GapMind for catabolism of small carbon sources

 

Alignments for a candidate for BPHYT_RS34240 in Dyella japonica UNC79MFTsu3.2

Align Monosaccharide-transporting ATPase; EC 3.6.3.17; Flags: Precursor (characterized, see rationale)
to candidate N515DRAFT_2414 N515DRAFT_2414 simple sugar transport system permease protein

Query= uniprot:B2T9V8
         (351 letters)



>FitnessBrowser__Dyella79:N515DRAFT_2414
          Length = 358

 Score =  137 bits (344), Expect = 6e-37
 Identities = 104/331 (31%), Positives = 162/331 (48%), Gaps = 17/331 (5%)

Query: 22  ALPASRGKRARSELARLRELALLPALALLIVIGAFISPSFLTK--------ANLISVLGA 73
           A+ +  G+  R  LA      LL  + LL   G F +P FL           NLI +   
Sbjct: 13  AISSRWGRGLRRCLAHPLLWPLLTLILLLAGNGLF-NPGFLALQWRDGHLYGNLIDIAHR 71

Query: 74  SAALALVVLAESLIVLTGKFDLSLESTVGIAPAVGAMLVMPAASAGFGMQWPAAAGLLAI 133
           +A LALV L  +L++     D+S+ + + IA  V A  +   ++ G    W A A  LA 
Sbjct: 72  AAPLALVSLGMTLVIALRGLDISVGAVLAIAATVAAWTIGHVSNDGLLPLWLAIAAALA- 130

Query: 134 VVVGAVIGFINGFLVVRLRLNAFIVTLAMLIVLRGMLVGATKGG--TLFDMPTSFFALAT 191
              GA+ G  NG+LVV   +   + TL +++  RG+    + G   TL+  P SF  L  
Sbjct: 131 --AGALCGLWNGWLVVGAGMQPIVATLILMVAGRGIAQSISGGQILTLYYAPYSF--LGN 186

Query: 192 TIVLGLPLSVWLAAAAFAIAAFMLRYHRLGRALYAIGGNPEAARAAGIRVERITWGVFVL 251
             VLGLP S+++ AA FA+    LR   LG  + AIG NP+AA  AG+R   IT G +V 
Sbjct: 187 GFVLGLPFSLFVVAAVFALLQLALRKTALGLFVRAIGHNPQAAHVAGVRARAITLGAYVF 246

Query: 252 GSILASVGGLIVTGYVGAINANQGNGMI-FTVFAAAVIGGISLDGGKGTMFGALTGVLLL 310
             I A++ GL+V+  V + +AN    ++      A  +GG  L GG+ ++ G+L G L++
Sbjct: 247 CGIAAALAGLLVSSNVNSADANNAGLLLELDAILAVALGGSLLGGGRFSLAGSLLGALII 306

Query: 311 GVVQNLLTLAQVPSFWIQAIYGAIILGSLMV 341
             +   +    VP     A+   ++   +++
Sbjct: 307 QALTTTIYAIGVPPQVNLAVKAVLVFAVMLL 337


Lambda     K      H
   0.326    0.140    0.397 

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: 273
Number of extensions: 15
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: 351
Length of database: 358
Length adjustment: 29
Effective length of query: 322
Effective length of database: 329
Effective search space:   105938
Effective search space used:   105938
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 (21.6 bits)
S2: 49 (23.5 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