GapMind for catabolism of small carbon sources

 

Alignments for a candidate for Dshi_0549 in Dyella japonica UNC79MFTsu3.2

Align ABC transporter for Xylitol, permease component 2 (characterized)
to candidate N515DRAFT_3133 N515DRAFT_3133 carbohydrate ABC transporter membrane protein 2, CUT1 family (TC 3.A.1.1.-)

Query= reanno::Dino:3607127
         (272 letters)



>FitnessBrowser__Dyella79:N515DRAFT_3133
          Length = 273

 Score =  135 bits (341), Expect = 7e-37
 Identities = 88/262 (33%), Positives = 141/262 (53%), Gaps = 4/262 (1%)

Query: 13  LLVLIITVCVFPFYWMVTTS-LKTQIVALEAPPVWIFEPTLSNYREALFEDGVLRTLINS 71
           LL+    V VFP  WM++ S ++    +   PP+     TL+NY E     G+ R L+NS
Sbjct: 13  LLIGSTLVAVFPLLWMLSVSFMRPGEASALPPPLLPTHATLANYHELFERAGMGRYLLNS 72

Query: 72  LIIAISTTFLALVLGVPAAFALARFEFRGKKDLWFWFITNRMISPIVLALPFFLIARNLG 131
           L ++ + T L+L   + A +A A+  F G++ L+   +   +I   V  LP FL+ + LG
Sbjct: 73  LGVSSAITLLSLAFNLMAGYAFAKLRFSGRERLFQVLLGGLVIPAQVAMLPLFLLLKYLG 132

Query: 132 LLDKHITLILIYLTFNLPIVIWIVTDQFRGIPYDLDEAARLEGASQFTIMRKICLPLAMP 191
           L++ +  +++  +     I  ++V    RGIP DL EAAR++GA +  I  +I LPL  P
Sbjct: 133 LVNSYAAVVVPAMATIFGI--FLVRQYARGIPDDLMEAARIDGAGELRIFVQIVLPLLKP 190

Query: 192 GVAVSAIFSFIFSWNELMFGLI-LTRSEAKTAPAMAVSFMEGYNLPYGKIMATSTLIVIP 250
            +   AIF+F+ +WN+ M+ LI LT  E  T P    S    +      +MA S + V+P
Sbjct: 191 IMVTLAIFTFLTAWNDFMWPLIALTGQEHYTLPIALASLSREHVQDSELMMAGSVVTVLP 250

Query: 251 VLIFALIASKQLVRGLTMGAVK 272
           VL+  L   +  ++GL +G+VK
Sbjct: 251 VLVLFLALQRYYLQGLLLGSVK 272


Lambda     K      H
   0.331    0.143    0.431 

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: 216
Number of extensions: 16
Number of successful extensions: 4
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: 272
Length of database: 273
Length adjustment: 25
Effective length of query: 247
Effective length of database: 248
Effective search space:    61256
Effective search space used:    61256
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.9 bits)
S2: 47 (22.7 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