GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gtsC in Polaromonas naphthalenivorans CJ2

Align ABC transporter for D-Glucose-6-Phosphate, permease component 1 (characterized)
to candidate WP_011803054.1 PNAP_RS18455 carbohydrate ABC transporter permease

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



>NCBI__GCF_000015505.1:WP_011803054.1
          Length = 289

 Score =  355 bits (910), Expect = e-103
 Identities = 176/279 (63%), Positives = 213/279 (76%), Gaps = 9/279 (3%)

Query: 12  LSRIAIYAVLILAVLLYLVPLVVMLLTSFKTPEDISSGNLLSWPTVVTGIGWVKAWAT-- 69
           LSR  +YAVL++A L +L P  VML TSFK  E I SGNLLS P  +    W  AW++  
Sbjct: 11  LSRALLYAVLLVAALFFLAPFYVMLATSFKDAEQIRSGNLLSPPASLNFDAWRLAWSSAC 70

Query: 70  -------VDGYFWNSIKITVPAVLISTAIGALNGYVLSFWRFKGSQLFFGLLLFGCFLPF 122
                  +  YFWNS+ + +PAVLISTA GA+NGYVLS W+F+GS+L FG LLFG F+PF
Sbjct: 71  TGVDCRGLQPYFWNSVSMAIPAVLISTAWGAVNGYVLSLWKFRGSELLFGFLLFGVFMPF 130

Query: 123 QTVLLPASFTLGKMGLASTTTGLVFVHVVYGLAFTTLFFRNYYVSIPDALIKAARLDGAG 182
           Q VLLP S  LG +GL+S+  GLV VH + G+A TTLFFRNYY +IP  L+ AAR+DGAG
Sbjct: 131 QVVLLPMSQVLGYLGLSSSIGGLVLVHCLAGMAGTTLFFRNYYTAIPKELVNAARMDGAG 190

Query: 183 FFTIFRQIILPMSTPIIMVCLIWQFTQIWNDFLFGVVFSSGDSQPITVALNNLVNTSTGA 242
           F+ IF +I+LP+STPI+MV LIWQFT IWNDFLFGV FS  DS+PITV LNN+ NTS+  
Sbjct: 191 FWRIFWRIVLPLSTPILMVTLIWQFTNIWNDFLFGVAFSGADSKPITVGLNNMANTSSSV 250

Query: 243 KEYNVDMAAAMIAGLPTLLVYVIAGKYFVRGLTAGAVKG 281
           K YNVDMAAA+IAGLPT+LVYV+AG+YFV+GLTAGAVKG
Sbjct: 251 KSYNVDMAAAVIAGLPTMLVYVLAGQYFVKGLTAGAVKG 289


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: 299
Number of extensions: 12
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: 289
Length adjustment: 26
Effective length of query: 255
Effective length of database: 263
Effective search space:    67065
Effective search space used:    67065
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 Apr 09 2024. 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