GapMind for catabolism of small carbon sources

 

Alignments for a candidate for sstT in Klebsiella michiganensis M5al

Align Serine/threonine transporter SstT; Na(+)/serine-threonine symporter (characterized)
to candidate BWI76_RS24715 BWI76_RS24715 serine/threonine transporter SstT

Query= SwissProt::P0AGE4
         (414 letters)



>FitnessBrowser__Koxy:BWI76_RS24715
          Length = 415

 Score =  701 bits (1809), Expect = 0.0
 Identities = 358/406 (88%), Positives = 389/406 (95%)

Query: 9   LFRRLAHGSLVKQILVGLVLGILLAWISKPAAEAVGLLGTLFVGALKAVAPILVLMLVMA 68
           L RRLA GSLVKQIL+GLVLG+LLA +SKPAA AVGLLGTLFVGALKAVAP+LVLMLVMA
Sbjct: 10  LLRRLAQGSLVKQILIGLVLGVLLATVSKPAAVAVGLLGTLFVGALKAVAPVLVLMLVMA 69

Query: 69  SIANHQHGQKTNIRPILFLYLLGTFSAALAAVVFSFAFPSTLHLSSSAGDISPPSGIVEV 128
           SIANHQ GQKT+IRPILFLYLLGTF+AAL AVVFSF FPSTLHL+++A  I+PPSGIVEV
Sbjct: 70  SIANHQQGQKTSIRPILFLYLLGTFAAALTAVVFSFIFPSTLHLNAAAESITPPSGIVEV 129

Query: 129 MRGLVMSMVSNPIDALLKGNYIGILVWAIGLGFALRHGNETTKNLVNDMSNAVTFMVKLV 188
           +RGL+MSMVSNPIDALL  NYIGILVWA+GLGFALRHGNETTKNL+ND+S+AVTF+VK+V
Sbjct: 130 LRGLLMSMVSNPIDALLNANYIGILVWAVGLGFALRHGNETTKNLINDVSHAVTFIVKVV 189

Query: 189 IRFAPIGIFGLVSSTLATTGFSTLWGYAQLLVVLVGCMLLVALVVNPLLVWWKIRRNPFP 248
           IRFAP+GIFGLV+STLATTGF TLWGYAQLL+VLVGCMLLVALV+NPLLV+WKIRRNP+P
Sbjct: 190 IRFAPLGIFGLVASTLATTGFETLWGYAQLLLVLVGCMLLVALVINPLLVFWKIRRNPYP 249

Query: 249 LVLLCLRESGVYAFFTRSSAANIPVNMALCEKLNLDRDTYSVSIPLGATINMAGAAITIT 308
           LVLLCLRESGVYAFFTRSSAANIPVNMAL EKLNLDRDTYSVSIPLGATINMAGAAITIT
Sbjct: 250 LVLLCLRESGVYAFFTRSSAANIPVNMALSEKLNLDRDTYSVSIPLGATINMAGAAITIT 309

Query: 309 VLTLAAVNTLGIPVDLPTALLLSVVASLCACGASGVAGGSLLLIPLACNMFGISNDIAMQ 368
           VLTLAAV+TL +PVDLPTALLLSVVASLCACGASGVAGGSLLLIPLACNMFGI ND+AMQ
Sbjct: 310 VLTLAAVHTLNVPVDLPTALLLSVVASLCACGASGVAGGSLLLIPLACNMFGIPNDVAMQ 369

Query: 369 VVAVGFIIGVLQDSCETALNSSTDVLFTAAACQAEDDRLANSALRN 414
           VVAVGFIIGVLQDSCETALNSSTDVLFTAAAC AED+++A +ALRN
Sbjct: 370 VVAVGFIIGVLQDSCETALNSSTDVLFTAAACIAEDEQIAKNALRN 415


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: 545
Number of extensions: 16
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: 415
Length adjustment: 31
Effective length of query: 383
Effective length of database: 384
Effective search space:   147072
Effective search space used:   147072
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.

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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