GapMind for catabolism of small carbon sources

 

Alignments for a candidate for ngcG in Dinoroseobacter shibae DFL-12

Align NgcG, component of N-Acetylglucosamine/N,N'-diacetyl chitobiose porter (NgcK (C) not identified) (characterized)
to candidate 3607838 Dshi_1246 binding-protein-dependent transport systems inner membrane component (RefSeq)

Query= TCDB::Q8RJU8
         (307 letters)



>FitnessBrowser__Dino:3607838
          Length = 282

 Score =  150 bits (378), Expect = 4e-41
 Identities = 85/282 (30%), Positives = 147/282 (52%), Gaps = 4/282 (1%)

Query: 28  PQKEKKEGTVLNVFSHGILVLWAFMVVLPLLWAVMTSFKDDASIF-GSPWSLPDKLH-FD 85
           P+  +K      +   G++ L   + +LPL+   + S K       G+ W  P +   F+
Sbjct: 3   PRPIEKAPRAAQLTYQGMIPLALILWLLPLIAVAIFSVKPAGDFAAGNYWGWPAEFAGFE 62

Query: 86  NWSRAWTEAHMGDYFLNTVLVVGGSLIGTLVLGSMAAYVLARFDFPGNRFIYYLFIGGMS 145
           N++R +T++ M  Y LN+ ++   ++IG + L  M  + L  + F GN  I+++FI G  
Sbjct: 63  NYARVFTDSEMPRYILNSFMITIPTVIGAVALSCMTGFALGIYRFRGNLLIFFMFIAGNF 122

Query: 146 FPIMLALVPLFYVVNNMGLLNTLHGLILVYIAYSLPFTVFFLTAFFRTLPSSVAEAAFVD 205
            P  + +VP+  +  +MGL NT  GL+L +IA+   F   F+  F R LP  + EAA V+
Sbjct: 123 VPFQILMVPVRDLTVDMGLYNTKTGLVLFHIAFQTGFCTLFMRNFIRALPYELIEAARVE 182

Query: 206 GASHTRTFFQIMLPMAKPGLISVGIFNFLGQWNQYMLPTVLNTDPDKRVLTQGLVQLAVS 265
           G +  R F+ ++LP+ KP + ++ +  F   WN Y    VL   P+ + +T G+      
Sbjct: 183 GVAEWRIFWFVVLPLMKPAIAALSVLIFTFIWNDYFWAVVLTQGPNAQPVTAGITSFNAQ 242

Query: 266 QGYKGDWSGLFAGLVMAMLPVLAAYIIFQRQVVQGLTAGALK 307
            G    ++ L AG ++A LP +  + + Q+  + GLT GA+K
Sbjct: 243 FGIA--YNMLSAGSLIAALPPVMMFFLMQKHFIAGLTLGAVK 282


Lambda     K      H
   0.326    0.141    0.440 

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: 264
Number of extensions: 12
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: 307
Length of database: 282
Length adjustment: 26
Effective length of query: 281
Effective length of database: 256
Effective search space:    71936
Effective search space used:    71936
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: 48 (23.1 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