GapMind for catabolism of small carbon sources

 

Alignments for a candidate for musK in Sinorhizobium meliloti 1021

Align ABC-type maltose transporter (EC 7.5.2.1) (characterized)
to candidate SM_b21106 SM_b21106 sugar ABC transporter ATP-binding protein

Query= BRENDA::Q8NMV1
         (376 letters)



>FitnessBrowser__Smeli:SM_b21106
          Length = 365

 Score =  310 bits (793), Expect = 5e-89
 Identities = 170/330 (51%), Positives = 219/330 (66%), Gaps = 14/330 (4%)

Query: 1   MATVTFKDASLSYPGAKEPTVKKFNLEIADGEFLVLVGPSGCGKSTTLRMLAGLENVTDG 60
           MA VT K     Y GA E  V   +LE+ D EF+ LVGPSGCGKSTTLRM+AGLE V+ G
Sbjct: 1   MAPVTLKKLVKRY-GALE-VVHGIDLEVKDREFIALVGPSGCGKSTTLRMIAGLEEVSGG 58

Query: 61  AIFIGDKDVTHVAPRDRDIAMVFQNYALYPHMTVGENMGFALKIAGKSQDEINKRVDEAA 120
           AI IG + V  + PR R+I+MVFQ+YALYPHMTV ENMGF+LKIAG+  +EI  RV EAA
Sbjct: 59  AIEIGGRKVNDLPPRARNISMVFQSYALYPHMTVAENMGFSLKIAGRPAEEIKTRVAEAA 118

Query: 121 ATLGLTEFLERKPKALSGGQRQRVAMGRAIVRNPQVFLMDEPLSNLDAKLRVQTRTQIAA 180
           A L L   LER+P  LSGGQRQRVAMGRAIVR P VFL DEPLSNLDAKLR Q RT+I  
Sbjct: 119 AILDLAHLLERRPSQLSGGQRQRVAMGRAIVRQPDVFLFDEPLSNLDAKLRTQVRTEIKK 178

Query: 181 LQRKLGVTTVYVTHDQTEALTMGDRIAVLKDGYLQQVGAPRELYDRPANVFVAGFIGSPA 240
           L  ++  T +YVTHDQ EA+T+ DRI +++DG+++QVG P +++ RPA  FVAGFIGSP 
Sbjct: 179 LHARMQATMIYVTHDQVEAMTLSDRIVIMRDGHIEQVGTPEDVFRRPATKFVAGFIGSPP 238

Query: 241 MNLGTFSVKDGD-ATSGHARIKLSPETLAAMTPEDNGRITIGFRPEALEIIPEGESTDL- 298
           MN+    + DG  A +  A + L P   + +   +  ++T G RP+  ++ P G      
Sbjct: 239 MNMEEAVLTDGKLAFASGATLPLPPRFRSLV--REGQKVTFGLRPD--DVYPSGHGLHAG 294

Query: 299 ------SIPIKLDFVEELGSDSFLYGKLVG 322
                  I + +   E LG+++ ++ +  G
Sbjct: 295 DADAVHEIELPVTITEPLGNETLVFTQFNG 324


Lambda     K      H
   0.316    0.135    0.380 

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: 402
Number of extensions: 18
Number of successful extensions: 1
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: 376
Length of database: 365
Length adjustment: 30
Effective length of query: 346
Effective length of database: 335
Effective search space:   115910
Effective search space used:   115910
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 (21.6 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