GapMind for catabolism of small carbon sources

 

Alignments for a candidate for SMc02869 in Sphingomonas koreensis DSMZ 15582

Align N-Acetyl-D-glucosamine ABC transport system, ATPase component (characterized)
to candidate Ga0059261_0341 Ga0059261_0341 ABC-type antimicrobial peptide transport system, ATPase component

Query= reanno::Smeli:SMc02869
         (352 letters)



>FitnessBrowser__Korea:Ga0059261_0341
          Length = 224

 Score =  117 bits (292), Expect = 4e-31
 Identities = 78/216 (36%), Positives = 113/216 (52%), Gaps = 13/216 (6%)

Query: 23  KTIRKAFGSHEVLKGIDLDVKDGEFVIFVGPSGCGKSTLLRTIAGLEDATSGSVQIDGVE 82
           +T  +      VL+GIDL V  GE V  +GPSG GKSTLL+ +  LE    GS++I GVE
Sbjct: 13  RTFSQGGADIHVLRGIDLTVGQGEIVALLGPSGSGKSTLLQAVGLLEGGFEGSIRISGVE 72

Query: 83  VGHVAPAKRGI------AMVFQSYALYPHLTVKDNMGLGLKQAGVPKAEIEEKVAKAAGM 136
           VG +    R +        V+Q + L P     +N+ L      +  A + +  A++ G+
Sbjct: 73  VGKLESHARTVTRRDKLGFVYQFHHLLPDFNALENVEL---PQLIQNATLADARARSEGL 129

Query: 137 LS---LEPYLARRPAELSGGQRQRVAIGRAIVREPKLFLFDEPLSNLDAALRVNTRLEIA 193
           L+   L   L  RP++LSGG++QRVA+ RA+   P L L DEP  NLD         E  
Sbjct: 130 LTALGLGARLTHRPSQLSGGEQQRVAVARALANRPALVLADEPTGNLDEHTADIVLAEFL 189

Query: 194 RLHRSLKATMIYVTHDQVEAMTLADKIVVLNAGRIE 229
           RL R   A  +  TH++  A  + D++V L+ G +E
Sbjct: 190 RLVRGEGAAALIATHNERLAAKM-DRVVRLHEGVLE 224


Lambda     K      H
   0.320    0.137    0.393 

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: 181
Number of extensions: 5
Number of successful extensions: 2
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: 352
Length of database: 224
Length adjustment: 26
Effective length of query: 326
Effective length of database: 198
Effective search space:    64548
Effective search space used:    64548
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 47 (22.7 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