GapMind for catabolism of small carbon sources

 

Aligments 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)



>lcl|FitnessBrowser__Koxy:BWI76_RS24715 BWI76_RS24715
           serine/threonine transporter SstT
          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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 on GapMind for carbon sources, or view the source code.

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