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_1821 N515DRAFT_1821 putative ABC transport system ATP-binding protein

Query= TCDB::Q00752
         (377 letters)



>lcl|FitnessBrowser__Dyella79:N515DRAFT_1821 N515DRAFT_1821 putative
           ABC transport system ATP-binding protein
          Length = 238

 Score =  131 bits (329), Expect = 2e-35
 Identities = 80/212 (37%), Positives = 117/212 (55%), Gaps = 10/212 (4%)

Query: 4   LNLNHIYKKYPNS--SHYSVEDFDLDIKNKEFIVFVGPSGCGKSTTLRMVAGLEDITKGE 61
           L + H+ K Y       Y++ DF++D+K  EF+   GPSG GK+T L +   LE  T GE
Sbjct: 2   LKMTHLSKVYRTEVVETYALRDFNIDVKEGEFVAVTGPSGSGKTTFLTIAGLLETFTGGE 61

Query: 62  LKIDGEVV---NDKAP---KDRDIAMVFQNYALYPHMSVYDNMAFGLKLRHYSKEAIDKR 115
             +DG  V   ND A    ++  I  +FQ + L P ++VYDN+   L+ R        +R
Sbjct: 62  YHLDGVEVSNLNDNARSKIRNEKIGFIFQAFNLIPDLNVYDNVEVPLRYRGMKALERKQR 121

Query: 116 VKEAAQILGLTEFLERKPADLSGGQRQRVAMGRAIVRDAKVFLMDEPLSNLDAKLRVSMR 175
           + +A + +GL    +  PA+LSGGQ+QRVA+ RA+    ++ L DEP  NLD ++   + 
Sbjct: 122 IMDALERVGLASRAKHYPAELSGGQQQRVAIARALAGSPRLLLADEPTGNLDTQMARGVM 181

Query: 176 AEIAKIHRRIGATTIYVTHDQTEAMTLADRIV 207
             + +IHR  GAT + VTHD  E  T A R V
Sbjct: 182 ELLEEIHRE-GATIVMVTHD-PELATRAQRNV 211


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: 211
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: 238
Length adjustment: 27
Effective length of query: 350
Effective length of database: 211
Effective search space:    73850
Effective search space used:    73850
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 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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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 preprint 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