GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gtsC in Pseudomonas stutzeri RCH2

Align ABC transporter for D-Galactose and D-Glucose, permease component 2 (characterized)
to candidate GFF1859 Psest_1898 ABC-type sugar transport system, permease component

Query= reanno::pseudo13_GW456_L13:PfGW456L13_1896
         (281 letters)



>FitnessBrowser__psRCH2:GFF1859
          Length = 280

 Score =  485 bits (1248), Expect = e-142
 Identities = 230/272 (84%), Positives = 254/272 (93%)

Query: 10  ISFSRIAIYATLLLAAAVYLIPLVVMLLTSFKSPEDIRTGNLLSWPTVIDGIGWIKAWDV 69
           ++  R+ IYATLLLA AVYL+PL+VMLLTSFK+PEDIRTGNLLSWP     +GW+ AWD 
Sbjct: 9   LTLGRLTIYATLLLACAVYLVPLIVMLLTSFKTPEDIRTGNLLSWPEAFSAMGWLTAWDS 68

Query: 70  VGGYFWNSVKITVPAVLISTFIGAMNGYVLSMWRFRGSQLFFGLLLFGCFLPFQTVLLPA 129
           +GGYFWNSVKI +PAVLIST +GA+NGYVLSMWRFRGSQLFFGLLLFGCFLPFQ +LLPA
Sbjct: 69  IGGYFWNSVKIVIPAVLISTALGALNGYVLSMWRFRGSQLFFGLLLFGCFLPFQVILLPA 128

Query: 130 SFTLGKFGLANTTTGLVLVHVVYGLAFTTLFFRNYYVSIPDALVKAARLDGAGFFTIFLK 189
           SFTLGK GLANTTTGLVLVHVVYGLAFTTLFFRN+YVS+PDALV+AARLDGAGFFTIF +
Sbjct: 129 SFTLGKLGLANTTTGLVLVHVVYGLAFTTLFFRNFYVSVPDALVRAARLDGAGFFTIFGR 188

Query: 190 ILLPMSIPIVMVCLIWQFTQIWNDFLFGVVFASGDAQPITVALNNLVNTSTGAKEYNVDM 249
           ILLPMS+PI+MVCLIWQFTQIWNDFLFGVVFASGD QP+TVALNNLVNTSTGAK+YNVDM
Sbjct: 189 ILLPMSVPIIMVCLIWQFTQIWNDFLFGVVFASGDTQPVTVALNNLVNTSTGAKQYNVDM 248

Query: 250 AAAMIAGLPTLLVYIFAGKYFLRGLTSGAVKG 281
           AAAMIAGLPTL+VY+ AGKYFLRGLT+GAVKG
Sbjct: 249 AAAMIAGLPTLVVYVVAGKYFLRGLTAGAVKG 280


Lambda     K      H
   0.329    0.143    0.447 

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: 370
Number of extensions: 6
Number of successful extensions: 1
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: 280
Length adjustment: 26
Effective length of query: 255
Effective length of database: 254
Effective search space:    64770
Effective search space used:    64770
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