GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gtsD in Sphingomonas koreensis DSMZ 15582

Align ABC transporter for D-Glucose-6-Phosphate, ATPase component (characterized)
to candidate Ga0059261_2293 Ga0059261_2293 cell division ATP-binding protein FtsE

Query= reanno::WCS417:GFF4321
         (386 letters)



>FitnessBrowser__Korea:Ga0059261_2293
          Length = 235

 Score =  108 bits (271), Expect = 1e-28
 Identities = 63/197 (31%), Positives = 104/197 (52%), Gaps = 7/197 (3%)

Query: 4   LELRNVNKTYGAGLPDTLKNIELSIKEGEFLILVGPSGCGKSTLMNCIAGLETITGGAIM 63
           ++  NV   YG G  +TL ++  ++  G F  + G SG GK++L+  +   +  T G + 
Sbjct: 5   VQFENVGLRYGTGA-ETLSDVSFTLSAGSFYFVTGASGAGKTSLLRLLYLAQRPTRGIVR 63

Query: 64  IGDQDVSGMSPKD-----RDIAMVFQSYALYPTMSVRENIEFGLKIRKMPQADIDAEVAR 118
           +  +D   +  K      R I +VFQ + L P +S  +N+   L++  +P+ADI+  V  
Sbjct: 64  LFGEDAGALPRKRLPGFRRRIGVVFQDFRLLPHLSAYDNVALPLRVAGIPEADIEGPVRE 123

Query: 119 VAKLLQIEHLLNRKPGQLSGGQQQRVAMGRALARRPKIYLFDEPLSNLDAKLRVEMRTEM 178
           +   + ++   + KP  LSGG+QQR+A+ RA+  RP+I + DEP  N+D  +  E    +
Sbjct: 124 MIAWVGLKDRDSAKPPTLSGGEQQRIAIARAVITRPEILIADEPTGNVDPDM-AERLLHL 182

Query: 179 KLMHQRLKTTTVYVTHD 195
                RL TT V  THD
Sbjct: 183 FDSLNRLGTTVVVATHD 199


Lambda     K      H
   0.318    0.135    0.382 

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: 239
Number of extensions: 13
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: 386
Length of database: 235
Length adjustment: 27
Effective length of query: 359
Effective length of database: 208
Effective search space:    74672
Effective search space used:    74672
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 48 (23.1 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