GapMind for catabolism of small carbon sources

 

Alignments for a candidate for sstT in Pseudomonas fluorescens FW300-N2C3

Align Serine/threonine transporter SstT; Na(+)/serine-threonine symporter (characterized)
to candidate AO356_01815 AO356_01815 serine/threonine protein kinase

Query= SwissProt::P0AGE4
         (414 letters)



>FitnessBrowser__pseudo5_N2C3_1:AO356_01815
          Length = 410

 Score =  557 bits (1435), Expect = e-163
 Identities = 280/401 (69%), Positives = 343/401 (85%)

Query: 11  RRLAHGSLVKQILVGLVLGILLAWISKPAAEAVGLLGTLFVGALKAVAPILVLMLVMASI 70
           +RL   SLV QI++GL+ GI+LAW++   A++   +G +FV ALKAVAPILV +LVMASI
Sbjct: 10  QRLKRTSLVTQIIIGLIAGIVLAWLAPDLAKSTAFIGKVFVSALKAVAPILVFVLVMASI 69

Query: 71  ANHQHGQKTNIRPILFLYLLGTFSAALAAVVFSFAFPSTLHLSSSAGDISPPSGIVEVMR 130
           ANH+HGQ+T+IRPILFLYLLGTF+AA+ AVV S  FPS+L LS+    ++ P GI EV++
Sbjct: 70  ANHKHGQETHIRPILFLYLLGTFAAAVVAVVASTLFPSSLVLSTQDVAVTAPGGISEVLQ 129

Query: 131 GLVMSMVSNPIDALLKGNYIGILVWAIGLGFALRHGNETTKNLVNDMSNAVTFMVKLVIR 190
            L++S+V NP+ AL+ GN+IGIL WAIG+G A+RH  +TT+ ++ D+SN VT +V+LVIR
Sbjct: 130 SLLLSVVDNPVRALMDGNFIGILAWAIGMGIAIRHAGQTTRTVLEDLSNGVTVIVRLVIR 189

Query: 191 FAPIGIFGLVSSTLATTGFSTLWGYAQLLVVLVGCMLLVALVVNPLLVWWKIRRNPFPLV 250
           FAP+GIFGLV+STLAT+GF  L GY QLL VL+GCML VALVVNPL+V+WK+RRNP+PLV
Sbjct: 190 FAPLGIFGLVASTLATSGFGALLGYLQLLTVLIGCMLFVALVVNPLIVFWKLRRNPYPLV 249

Query: 251 LLCLRESGVYAFFTRSSAANIPVNMALCEKLNLDRDTYSVSIPLGATINMAGAAITITVL 310
             CLRESG+ AFFTRSSAANIPVN+ L ++L L  DTYSVSIPLGATINMAGAAITITVL
Sbjct: 250 FTCLRESGITAFFTRSSAANIPVNLELSKRLGLHEDTYSVSIPLGATINMAGAAITITVL 309

Query: 311 TLAAVNTLGIPVDLPTALLLSVVASLCACGASGVAGGSLLLIPLACNMFGISNDIAMQVV 370
           TLAAV+TLGI VD+PTA+LLSVVA++CACGASGVAGGSLLLIPLAC++FGI ++IAMQVV
Sbjct: 310 TLAAVHTLGIVVDVPTAVLLSVVAAICACGASGVAGGSLLLIPLACSLFGIPSEIAMQVV 369

Query: 371 AVGFIIGVLQDSCETALNSSTDVLFTAAACQAEDDRLANSA 411
           AVGFIIGVLQDS ETALNSSTDVLFTAAAC  E+++LA +A
Sbjct: 370 AVGFIIGVLQDSAETALNSSTDVLFTAAACLGEEEKLARTA 410


Lambda     K      H
   0.325    0.138    0.405 

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: 430
Number of extensions: 7
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: 414
Length of database: 410
Length adjustment: 31
Effective length of query: 383
Effective length of database: 379
Effective search space:   145157
Effective search space used:   145157
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.6 bits)
S2: 50 (23.9 bits)

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

Links

Downloads

Related tools

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