GapMind for catabolism of small carbon sources

 

Alignments for a candidate for ngcG in Stenotrophomonas chelatiphaga DSM 21508

Align NgcG, component of N-Acetylglucosamine/N,N'-diacetyl chitobiose porter (NgcK (C) not identified) (characterized)
to candidate WP_042615044.1 ABB28_RS00970 carbohydrate ABC transporter permease

Query= TCDB::Q8RJU8
         (307 letters)



>NCBI__GCF_001431535.1:WP_042615044.1
          Length = 278

 Score =  162 bits (411), Expect = 6e-45
 Identities = 93/266 (34%), Positives = 153/266 (57%), Gaps = 8/266 (3%)

Query: 44  GILVLWAFMVVLPLLWAVMTSFKD--DASIFGSPWSLPDKLHFDNWSRAWTEAHMGDYFL 101
           G+LVL A + + PLLW V  S     +A+ F  P + P  + F N+   +    MG  F 
Sbjct: 18  GLLVL-ALVSLAPLLWMVSVSVMPAGEATTFPPPLT-PSHVTFANYHELFARTGMGVNFA 75

Query: 102 NTVLVVGGSLIGTLVLGSMAAYVLARFDFPGNRFIYYLFIGGMSFPIMLALVPLFYVVNN 161
           N++LV     +G+L+L +MA Y  A+  F G   ++ + +  +  P  +A++PLF ++  
Sbjct: 76  NSLLVSVAITLGSLLLNTMAGYAFAKLRFVGRDRLFQVLMAALVIPAQVAMLPLFLLMKQ 135

Query: 162 MGLLNTLHGLILVYIAYSLPFTVFFLTAFFRTLPSSVAEAAFVDGASHTRTFFQIMLPMA 221
           +GL+N+  G+I+  +A    F +F +  + R++P  + EAA +DGA   R FFQI+LPM 
Sbjct: 136 LGLVNSFGGVIVPALA--TVFGIFLVRQYARSIPDELLEAARMDGAGEMRIFFQIVLPML 193

Query: 222 KPGLISVGIFNFLGQWNQYMLPTVLNTDPDKRVLTQGLVQLAVSQGYKGDWSGLFAGLVM 281
           KP L+++ IF F+G WN +M P ++ TD +   L   L  L  S+ +  D   + AG V+
Sbjct: 194 KPVLVTLSIFTFMGAWNDFMWPLIVLTDQEHYTLPVALATL--SREHIMDVEMMMAGAVV 251

Query: 282 AMLPVLAAYIIFQRQVVQGLTAGALK 307
            ++PVLA +++ QR  +QGL  G++K
Sbjct: 252 TVIPVLALFLLLQRYYIQGLMLGSVK 277


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: 261
Number of extensions: 14
Number of successful extensions: 4
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 1
Length of query: 307
Length of database: 278
Length adjustment: 26
Effective length of query: 281
Effective length of database: 252
Effective search space:    70812
Effective search space used:    70812
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.

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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