GapMind for catabolism of small carbon sources

 

Alignments for a candidate for malK in Paucidesulfovibrio gracilis DSM 16080

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_200806763.1 B5D49_RS03200 ABC transporter ATP-binding protein

Query= TCDB::Q00752
         (377 letters)



>NCBI__GCF_900167125.1:WP_200806763.1
          Length = 406

 Score =  223 bits (567), Expect = 1e-62
 Identities = 113/257 (43%), Positives = 173/257 (67%), Gaps = 14/257 (5%)

Query: 20  SVEDFDLDIKNKEFIVFVGPSGCGKSTTLRMVAGLEDITKGELKIDGEVVNDKAPKDRDI 79
           +V++ DL I+  E +  +GPSGCGK+T LRM+AGLE  TKG++ I G  +ND     R++
Sbjct: 59  AVQETDLTIETGELVTLLGPSGCGKTTILRMIAGLETPTKGDIYIKGRRINDTPIHKRNL 118

Query: 80  AMVFQNYALYPHMSVYDNMAFGLKLRHYSKEAIDKRVKEAAQILGLTEFLERKPADLSGG 139
            M+FQNYAL+PH ++++N+AFGLK R+ S+E + ++V +A +++ L    +R  + LSGG
Sbjct: 119 GMIFQNYALFPHKTIFENVAFGLKYRNVSREEMREKVAQALEMVRLPGVEKRYASQLSGG 178

Query: 140 QRQRVAMGRAIVRDAKVFLMDEPLSNLDAKLRVSMRAEIAKIHRRIGATTIYVTHDQTEA 199
           Q+QR+A+ RAIV +  V LMDEPLS LD KLR  MR EI  I +++  TT++VTHDQ EA
Sbjct: 179 QQQRIALARAIVIEPDVLLMDEPLSALDEKLREEMRMEIDNIQQQLNLTTLFVTHDQREA 238

Query: 200 MTLADRIVIMSSTKNEDGSGTIGRVEQVGTPQELYNRPANKFVAGFIGSPAMNFFDVTIK 259
           ++++++IV+M            GR +Q GTP+++Y+ P N FVA F+G    NFFD  + 
Sbjct: 239 LSMSNKIVVMKD----------GRKQQEGTPEDVYDYPDNYFVADFLGH--ANFFDARVL 286

Query: 260 DGHLVSKDGLTIAVTEG 276
           +  ++  D + + + EG
Sbjct: 287 E--VLDNDQVRVRIAEG 301


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: 359
Number of extensions: 12
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: 377
Length of database: 406
Length adjustment: 31
Effective length of query: 346
Effective length of database: 375
Effective search space:   129750
Effective search space used:   129750
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