GapMind for catabolism of small carbon sources

 

Alignments for a candidate for sstT in Shewanella amazonensis SB2B

Align Serine/threonine transporter SstT; Na(+)/serine-threonine symporter (characterized)
to candidate 6938067 Sama_2200 serine/threonine transporter SstT (RefSeq)

Query= SwissProt::P0AGE4
         (414 letters)



>FitnessBrowser__SB2B:6938067
          Length = 405

 Score =  520 bits (1339), Expect = e-152
 Identities = 270/404 (66%), Positives = 328/404 (81%), Gaps = 2/404 (0%)

Query: 1   MTTQRSPGLFRRLAHGSLVKQILVGLVLGILLAWISKPAAEAVGLLGTLFVGALKAVAPI 60
           M+T++S  L    A GSLV QI VG++ G+ LA  S  AA  V  LG LFVGALKA+AP+
Sbjct: 1   MSTEKS--LLANAAGGSLVLQIFVGIIAGVALAGFSPEAANQVAFLGDLFVGALKAIAPV 58

Query: 61  LVLMLVMASIANHQHGQKTNIRPILFLYLLGTFSAALAAVVFSFAFPSTLHLSSSAGDIS 120
           LV +LV +SIAN   G +TN+RPI+ LYL+GTF+AAL AV+ SFAFP++L L  +A   +
Sbjct: 59  LVFVLVASSIANQVSGAQTNMRPIILLYLVGTFAAALTAVLMSFAFPTSLVLIDAAAGAN 118

Query: 121 PPSGIVEVMRGLVMSMVSNPIDALLKGNYIGILVWAIGLGFALRHGNETTKNLVNDMSNA 180
           PP GI +V+  L+  +V NP++AL+  NYIG+L W +GLG ALRH + +TKN+++D+S+ 
Sbjct: 119 PPEGIGQVLNTLLFKLVDNPVNALINANYIGLLAWGVGLGIALRHASTSTKNMLHDVSHG 178

Query: 181 VTFMVKLVIRFAPIGIFGLVSSTLATTGFSTLWGYAQLLVVLVGCMLLVALVVNPLLVWW 240
           V+ +V+ VI  APIGIFGLV++T+A TGF  L  YAQLL VL+G M ++A VVNPL+V+ 
Sbjct: 179 VSQLVRFVICLAPIGIFGLVAATIAQTGFEALAAYAQLLGVLLGAMAVIAFVVNPLIVFL 238

Query: 241 KIRRNPFPLVLLCLRESGVYAFFTRSSAANIPVNMALCEKLNLDRDTYSVSIPLGATINM 300
           KIRRNP+PLV  CLRESGV AFFTRSSAANIPVNMALCE+L L  DTYSVSIPLGATINM
Sbjct: 239 KIRRNPYPLVFKCLRESGVTAFFTRSSAANIPVNMALCERLKLHEDTYSVSIPLGATINM 298

Query: 301 AGAAITITVLTLAAVNTLGIPVDLPTALLLSVVASLCACGASGVAGGSLLLIPLACNMFG 360
           AGAAITITVLTLAAV+TLGI VDL TALLLSV+A++ ACGASGVAGGSLLLIPLAC++FG
Sbjct: 299 AGAAITITVLTLAAVHTLGIEVDLATALLLSVIAAVSACGASGVAGGSLLLIPLACSLFG 358

Query: 361 ISNDIAMQVVAVGFIIGVLQDSCETALNSSTDVLFTAAACQAED 404
           ISNDIAMQVVAVGF IGV+QDS ETALNSSTDVLFTAAAC+A +
Sbjct: 359 ISNDIAMQVVAVGFTIGVIQDSAETALNSSTDVLFTAAACEAAE 402


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: 451
Number of extensions: 17
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: 405
Length adjustment: 31
Effective length of query: 383
Effective length of database: 374
Effective search space:   143242
Effective search space used:   143242
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