GapMind for catabolism of small carbon sources

 

Alignments for a candidate for sstT in Pseudomonas stutzeri RCH2

Align Serine/threonine transporter SstT; Na(+)/serine-threonine symporter (characterized)
to candidate GFF2430 Psest_2478 Na+/serine symporter

Query= SwissProt::P0AGE4
         (414 letters)



>FitnessBrowser__psRCH2:GFF2430
          Length = 408

 Score =  534 bits (1376), Expect = e-156
 Identities = 271/399 (67%), Positives = 331/399 (82%)

Query: 7   PGLFRRLAHGSLVKQILVGLVLGILLAWISKPAAEAVGLLGTLFVGALKAVAPILVLMLV 66
           P + R ++  SLV QI+VGLV G LLA     AA++V LLG LFV ALKAVAPILV +LV
Sbjct: 5   PRVIRFISRTSLVAQIVVGLVAGALLALFLPAAAKSVALLGDLFVQALKAVAPILVFVLV 64

Query: 67  MASIANHQHGQKTNIRPILFLYLLGTFSAALAAVVFSFAFPSTLHLSSSAGDISPPSGIV 126
            +S+ANH+ GQ T+IRPI+ LY LGT SA+  AV+ SF FP+TL L S A D++PPSG+ 
Sbjct: 65  TSSLANHKRGQPTHIRPIILLYALGTLSASAVAVLASFMFPTTLTLVSGAADVTPPSGVG 124

Query: 127 EVMRGLVMSMVSNPIDALLKGNYIGILVWAIGLGFALRHGNETTKNLVNDMSNAVTFMVK 186
            V++ L+ ++  NP+ ALL GN+IGIL WAIGLGFA RH  ++T+ L+ D+S+ VT +VK
Sbjct: 125 AVLQTLLFNVADNPVRALLNGNFIGILAWAIGLGFAFRHAQDSTRRLIGDLSDGVTLIVK 184

Query: 187 LVIRFAPIGIFGLVSSTLATTGFSTLWGYAQLLVVLVGCMLLVALVVNPLLVWWKIRRNP 246
           +VIRFAP+G+FGLV+ TLA +GF  L GY +LL+VLVG ML +ALV+NPL+V+W+IRRNP
Sbjct: 185 VVIRFAPLGVFGLVAGTLADSGFDVLLGYLRLLLVLVGAMLFMALVMNPLIVFWQIRRNP 244

Query: 247 FPLVLLCLRESGVYAFFTRSSAANIPVNMALCEKLNLDRDTYSVSIPLGATINMAGAAIT 306
           +PLV  CLRESG+ AFFTRSSAANIPVNM LC++L L +DTYSVSIPLGATINM GAAIT
Sbjct: 245 YPLVFTCLRESGITAFFTRSSAANIPVNMQLCQRLGLHKDTYSVSIPLGATINMGGAAIT 304

Query: 307 ITVLTLAAVNTLGIPVDLPTALLLSVVASLCACGASGVAGGSLLLIPLACNMFGISNDIA 366
           ITVLTLAAVNTLGI VD+ TA+LLS++A++CACGASGVAGGSLLLIPLAC++FGISND+A
Sbjct: 305 ITVLTLAAVNTLGIQVDIATAVLLSLLAAVCACGASGVAGGSLLLIPLACSLFGISNDLA 364

Query: 367 MQVVAVGFIIGVLQDSCETALNSSTDVLFTAAACQAEDD 405
           MQVVAVGFIIGV+QDS ETALNSSTDVLFTAA+C A  D
Sbjct: 365 MQVVAVGFIIGVVQDSAETALNSSTDVLFTAASCIAHGD 403


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: 434
Number of extensions: 13
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: 408
Length adjustment: 31
Effective length of query: 383
Effective length of database: 377
Effective search space:   144391
Effective search space used:   144391
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