GapMind for catabolism of small carbon sources

 

Alignments for a candidate for malK in Chryseobacterium angstadtii KM

Align MsmK aka SMU.882, component of The raffinose/stachyose transporter, MsmEFGK (MalK (3.A.1.1.27) can probably substitute for MsmK; Webb et al., 2008). This system may also transport melibiose, isomaltotriose and sucrose as well as isomaltosaccharides (characterized)
to candidate WP_048505507.1 ACM46_RS05225 ABC transporter ATP-binding protein

Query= TCDB::Q00752
         (377 letters)



>NCBI__GCF_001045465.1:WP_048505507.1
          Length = 252

 Score =  123 bits (308), Expect = 6e-33
 Identities = 72/237 (30%), Positives = 124/237 (52%), Gaps = 12/237 (5%)

Query: 4   LNLNHIYKKYPNSSHYSVEDFDLDIKNKEFIVFVGPSGCGKSTTLRMVAGLEDITKGELK 63
           + + ++YKKY N+  +SV D  L+I  +E    +GP+G GK+T + M++GL   T G+ K
Sbjct: 6   IEIKNLYKKYKNADEFSVNDISLNIDKQEIYGILGPNGAGKTTLISMLSGLIKPTSGQFK 65

Query: 64  IDGEVVNDKAPKDRD-IAMVFQNYALYPHMSVYDNMAFGLKLRHYSKEAIDKRVKEAAQI 122
           I+G        K R  I +V Q YALYP ++  +N+ F   L       + K + E+ +I
Sbjct: 66  INGLSPQKDGFKLRQIIGIVPQEYALYPTLTAKENLMFFGSLYGLKHRQLSKAIDESLEI 125

Query: 123 LGLTEFLERKPADLSGGQRQRVAMGRAIVRDAKVFLMDEPLSNLDAKLRVSMRAEIAKIH 182
           +GL +F ++K    SGG ++R  +    + + KV  +DEP   +D + +  +   + +++
Sbjct: 126 MGLAKFADKKVEQFSGGMKRRCNLIAGTLHNPKVLFLDEPTVGVDVQSKKVIIDFLQELN 185

Query: 183 RRIGATTIYVTHDQTEAMTLADRIVIMSSTKNEDGSGTIGRVEQVGTPQELYNRPAN 239
           +  G   IY +H  +EA     +I I+            GR+  VGTP+EL  + +N
Sbjct: 186 KN-GTCIIYTSHHLSEAEEFCTKIAIIDR----------GRIHAVGTPEELVAQISN 231


Lambda     K      H
   0.318    0.135    0.375 

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: 225
Number of extensions: 10
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: 377
Length of database: 252
Length adjustment: 27
Effective length of query: 350
Effective length of database: 225
Effective search space:    78750
Effective search space used:    78750
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 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