GapMind for catabolism of small carbon sources

 

Alignments for a candidate for malK in Sinorhizobium meliloti 1021

Align Maltose/maltodextrin import ATP-binding protein MalK; EC 7.5.2.1 (characterized)
to candidate SMc04140 SMc04140 ABC transporter ATP-binding protein

Query= SwissProt::P19566
         (369 letters)



>FitnessBrowser__Smeli:SMc04140
          Length = 360

 Score =  380 bits (975), Expect = e-110
 Identities = 202/359 (56%), Positives = 249/359 (69%), Gaps = 2/359 (0%)

Query: 3   SVQLRNVTKAWGDVVVSKDINLDIHDGEFVVFVGPSGCGKSTLLRMIAGLETITSGDLFI 62
           SV L+ V K +G + V   I+L I  GEF VFVGPSGCGKSTLLRMIAGLE I+ G L +
Sbjct: 4   SVVLQKVEKRYGALDVIHGIDLTIDPGEFAVFVGPSGCGKSTLLRMIAGLEEISGGTLML 63

Query: 63  GETRMNDIPPAERGVGMVFQSYALYPHLSVAENMSFGLKLAGAKKEVMNQRVNQVAEVLQ 122
              RMN++ PA RG+ MVFQSYALYPH+SV +N++FGL+ AG KK  +  +V + AE+LQ
Sbjct: 64  DSDRMNEVAPARRGIAMVFQSYALYPHMSVYKNLAFGLETAGFKKAEIEPKVRRAAEILQ 123

Query: 123 LAHLLERKPKALSGGQRQRVAIGRTLVAEPRVFLLDEPLSNLDAALRVQMRIEISRLHKR 182
           +  LL+RKPKALSGGQRQRVAIGR +V EPR+FL DEPLSNLDA LRVQMR+EISRLH+ 
Sbjct: 124 IEKLLDRKPKALSGGQRQRVAIGRAIVREPRIFLFDEPLSNLDAELRVQMRVEISRLHRD 183

Query: 183 LGRTMIYVTHDQVEAMTLADKIVVLDAGRVAQVGKPLELYHYPADRFVAGFIGSPKMNFL 242
           LG TMIYVTHDQVEAMT+ADKIVVL++GR+ QVG PL+LY+ P +RFVAGFIGSPKMNFL
Sbjct: 184 LGNTMIYVTHDQVEAMTMADKIVVLNSGRIEQVGAPLDLYNNPVNRFVAGFIGSPKMNFL 243

Query: 243 PVKVTATAIEQVQVELPNRQQIWLPVESRGVQVGANMSLGIRPEHLLPSDIADVTLEGEV 302
             ++      +  +E+     I LP    G   G +++ GIRPEHL   +         V
Sbjct: 244 KARIADVTGSETAIEVCG-GTIRLPRRLNGATQGQDVTFGIRPEHLSAREGGIELATVNV 302

Query: 303 QVVEQLGHETQIHIQIPAIRQNLVYRQNDVVLVEEGATFAIGLPPERCHLFREDGSACR 361
           ++VE LG ET ++  I   RQ L         VE G+  A+   P RCH+F  DG A R
Sbjct: 303 EIVENLGGETMLY-GITPDRQQLTVALEGQQKVERGSNLAVHFDPSRCHVFGADGRAMR 360


Lambda     K      H
   0.321    0.138    0.396 

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: 387
Number of extensions: 11
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: 369
Length of database: 360
Length adjustment: 29
Effective length of query: 340
Effective length of database: 331
Effective search space:   112540
Effective search space used:   112540
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 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:

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