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_007675527.1 BN137_RS07340 carbohydrate ABC transporter permease

Query= TCDB::Q8RJU8
         (307 letters)



>NCBI__GCF_000319285.1:WP_007675527.1
          Length = 280

 Score =  125 bits (313), Expect = 1e-33
 Identities = 79/273 (28%), Positives = 131/273 (47%), Gaps = 21/273 (7%)

Query: 46  LVLWAFMVVLPLLWAVMTSFKDDASIFGSPWSLPDKLHFDNWSRAWTEAHMGD------- 98
           L L+    +LP    +MTSFK               LH   + + WT AH  D       
Sbjct: 17  LALFLIATLLPFFVMLMTSFKSPKEAIS--------LHPTLFPQHWTLAHYLDIFNPIIF 68

Query: 99  ----YFLNTVLVVGGSLIGTLVLGSMAAYVLARFDFPGNRFIYYLFIGGMSFPIMLALVP 154
               YF N+++V   +    + +G + AY L++  F G   I   F     F  +L +VP
Sbjct: 69  PFVTYFRNSLVVSVIASGVAVFIGILGAYALSKLRFKGRMTINASFYAVYMFSGILLVVP 128

Query: 155 LFYVVNNMGLLNTLHGLILVYIAYSLPFTVFFLTAFFRTLPSSVAEAAFVDGASHTRTFF 214
           LF ++  +G+ +T   +I+  +  +LP  VF L ++F T+P  + EAA +DG +  +  F
Sbjct: 129 LFKIITALGIYDTQLAIIVTMVTQTLPTAVFMLKSYFDTIPDEIEEAAMMDGLNRLQIIF 188

Query: 215 QIMLPMAKPGLISVGIFNFLGQWNQYMLPTVLNTDPDKRVLTQGLVQLAVSQGYKGDWSG 274
           +I +P+A  GL+SV ++ F+  WN Y+  ++  +      L  GL  L  +  Y   W  
Sbjct: 189 RITVPLAVSGLVSVFVYCFMVAWNDYLFASIFLSSASNFTLPVGLNTLFSTPDY--IWGR 246

Query: 275 LFAGLVMAMLPVLAAYIIFQRQVVQGLTAGALK 307
           + A  ++  LPV+  Y + +R +  GLT G +K
Sbjct: 247 MMAASLVTALPVVVMYALSERFIKSGLTDGGVK 279



 Score = 23.1 bits (48), Expect = 0.008
 Identities = 11/21 (52%), Positives = 13/21 (61%)

Query: 170 GLILVYIAYSLPFTVFFLTAF 190
           GL L  IA  LPF V  +T+F
Sbjct: 16  GLALFLIATLLPFFVMLMTSF 36


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: 263
Number of extensions: 17
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: 2
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 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