GapMind for catabolism of small carbon sources

 

Aligments for a candidate for malK in Dyella japonica UNC79MFTsu3.2

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 N515DRAFT_4212 N515DRAFT_4212 multiple sugar transport system ATP-binding protein

Query= TCDB::Q00752
         (377 letters)



>lcl|FitnessBrowser__Dyella79:N515DRAFT_4212 N515DRAFT_4212 multiple
           sugar transport system ATP-binding protein
          Length = 364

 Score =  338 bits (866), Expect = 2e-97
 Identities = 187/381 (49%), Positives = 253/381 (66%), Gaps = 26/381 (6%)

Query: 1   MVELNLNHIYKKYPNSSHYSVEDFDLDIKNKEFIVFVGPSGCGKSTTLRMVAGLEDITKG 60
           M ++ L+ + K YPN  H  V +   +I + E +V VGPSGCGK+T LRM+AGLE I+ G
Sbjct: 1   MAKVRLDKLRKVYPNG-HVGVAEASFEIADGELLVLVGPSGCGKTTLLRMIAGLESISGG 59

Query: 61  ELKIDGEVVNDKAPKDRDIAMVFQNYALYPHMSVYDNMAFGLKLRHYSKEAIDKRVKEAA 120
            L I   VVND APKDRDIAMVFQNYALYPHM+V +N+ FGLKLR   K  I++RV EAA
Sbjct: 60  TLSIGERVVNDIAPKDRDIAMVFQNYALYPHMTVAENLGFGLKLRGQPKAEIERRVAEAA 119

Query: 121 QILGLTEFLERKPADLSGGQRQRVAMGRAIVRDAKVFLMDEPLSNLDAKLRVSMRAEIAK 180
           ++L L + L+ +PA LSGGQRQRVA+GRA+VRD KVFL+DEPLSNLDAKLR+SMR EIA+
Sbjct: 120 RMLELEQRLDSRPAALSGGQRQRVALGRALVRDPKVFLLDEPLSNLDAKLRLSMRVEIAR 179

Query: 181 IHRRIGATTIYVTHDQTEAMTLADRIVIMSSTKNEDGSGTIGRVEQVGTPQELYNRPANK 240
           IH+R+ AT +YVTHDQ EAMTL  RIV+++           G ++Q+ TP  LY+ PAN 
Sbjct: 180 IHQRLKATMVYVTHDQIEAMTLGQRIVVLNG----------GVIQQIDTPMNLYDTPANL 229

Query: 241 FVAGFIGSPAMNFFDVTIKDGHLVSKDGLTIAVTEGQLKMLE------SKGFKNKNLIFG 294
           FVAGF+GSPAMN     +  G L    G  +A+ +G+L + E       + +++++++ G
Sbjct: 230 FVAGFLGSPAMN-----LLRGILYRDGGWKLAMPQGELVLGELPQGAALEAWRDRDIVVG 284

Query: 295 IRPEDISSSLLVQETYPDATVDAEVVVSELLGSETMLYLKLGQTEFAARVDARDFHEPGE 354
           +RPED    LL+      A + A++ V E +G+E  L L+ G+    +R+  R+   PG 
Sbjct: 285 LRPED----LLLCADAAGAALAAQLEVVEPVGNEVFLNLRHGELALVSRMPPRELPAPGS 340

Query: 355 KVSLTFNVAKGHFFDAETEAA 375
            +   F   + HFFDA+ E A
Sbjct: 341 TLHFGFAPERLHFFDAKGEGA 361


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: 384
Number of extensions: 18
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: 364
Length adjustment: 30
Effective length of query: 347
Effective length of database: 334
Effective search space:   115898
Effective search space used:   115898
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