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 3608623 Dshi_2016 binding-protein-dependent transport systems inner membrane component (RefSeq)

Query= TCDB::Q8RJU8
         (307 letters)



>FitnessBrowser__Dino:3608623
          Length = 284

 Score =  140 bits (353), Expect = 3e-38
 Identities = 84/274 (30%), Positives = 141/274 (51%), Gaps = 7/274 (2%)

Query: 32  KKEGTVLNVFSHGILVLWAFMVVLPLLWAVMTSFKDDASIFGSPWSL-PDKLHFDNWSRA 90
           +K G  L +   G+++  AF +  P+  A + S      I   P  L P     +N++RA
Sbjct: 9   EKRGLGLWLTHLGLIIGVAF-IFFPIWLAFVASTVSQPEIVRPPMPLLPGDQLVENYTRA 67

Query: 91  WTEAHMGDYFL---NTVLVVGGSLIGTLVLGSMAAYVLARFDFPGNRFIYYLFIGGMSFP 147
            T        L   N++++  G  +G + +  ++A+ +  F FPG    ++L    +  P
Sbjct: 68  LTAGINAPVALMLGNSLIMALGIALGKIAISLLSAFAIVYFRFPGRMLFFWLIFLTLMLP 127

Query: 148 IMLALVPLFYVVNNMGLLNTLHGLILVYIAYSLPFTVFFLTAFFRTLPSSVAEAAFVDGA 207
           + + +VP + V+ N G+LN+  GLIL  +A +     F    FF T+P  +AEAA VDGA
Sbjct: 128 VEVRIVPTYEVIANFGMLNSYQGLILPLVASAT--ATFLFRQFFMTVPDELAEAARVDGA 185

Query: 208 SHTRTFFQIMLPMAKPGLISVGIFNFLGQWNQYMLPTVLNTDPDKRVLTQGLVQLAVSQG 267
              R FF I+LPM++  + ++ +  F+  WNQY+ P ++ TDP+   +  G+ Q+  S  
Sbjct: 186 RPMRFFFDILLPMSRTNIAALFVILFIYGWNQYLWPLLITTDPEMNTIVMGIKQMFPSGD 245

Query: 268 YKGDWSGLFAGLVMAMLPVLAAYIIFQRQVVQGL 301
              DW  + A  ++AM+P +   I  QR  V+GL
Sbjct: 246 DTADWPVIMATSILAMVPPVIVVITMQRLFVRGL 279


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: 285
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: 307
Length of database: 284
Length adjustment: 26
Effective length of query: 281
Effective length of database: 258
Effective search space:    72498
Effective search space used:    72498
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