GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gtsC in Phaeobacter inhibens BS107

Align ABC transporter for D-Glucose-6-Phosphate, permease component 1 (characterized)
to candidate GFF3854 PGA1_78p00180 putative sn-glycerol-3-phosphate transport system permease protein UgpE

Query= reanno::WCS417:GFF4322
         (281 letters)



>FitnessBrowser__Phaeo:GFF3854
          Length = 309

 Score =  280 bits (715), Expect = 4e-80
 Identities = 137/284 (48%), Positives = 195/284 (68%), Gaps = 9/284 (3%)

Query: 7   KPAISLSRIAIYAVLILAVLLYLVPLVVMLLTSFKTPEDISSGNLLSWPTVVTGIGWVKA 66
           K  +S   + +Y  L+L  L YL+PL VM++TS K   +I  GN+ S P  +T   W+KA
Sbjct: 26  KTRVSRRNVMLYGTLLLIALYYLLPLYVMVVTSLKGMPEIRLGNIFSPPVEITFQPWIKA 85

Query: 67  WATV------DGY---FWNSIKITVPAVLISTAIGALNGYVLSFWRFKGSQLFFGLLLFG 117
           W+        DG    F NSIKI VP+V +S AI ++NGY L+ WRFKGS+ FF +L+ G
Sbjct: 86  WSEACTGINCDGLSRGFGNSIKILVPSVALSIAIASVNGYALANWRFKGSETFFTILIIG 145

Query: 118 CFLPFQTVLLPASFTLGKMGLASTTTGLVFVHVVYGLAFTTLFFRNYYVSIPDALIKAAR 177
            F+P+QT+L P    L ++ L  +  GLV VH ++G+   TL FRNY+ S+P+ L KAAR
Sbjct: 146 AFIPYQTMLYPIVIILRELKLMGSLWGLVLVHSIFGMPILTLLFRNYFSSLPEELFKAAR 205

Query: 178 LDGAGFFTIFRQIILPMSTPIIMVCLIWQFTQIWNDFLFGVVFSSGDSQPITVALNNLVN 237
           +DGAGF+ I+ ++++PMS PI +V +I Q T IWNDFLFGV+++  ++ P+TV LNN+VN
Sbjct: 206 VDGAGFWGIYLRVMVPMSIPIFVVAMILQVTGIWNDFLFGVIYTKPETYPMTVQLNNIVN 265

Query: 238 TSTGAKEYNVDMAAAMIAGLPTLLVYVIAGKYFVRGLTAGAVKG 281
           +  G KEYNV+MAA ++ GL  L++Y+++GK FVRG+ AGAVKG
Sbjct: 266 SVQGVKEYNVNMAATLLTGLVPLVIYLVSGKLFVRGIAAGAVKG 309


Lambda     K      H
   0.328    0.141    0.435 

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: 251
Number of extensions: 11
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: 281
Length of database: 309
Length adjustment: 26
Effective length of query: 255
Effective length of database: 283
Effective search space:    72165
Effective search space used:    72165
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