GapMind for catabolism of small carbon sources

 

Alignments for a candidate for malG in Sinorhizobium meliloti 1021

Align MalG, component of Maltose/Maltotriose/maltodextrin (up to 7 glucose units) transporters MalXFGK (MsmK (3.A.1.1.28) can probably substitute for MalK; Webb et al., 2008) (characterized)
to candidate SMc04137 SMc04137 ABC transporter permease

Query= TCDB::Q8DT26
         (278 letters)



>FitnessBrowser__Smeli:SMc04137
          Length = 295

 Score =  134 bits (338), Expect = 2e-36
 Identities = 81/269 (30%), Positives = 138/269 (51%), Gaps = 4/269 (1%)

Query: 12  IYALLILLSFIWLFPIIWVILTSFRGEGTAYVPYII-PKTWTLDNYIKLFTNSSFPFGRW 70
           ++A LI  S   ++P++W+I  S R E   +    + P +    +Y++ +      FGR+
Sbjct: 28  VHAALIAASIAMIYPLLWMISASVRPEDEIFASTSLWPSSVDFSSYVRGWFGLDVSFGRF 87

Query: 71  FLNTLIVSTATCVLSTSITVAMAYSLSRIKFKHRNGFLKLALVLNMFPGFMSMIAVYYIL 130
           F N+L+++  T V +       AY+ +R++F  RN +  + L   M P  +++I  Y + 
Sbjct: 88  FWNSLVIAVLTVVGNVVACSLAAYAFARLRFAGRNFWFAIMLGTMMIPYHVTLIPQYVLF 147

Query: 131 KALNLTQTLTSLVLV-YSSGAALTFYIAKGFFDTIPYSLDESAMIDGATRKDIFLKITLP 189
             L    T   LV+  + +  A   ++   FF  IP  LDE+AM+DG     I+ KI LP
Sbjct: 148 LDLGWVNTFLPLVVPKFLASDAFFIFLMVQFFRGIPRELDEAAMMDGCGAWRIYWKIMLP 207

Query: 190 LSKPIIVYTALLAFIAPWIDFIFAQVILGDATSKYTVAIGLFSMLQADTINNWFMAFAAG 249
           LS P++   A+ +FI  W DF    + L D  S YT+ +GL + + + + ++W   FA  
Sbjct: 208 LSLPVLATAAIFSFIWTWDDFFGPLIYLNDMNS-YTIQLGLRTFVDSSSTSDWGGLFAM- 265

Query: 250 SVLIAIPITILFIFMQKYYVEGITGGSVK 278
           S L  +P+   F+F Q+  +EGI    +K
Sbjct: 266 STLSLVPVFFFFLFFQRLLIEGIATTGMK 294


Lambda     K      H
   0.330    0.142    0.428 

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: 227
Number of extensions: 15
Number of successful extensions: 5
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: 278
Length of database: 295
Length adjustment: 26
Effective length of query: 252
Effective length of database: 269
Effective search space:    67788
Effective search space used:    67788
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.8 bits)
S2: 47 (22.7 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