GapMind for catabolism of small carbon sources

 

Alignments for a candidate for mtlK in Desulfoscipio geothermicus DSM 3669

Align SmoK aka POLK, component of Hexitol (glucitol; mannitol) porter (characterized)
to candidate WP_092484009.1 BM299_RS11075 ABC transporter ATP-binding protein

Query= TCDB::P54933
         (332 letters)



>NCBI__GCF_900115975.1:WP_092484009.1
          Length = 344

 Score =  191 bits (484), Expect = 3e-53
 Identities = 113/345 (32%), Positives = 189/345 (54%), Gaps = 29/345 (8%)

Query: 4   ITLRNVQKRFGEAVVIPSLDLDIEDGEFVVFVGPSGCGKSTLLRLIAGLEDVSDGQIMID 63
           + L +V  + GE  ++  ++L++++GE+ + +GP+G GK+ +L  IAG+     G I   
Sbjct: 2   LRLEHVTVKLGEFQLL-DINLEVQEGEYFIILGPTGTGKTVILETIAGMYRPDKGTIRFK 60

Query: 64  GRDATEMPPAKRGLAMVFQSYALYPHMTVKKNIAFPLRMAKMEPQEIERRVSNAAKILNL 123
            R+   + P +R +  V+Q YAL+PH+TVK+NI F  ++ K+  + I+ ++     +L +
Sbjct: 61  ERNLATLAPEQRKVGFVYQDYALFPHLTVKENIIFGAQIRKLPKKIIKSKLDELVAMLGI 120

Query: 124 TNYLDRRPGQLSGGQRQRVAIGRAIVREPAAFLFDEPLSNLDAALRVNMRLEITELHQSL 183
            + L+R P  LSGG++QR A+ RA++  P   L DEPLS LD   + N + E+ ++HQ+L
Sbjct: 121 GHLLNRHPSTLSGGEQQRTALARALIISPEILLLDEPLSALDPRSKENFQEELKKIHQTL 180

Query: 184 ETTMIYVTHDQVEAMTMADKIVVLNAGRIEQVGSPLTLYRNPANLFVAGFIGSPKMNLIE 243
           +TT ++VTHD  EAM +ADKI V++ G+I QVG+P  ++  P N FVA F+G    N+ E
Sbjct: 181 KTTTLHVTHDFNEAMYLADKIGVMHQGQIIQVGTPQEIFYKPQNDFVASFVGIE--NIFE 238

Query: 244 GP----------------EAAKHGATTIGIRPEHIDLSREA------GAWEGEVGVSEHL 281
           G                    K G   + + PE I LS+E         + G+V    + 
Sbjct: 239 GQVNDDKVSLAPDVDIFVNTGKQGKVKVAVPPEDIALSKEPFDLCYHYQFNGKVLNISNQ 298

Query: 282 GSDTFLHVHVAGMPTL---TVRTGGEFGVHHGDRVWLTPQADKIH 323
           G+ + + + + G+P +   T R   E  +  GD +W    +   H
Sbjct: 299 GALSKITIDI-GIPLVCFATTRFVKETAITVGDNLWAGFNSSSTH 342


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: 291
Number of extensions: 18
Number of successful extensions: 2
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: 344
Length adjustment: 28
Effective length of query: 304
Effective length of database: 316
Effective search space:    96064
Effective search space used:    96064
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 Apr 09 2024. 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