GapMind for catabolism of small carbon sources

 

Alignments for a candidate for SLC2A2 in Lactobacillus silagei IWT126

Align Solute carrier family 2, facilitated glucose transporter member 2; Glucose transporter type 2, liver; GLUT-2 (characterized)
to candidate WP_054656487.1 CES79_RS12280 sugar porter family MFS transporter

Query= SwissProt::P11168
         (524 letters)



>NCBI__GCF_002217945.1:WP_054656487.1
          Length = 455

 Score =  177 bits (448), Expect = 1e-48
 Identities = 131/407 (32%), Positives = 204/407 (50%), Gaps = 18/407 (4%)

Query: 102 SSFAVGGMTASFFGGWLGDTLGRIKAMLVANILSLVGALLMGFSKLGPSHILIIAGRSIS 161
           S+   G +      G L D LGR K +L++ ++  V +LL G +    S  LII  R   
Sbjct: 54  SAVMFGAIFGGALAGQLSDRLGRRKMILISAVIFAVFSLLSGIAPNDGSIYLIIV-RIFL 112

Query: 162 GLYCGLISGLVPMYIGEIAPTALRGALGTFHQLAIVTGILISQIIGLEFILGNYDL---W 218
           GL  G  S LVP Y+ E+AP  LRG L   +Q  IV+G+LIS I  ++F+L        W
Sbjct: 113 GLAVGAASALVPPYMSELAPARLRGRLSGLNQTMIVSGMLISYI--MDFVLKGLPTGWGW 170

Query: 219 HILLGLSGVRAILQSLLLFFCPESPRYLYIKLDEEVKAKQSLKRLR-GYDDVTKDINEMR 277
            ++L  + V AI+    +   PESPR+L +K  +E  AK+ L  +R   D++  ++ +++
Sbjct: 171 RVMLAFAAVPAIILFFGVLRLPESPRFL-VKHGDEEAAKRVLSYVRDSQDEIDGELKDIK 229

Query: 278 KEREEASSEQKVSIIQLFTNSSYRQPILVALMLHVAQQFSGINGIFYYSTSIFQTA---G 334
           K   + ++  K +         YR  ++  + +   QQF G N IFYY   I + A    
Sbjct: 230 KTASQETAASKSTHYSTLFTGKYRYLVIAGVGVAAFQQFQGANAIFYYIPLIVEKATGSA 289

Query: 335 ISKPVYATIGVGAVNMVFTAVSVFLVEKAGRRSLFLIGMSGMFVCAIFMSVGLVLLNKFS 394
            S  +   I  G + ++ + + + + EK  RR+L ++G S M   + F+     ++NK  
Sbjct: 290 ASNALMWPIIQGVILVLGSLLYMAIAEKFKRRTLIMMGGSVM-ALSFFLP---AIINKMD 345

Query: 395 WMSYVSMIAIFL--FVSFFEIGPGPIPWFMVAEFFSQGPRPAALAIAAFSNWTCNFIVAL 452
             +   MI +FL  +V+F+     P+ W +V E F    R  A  +A+  NW  +F V L
Sbjct: 346 PNANPMMIVVFLSIYVAFYSFTWAPLTWVIVGEMFPLAIRGKAAGLASSFNWIGSFAVGL 405

Query: 453 CFQYI-ADFCGPYVFFLFAGVLLAFTLFTFFKVPETKGKSFEEIAAE 498
            F  + A      VF +F  + +   LFT F VPETKGK+ EEI AE
Sbjct: 406 LFPIMTAAMSQEAVFAIFGAICVLGVLFTHFFVPETKGKTLEEIEAE 452


Lambda     K      H
   0.326    0.140    0.418 

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: 582
Number of extensions: 39
Number of successful extensions: 7
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 1
Length of query: 524
Length of database: 455
Length adjustment: 34
Effective length of query: 490
Effective length of database: 421
Effective search space:   206290
Effective search space used:   206290
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.7 bits)
S2: 52 (24.6 bits)

This GapMind analysis is from Sep 24 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