y  V++P +RPVF +AL+I++   IK +DLV A T GG
Sbjct: 197 LRGIDEDIWKAARVDGIGVTKTYVRVIIPMMRPVFVTALVIIASGIIKLYDLVVAQTNGG 256

Query: 249 PGYSSDLPAMFMYSFTFSRGQMGMGSASAILMLGAILAILVPYLYSELRSKR 300
           PG SS++PA ++ ++ F    +G G A++ +ML +++ ILVP+ Y E   K+
Sbjct: 257 PGISSEVPAKYVINYMFEAQNLGQGFAASTMMLLSVIIILVPWAYLEFGGKK 308


Lambda     K      H
   0.330    0.142    0.455 

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: 281
Number of extensions: 10
Number of successful extensions: 2
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: 302
Length of database: 310
Length adjustment: 27
Effective length of query: 275
Effective length of database: 283
Effective search space:    77825
Effective search space used:    77825
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: 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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 on GapMind for carbon sources, or view the source code.

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