GapMind for catabolism of small carbon sources

 

Aligments for a candidate for malK in Dinoroseobacter shibae DFL-12

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 3607124 Dshi_0546 ABC transporter related (RefSeq)

Query= TCDB::Q00752
         (377 letters)



>lcl|FitnessBrowser__Dino:3607124 Dshi_0546 ABC transporter related
           (RefSeq)
          Length = 338

 Score =  302 bits (774), Expect = 8e-87
 Identities = 177/374 (47%), Positives = 237/374 (63%), Gaps = 47/374 (12%)

Query: 1   MVELNLNHIYKKYPNSSHYSVEDFDLDIKNKEFIVFVGPSGCGKSTTLRMVAGLEDITKG 60
           M  + ++ I K Y  +   ++ D +LDI++ EF+VFVGPSGCGKST LR +AGLE ++ G
Sbjct: 1   MAGIKIDKINKFYGTTQ--ALFDINLDIEDGEFVVFVGPSGCGKSTLLRTLAGLEGVSSG 58

Query: 61  ELKIDGEVVNDKAPKDRDIAMVFQNYALYPHMSVYDNMAFGLKLRHYSKEAIDKRVKEAA 120
            ++I G  V    P DRD+AMVFQ+YALYPHM+V +NM FG+K+  +  +   +R+ EAA
Sbjct: 59  RIEIGGRDVTTVEPADRDLAMVFQSYALYPHMTVRENMEFGMKVNGFEPDLRKERIAEAA 118

Query: 121 QILGLTEFLERKPADLSGGQRQRVAMGRAIVRDAKVFLMDEPLSNLDAKLRVSMRAEIAK 180
           ++L L ++L+RKP  LSGGQRQRVA+GRAIV++  VFL DEPLSNLDAKLRV MR E+  
Sbjct: 119 RVLQLEDYLDRKPGQLSGGQRQRVAIGRAIVKNPSVFLFDEPLSNLDAKLRVQMRVELEG 178

Query: 181 IHRRIGATTIYVTHDQTEAMTLADRIVIMSSTKNEDGSGTIGRVEQVGTPQELYNRPANK 240
           +H+++GAT IYVTHDQ EAMT+AD+IV+++           GR+EQVG+P +LY++P ++
Sbjct: 179 LHKQLGATMIYVTHDQVEAMTMADKIVVLNR----------GRIEQVGSPMDLYHKPNSR 228

Query: 241 FVAGFIGSPAMNFF--DVTIKDGHLVSKDGLTIAVTEGQLKMLESKGFKNKNLIFGIRPE 298
           FVA FIGSPAMN F  DV ++D   +S D     V                    G RPE
Sbjct: 229 FVAEFIGSPAMNVFSSDVGLQD---ISLDASAAFV--------------------GCRPE 265

Query: 299 DISSSLLVQETYPDAT--VDAEVVVSELLGSETMLYLKL-GQTEFAARVDARDFHEPGEK 355
            I       E  PD    + A V V E LG E++LYL L G  +  ARV   D  + G  
Sbjct: 266 HI-------EIVPDGDGHIAATVHVKERLGGESLLYLGLKGGGQIVARVGGDDETKVGAA 318

Query: 356 VSLTFNVAKGHFFD 369
           VSL F+  + H FD
Sbjct: 319 VSLRFSRHRLHQFD 332


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: 377
Number of extensions: 16
Number of successful extensions: 4
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: 338
Length adjustment: 29
Effective length of query: 348
Effective length of database: 309
Effective search space:   107532
Effective search space used:   107532
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: 49 (23.5 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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 on GapMind for carbon sources, or view the source code.

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