Alignments for a candidate for sstT in Shewanella sp. ANA-3

GapMind for catabolism of small carbon sources

Alignments for a candidate for sstT in Shewanella sp. ANA-3

Align Serine/threonine transporter SstT; Na(+)/serine-threonine symporter (characterized)
to candidate 7024234 Shewana3_1426 serine/threonine transporter SstT (RefSeq)

Query= SwissProt::P0AGE4
         (414 letters)



>FitnessBrowser__ANA3:7024234
          Length = 408

 Score =  520 bits (1338), Expect = e-152
 Identities = 265/403 (65%), Positives = 328/403 (81%)

Query: 4   QRSPGLFRRLAHGSLVKQILVGLVLGILLAWISKPAAEAVGLLGTLFVGALKAVAPILVL 63
           ++   L  +LA+GSLV QILVG++ G+ LA  S  AA+ V  LG+LFVGALKA+APILV 
Sbjct: 2   KQESSLLAKLANGSLVLQILVGIIAGVSLASFSHEAAKQVAFLGSLFVGALKAIAPILVF 61

Query: 64  MLVMASIANHQHGQKTNIRPILFLYLLGTFSAALAAVVFSFAFPSTLHLSSSAGDISPPS 123
           +LV +SIAN +   +TN+RPI+ LYL GTF+AAL AVV S  FP+ L L +     SPP 
Sbjct: 62  ILVASSIANQKKNTQTNMRPIVVLYLFGTFAAALTAVVLSMMFPTNLVLVAGVEGTSPPQ 121

Query: 124 GIVEVMRGLVMSMVSNPIDALLKGNYIGILVWAIGLGFALRHGNETTKNLVNDMSNAVTF 183
           GI EV+  L+  +V NP++AL+ GNYIGIL W +GLG AL H +++TK +  D+S+ ++ 
Sbjct: 122 GIGEVINTLLFKLVDNPVNALMTGNYIGILAWGVGLGLALHHASDSTKQVFADVSHGISQ 181

Query: 184 MVKLVIRFAPIGIFGLVSSTLATTGFSTLWGYAQLLVVLVGCMLLVALVVNPLLVWWKIR 243
           MV+ +IR APIGIFGLV++T A TGF+ + GYA+LL VL+G M ++AL+VNPL+V+ KI+
Sbjct: 182 MVRFIIRLAPIGIFGLVAATFAETGFAAIAGYAKLLAVLLGAMAIIALIVNPLIVYVKIK 241

Query: 244 RNPFPLVLLCLRESGVYAFFTRSSAANIPVNMALCEKLNLDRDTYSVSIPLGATINMAGA 303
           RNP+PLV+ CLRESGV AFFTRSSAANIPVNMALCEKL L  DTYSVSIPLGATINM GA
Sbjct: 242 RNPYPLVIRCLRESGVTAFFTRSSAANIPVNMALCEKLKLHEDTYSVSIPLGATINMGGA 301

Query: 304 AITITVLTLAAVNTLGIPVDLPTALLLSVVASLCACGASGVAGGSLLLIPLACNMFGISN 363
           AITITVLTLAA +TLGI VDL TALLLSVVA++ ACGASGVAGGSLLLIPLAC++FGISN
Sbjct: 302 AITITVLTLAAAHTLGIQVDLLTALLLSVVAAISACGASGVAGGSLLLIPLACSLFGISN 361

Query: 364 DIAMQVVAVGFIIGVLQDSCETALNSSTDVLFTAAACQAEDDR 406
           D+AMQVVAVGFIIGV+QD+ ETALNSSTDV+FTAAAC+A +++
Sbjct: 362 DVAMQVVAVGFIIGVIQDAAETALNSSTDVIFTAAACEAAENK 404


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: 435
Number of extensions: 14
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:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

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:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

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:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

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

GapMind for catabolism of small carbon sources