GapMind for catabolism of small carbon sources

 

Alignments for a candidate for ngcG in Cronobacter condimenti 1330

Align NgcG, component of N-Acetylglucosamine/N,N'-diacetyl chitobiose porter (NgcK (C) not identified) (characterized)
to candidate WP_007665545.1 BN137_RS16135 carbohydrate ABC transporter permease

Query= TCDB::Q8RJU8
         (307 letters)



>NCBI__GCF_000319285.1:WP_007665545.1
          Length = 281

 Score =  154 bits (388), Expect = 3e-42
 Identities = 80/254 (31%), Positives = 138/254 (54%), Gaps = 1/254 (0%)

Query: 54  VLPLLWAVMTSFKDDASIFGSPWSLPDKLHFDNWSRAWTEAHMGDYFLNTVLVVGGSLIG 113
           V P  +A+++S ++   +F +P   P   H+DN+  A  +  +    LN+VLV   ++  
Sbjct: 28  VFPFYYAIISSLREGQELF-TPAYFPTGWHWDNYVVALVDNGIARSLLNSVLVAAVTVGL 86

Query: 114 TLVLGSMAAYVLARFDFPGNRFIYYLFIGGMSFPIMLALVPLFYVVNNMGLLNTLHGLIL 173
            L +   AA+ LAR  F G R + +  +    FP +  L  +F +V  +GL ++L  L++
Sbjct: 87  CLFVSVTAAFALARVPFRGRRVLLFTILCVSMFPQVAVLTGMFELVRFLGLYDSLGALVI 146

Query: 174 VYIAYSLPFTVFFLTAFFRTLPSSVAEAAFVDGASHTRTFFQIMLPMAKPGLISVGIFNF 233
            Y  +SLPFTV+ LT F +++P  + EAA VDGA       +I  P+  P +++ G+  F
Sbjct: 147 SYTTFSLPFTVWVLTTFMKSIPVELEEAAIVDGAKTGTIIRRIFAPVLAPAMVTTGLLAF 206

Query: 234 LGQWNQYMLPTVLNTDPDKRVLTQGLVQLAVSQGYKGDWSGLFAGLVMAMLPVLAAYIIF 293
           +G WN++M         DKR +   +   + +  Y+  W  + A  V+  LP++   +IF
Sbjct: 207 IGAWNEFMFALTFIISGDKRTVPVAISLFSGASSYELPWGSIMAASVVVTLPIIVLVLIF 266

Query: 294 QRQVVQGLTAGALK 307
           Q+++V GLT+GA+K
Sbjct: 267 QKRIVSGLTSGAIK 280


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: 248
Number of extensions: 9
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: 281
Length adjustment: 26
Effective length of query: 281
Effective length of database: 255
Effective search space:    71655
Effective search space used:    71655
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 24 2021. The underlying query database was built on Sep 17 2021.

Links

Downloads

Related tools

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