GapMind for catabolism of small carbon sources

 

Alignments 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)



>FitnessBrowser__Phaeo:GFF3853
          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:

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