GapMind for catabolism of small carbon sources

 

Alignments for a candidate for mtlG in Cronobacter condimenti 1330

Align SmoG, component of Hexitol (glucitol; mannitol) porter (characterized)
to candidate WP_007675527.1 BN137_RS07340 carbohydrate ABC transporter permease

Query= TCDB::O30833
         (276 letters)



>NCBI__GCF_000319285.1:WP_007675527.1
          Length = 280

 Score =  115 bits (287), Expect = 1e-30
 Identities = 80/266 (30%), Positives = 139/266 (52%), Gaps = 7/266 (2%)

Query: 15  LAAWTIAFLI-FFPILWTVLMSFKSEGDAIKAPFAMLFSDWTLQSYADVQERS--NYARH 71
           LA + IA L+ FF +L T   SFKS  +AI     +    WTL  Y D+       +  +
Sbjct: 17  LALFLIATLLPFFVMLMT---SFKSPKEAISLHPTLFPQHWTLAHYLDIFNPIIFPFVTY 73

Query: 72  FMNSVVISLGSTLVALAIAIPAAWAMAFVPGRRTKDVLMWMLSTKMMPAVGVLIPLYLIF 131
           F NS+V+S+ ++ VA+ I I  A+A++ +  +    +     +  M   + +++PL+ I 
Sbjct: 74  FRNSLVVSVIASGVAVFIGILGAYALSKLRFKGRMTINASFYAVYMFSGILLVVPLFKII 133

Query: 132 RDTGLLDTRIGLVIVLTLINLPIVVWMLYTYFKEIPGEILEAARMDGATLGSEILYILTP 191
              G+ DT++ +++ +    LP  V+ML +YF  IP EI EAA MDG      I  I  P
Sbjct: 134 TALGIYDTQLAIIVTMVTQTLPTAVFMLKSYFDTIPDEIEEAAMMDGLNRLQIIFRITVP 193

Query: 192 MAVPGIASTLLLNVILAWNE-AFWTLQLTTSRAAPLTQFIASYSSPEGLFYAKLSAASTM 250
           +AV G+ S  +   ++AWN+  F ++ L+++    L   + +  S     + ++ AAS +
Sbjct: 194 LAVSGLVSVFVYCFMVAWNDYLFASIFLSSASNFTLPVGLNTLFSTPDYIWGRMMAASLV 253

Query: 251 AIAPILILGWFSQKQLVRGLTFGAVK 276
              P++++   S++ +  GLT G VK
Sbjct: 254 TALPVVVMYALSERFIKSGLTDGGVK 279


Lambda     K      H
   0.327    0.137    0.416 

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: 173
Number of extensions: 9
Number of successful extensions: 4
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: 276
Length of database: 280
Length adjustment: 25
Effective length of query: 251
Effective length of database: 255
Effective search space:    64005
Effective search space used:    64005
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 (21.7 bits)
S2: 47 (22.7 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