GapMind for catabolism of small carbon sources

 

Alignments for a candidate for malK_Aa in Sphingomonas koreensis DSMZ 15582

Align ABC-type maltose transporter (EC 7.5.2.1) (characterized)
to candidate Ga0059261_2293 Ga0059261_2293 cell division ATP-binding protein FtsE

Query= BRENDA::Q70HW1
         (384 letters)



>FitnessBrowser__Korea:Ga0059261_2293
          Length = 235

 Score =  104 bits (259), Expect = 3e-27
 Identities = 59/186 (31%), Positives = 99/186 (53%), Gaps = 6/186 (3%)

Query: 15  GQTEPTVKDFNLDIQDKEFTVFVGPSGCGKTTTLRMIAGLEDITEGNLYIGDRRVNDVPP 74
           G    T+ D +  +    F    G SG GKT+ LR++   +  T G + +       +P 
Sbjct: 15  GTGAETLSDVSFTLSAGSFYFVTGASGAGKTSLLRLLYLAQRPTRGIVRLFGEDAGALPR 74

Query: 75  KD-----RDIAMVFQNYALYPHMTVYQNMAFGLKLRKVPKAEIDRRVQEAAKILDIAHLL 129
           K      R I +VFQ++ L PH++ Y N+A  L++  +P+A+I+  V+E    + +    
Sbjct: 75  KRLPGFRRRIGVVFQDFRLLPHLSAYDNVALPLRVAGIPEADIEGPVREMIAWVGLKDRD 134

Query: 130 DRKPKALSGGQRQRVALGRAIVREPQVFLMDEPLSNLDAKLRVQMRAEIRKLHQRLQTTV 189
             KP  LSGG++QR+A+ RA++  P++ + DEP  N+D  +  ++      L+ RL TTV
Sbjct: 135 SAKPPTLSGGEQQRIAIARAVITRPEILIADEPTGNVDPDMAERLLHLFDSLN-RLGTTV 193

Query: 190 IYVTHD 195
           +  THD
Sbjct: 194 VVATHD 199


Lambda     K      H
   0.321    0.138    0.395 

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: 219
Number of extensions: 7
Number of successful extensions: 3
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: 384
Length of database: 235
Length adjustment: 27
Effective length of query: 357
Effective length of database: 208
Effective search space:    74256
Effective search space used:    74256
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: 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