GapMind for catabolism of small carbon sources

 

Alignments for a candidate for mtlK in Desulfovibrio vulgaris Hildenborough

Align SmoK aka POLK, component of Hexitol (glucitol; mannitol) porter (characterized)
to candidate 206675 DVU1236 amino acid ABC transporter, ATP-binding protein

Query= TCDB::P54933
         (332 letters)



>MicrobesOnline__882:206675
          Length = 247

 Score =  158 bits (400), Expect = 1e-43
 Identities = 90/227 (39%), Positives = 136/227 (59%), Gaps = 6/227 (2%)

Query: 4   ITLRNVQKRFGEAVVIPSLDLDIEDGEFVVFVGPSGCGKSTLLRLIAGLEDVSDGQIMID 63
           I++RNV K FGE   +  + LD++ GE VV +GPSG GKSTLLR I  LE+V  G I++D
Sbjct: 9   ISIRNVWKFFGELTALHDVSLDVQAGEKVVIIGPSGSGKSTLLRSINRLENVDKGSIIVD 68

Query: 64  GRDA----TEMPPAKRGLAMVFQSYALYPHMTVKKNIAF-PLRMAKMEPQEIERRVSNAA 118
           G+D     +++   ++ L MVFQS+ L+PH TV +N+   P+R+ K+   E E R  +  
Sbjct: 69  GKDIRAEDSDINVIRQDLGMVFQSFNLFPHKTVLQNLTMAPMRLRKVPRDEAESRALDLL 128

Query: 119 KILNLTNYLDRRPGQLSGGQRQRVAIGRAIVREPAAFLFDEPLSNLDAALRVNMRLEITE 178
           K + +++  +  P  LSGGQ+QRVAI RA+   P   LFDEP S LD  + +   L++  
Sbjct: 129 KKVGISDKANVYPAMLSGGQQQRVAIARALAMNPKIMLFDEPTSALDPEM-IGEVLDVMV 187

Query: 179 LHQSLETTMIYVTHDQVEAMTMADKIVVLNAGRIEQVGSPLTLYRNP 225
                  TM+ VTH+   A  +AD+I+ ++ G+I + G+P   +  P
Sbjct: 188 TLAKEGMTMVCVTHEMGFAREVADRIIFMDHGQILEQGTPQHFFEAP 234


Lambda     K      H
   0.320    0.137    0.400 

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: 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: 332
Length of database: 247
Length adjustment: 26
Effective length of query: 306
Effective length of database: 221
Effective search space:    67626
Effective search space used:    67626
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: 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