GapMind for catabolism of small carbon sources

 

Alignments for a candidate for malK in Malonomonas rubra DSM 5091

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_072908814.1 BUB13_RS11050 glycine betaine/L-proline ABC transporter ATP-binding protein ProV

Query= TCDB::Q00752
         (377 letters)



>NCBI__GCF_900142125.1:WP_072908814.1
          Length = 415

 Score =  163 bits (412), Expect = 9e-45
 Identities = 97/264 (36%), Positives = 149/264 (56%), Gaps = 21/264 (7%)

Query: 21  VEDFDLDIKNKEFIVFVGPSGCGKSTTLRMVAGLEDITKGELKIDGEVV----NDKAPKD 76
           V+D   +I   E  V +G SG GKST +RM+  L + T G++ IDGE +    +D+  K 
Sbjct: 46  VQDASFEIFKGEIFVIMGLSGSGKSTMVRMLNRLIEPTSGQVLIDGEDIVAMNDDQLVKV 105

Query: 77  R--DIAMVFQNYALYPHMSVYDNMAFGLKLRHYSKEAIDKRVKEAAQILGLTEFLERKPA 134
           R   ++MVFQ++AL PHM+V  N AFGL++    K+  ++R  +A + +GL  + E  P 
Sbjct: 106 RRAKLSMVFQSFALMPHMTVLQNAAFGLEMDGVDKQTREQRALQALEQVGLEAWAESMPD 165

Query: 135 DLSGGQRQRVAMGRAIVRDAKVFLMDEPLSNLDAKLRVSMRAEIAKIHRRIGATTIYVTH 194
           +LSGG +QRV + R +  D  + LMDE  S LD  +R  M+ E+ K+  +   T ++++H
Sbjct: 166 ELSGGMQQRVGLARGLAVDPDILLMDEAFSALDPLIRTEMQDELLKLQAKAKRTIVFISH 225

Query: 195 DQTEAMTLADRIVIMSSTKNEDGSGTIGRVEQVGTPQELYNRPANKFVAGFI-GSPAMNF 253
           D  EAM + DRI IM            GRV QVGTP+E+   PA+ +V  F  G    N 
Sbjct: 226 DLDEAMRIGDRIAIMEG----------GRVVQVGTPEEILQNPADDYVRAFFRGVDPTNI 275

Query: 254 FDVTIKDGHLVSKDGLTIAVTEGQ 277
               +  G + ++  +TI +T+G+
Sbjct: 276 ----LTAGDIATQTQVTIPITDGK 295


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: 325
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: 415
Length adjustment: 31
Effective length of query: 346
Effective length of database: 384
Effective search space:   132864
Effective search space used:   132864
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: 50 (23.9 bits)

This GapMind analysis is from Apr 09 2024. 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