GapMind for catabolism of small carbon sources

 

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

Align Sodium:dicarboxylate symporter (characterized, see rationale)
to candidate 7023412 Shewana3_0642 sodium:dicarboxylate symporter (RefSeq)

Query= uniprot:A1S570
         (437 letters)



>FitnessBrowser__ANA3:7023412
          Length = 416

 Score =  318 bits (816), Expect = 2e-91
 Identities = 163/401 (40%), Positives = 250/401 (62%), Gaps = 3/401 (0%)

Query: 11  LTGKILIGMGAGILIGLLLRNFFGGSEWVQDYITEGFFHVIGTIFINSLKMLVVPLVFIS 70
           L+ +I IG+ AG+++G L++ F     +    + E     +GT+F+N + MLVVPLVF+S
Sbjct: 5   LSTRIFIGLFAGLILGTLVQYFLNDIGFFSGNLVE-LAGGVGTMFVNMIMMLVVPLVFVS 63

Query: 71  LVCGTCSLSEPSKLGRLGGKTLAFYLFTTAIALVVAISAAVLVQPGNA--SLASESMQYS 128
           +VCG C L +    GRLGGKT  FY+  T +A+  A+   +L+ PG      +++ +  +
Sbjct: 64  IVCGVCELQDLKSFGRLGGKTFGFYIVNTLVAISTALLVVLLLDPGKGVDMSSTDGVAIT 123

Query: 129 AKEAPSLADVLINIVPSNPMKALSEGNMLQIIIFAVIFGFAISHIGERGRRVAALFDDLN 188
           A E PSL  +LI+IVP NP+ A   GNMLQ+I  A++ G  I  +GE        F   N
Sbjct: 124 ATELPSLMALLIDIVPRNPVAAFMSGNMLQVIFMALMLGGVIKSLGEHVAGAVQGFQTAN 183

Query: 189 EVIMRVVTLIMQLAPYGVFALMGKLALTLGMETLESVIKYFMLVLVVLLFHGFVVYPTLL 248
           +++M++++++M LAPYGVFALM KL  TL      SV++Y +++L +LL   FVVYP  +
Sbjct: 184 KIMMKLISVVMSLAPYGVFALMFKLGATLDAAVFISVLEYVVIILALLLLWIFVVYPLAV 243

Query: 249 KLFSGLSPLMFIRKMRDVQLFAFSTASSNATLPVTMEASEHRLGADNKVASFTLPLGATI 308
             F+ +S   F  K ++  LF+ STASSNAT+PVTM     +LG +  VA F +PLGAT+
Sbjct: 244 GFFTPISAKSFREKTQEQVLFSLSTASSNATIPVTMRTLTEKLGVNRAVAGFGVPLGATM 303

Query: 309 NMDGTAIMQGVATVFIAQVFGIDLTITDYAMVVMTATLASIGTAGVPGVGLVMLAMVLNQ 368
           NM G AI   +A  F+A  FG+ +T      ++ +  L S+G  GVPG G+VM+ ++++Q
Sbjct: 304 NMGGVAIYITIAIFFVANAFGMPITSEQLPSLLFSIFLLSVGAGGVPGGGMVMIGVLIHQ 363

Query: 369 VGLPVEGIALILGVDRMLDMVRTAVNVTGDTVATVVIAKSE 409
           +GLP+E  A++  +DR++DMV T+ NV GDT    ++ ++E
Sbjct: 364 MGLPIEAFAIVAALDRIIDMVLTSCNVVGDTAVLTIVDQTE 404


Lambda     K      H
   0.325    0.139    0.388 

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: 407
Number of extensions: 18
Number of successful extensions: 2
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: 437
Length of database: 416
Length adjustment: 32
Effective length of query: 405
Effective length of database: 384
Effective search space:   155520
Effective search space used:   155520
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: 51 (24.3 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