GapMind for catabolism of small carbon sources

 

Alignments for a candidate for ngcG in Pseudomonas fluorescens FW300-N2C3

Align NgcG, component of N-Acetylglucosamine/N,N'-diacetyl chitobiose porter (NgcK (C) not identified) (characterized)
to candidate AO356_28580 AO356_28580 sugar ABC transporter permease

Query= TCDB::Q8RJU8
         (307 letters)



>FitnessBrowser__pseudo5_N2C3_1:AO356_28580
          Length = 280

 Score =  145 bits (365), Expect = 1e-39
 Identities = 85/263 (32%), Positives = 140/263 (53%), Gaps = 4/263 (1%)

Query: 45  ILVLWAFMVVLPLLWAVMTSFKDDASIFGSPWSLPDKLHFDNWSRAWTEAHMGDYFLNTV 104
           IL+++A   V P  +A++TS K  +++F   + + D+  F N++    +A       N++
Sbjct: 21  ILLVYA---VFPFYYAIVTSLKPSSALFQVSYWI-DQPDFSNYAAVLNQASFLRAIGNSL 76

Query: 105 LVVGGSLIGTLVLGSMAAYVLARFDFPGNRFIYYLFIGGMSFPIMLALVPLFYVVNNMGL 164
           +V    +   L L   AAY L R  F G   +  + +G   FP +  L  LF V+  +GL
Sbjct: 77  VVALCVVALALFLSLTAAYALGRVKFRGRGPVLMMVLGVSMFPQVAVLSGLFEVIRALGL 136

Query: 165 LNTLHGLILVYIAYSLPFTVFFLTAFFRTLPSSVAEAAFVDGASHTRTFFQIMLPMAKPG 224
            NT   LIL Y  ++LPFTV+ LT F   LP  + EAA +DGAS   T  +++LP+  P 
Sbjct: 137 YNTSWALILSYTIFTLPFTVWVLTTFMGQLPHELEEAAIMDGASPWVTLTRVLLPLLWPA 196

Query: 225 LISVGIFNFLGQWNQYMLPTVLNTDPDKRVLTQGLVQLAVSQGYKGDWSGLFAGLVMAML 284
           L++ G+  F+  WN+++          +R +   +  ++    ++  W  L A  V+  +
Sbjct: 197 LVTTGLLAFIAAWNEFLFALTFTLTDSQRTVPVAIALISGGSPHELPWGLLMAASVLVTV 256

Query: 285 PVLAAYIIFQRQVVQGLTAGALK 307
           P++   +IFQR++V GLTAGALK
Sbjct: 257 PLVILVLIFQRRIVSGLTAGALK 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: 256
Number of extensions: 17
Number of successful extensions: 1
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: 280
Length adjustment: 26
Effective length of query: 281
Effective length of database: 254
Effective search space:    71374
Effective search space used:    71374
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