GapMind for catabolism of small carbon sources

 

Alignments for a candidate for mtlK in Thiothrix lacustris DSM 21227

Align SmoK aka POLK, component of Hexitol (glucitol; mannitol) porter (characterized)
to candidate WP_028489030.1 Q394_RS0109195 ABC transporter ATP-binding protein

Query= TCDB::P54933
         (332 letters)



>NCBI__GCF_000621325.1:WP_028489030.1
          Length = 348

 Score =  345 bits (886), Expect = e-100
 Identities = 191/339 (56%), Positives = 236/339 (69%), Gaps = 7/339 (2%)

Query: 1   MGKITLRNVQKRFGEAVVIPSLDLDIEDGEFVVFVGPSGCGKSTLLRLIAGLEDVSDGQI 60
           M  + L+NV K +G+   I  + L+I+ GEF+VFVGPSGCGKSTLLR+IAGLE ++ GQ+
Sbjct: 1   MAFLELKNVDKYYGKLHAIKQVSLEIQSGEFIVFVGPSGCGKSTLLRMIAGLEVINGGQL 60

Query: 61  MIDGRDATEMPPAKRGLAMVFQSYALYPHMTVKKNIAFPLRMAKMEPQEIERRVSNAAKI 120
           ++DGRD TE+PP++R LAMVFQSYALYPHMTV++N++F LR+AK++P  I+ +V  AA  
Sbjct: 61  ILDGRDITEVPPSQRDLAMVFQSYALYPHMTVEENMSFALRLAKVDPAIIQEKVKMAADK 120

Query: 121 LNLTNYLDRRPGQLSGGQRQRVAIGRAIVREPAAFLFDEPLSNLDAALRVNMRLEITELH 180
           LNLT YL R P  LSGGQRQRVAIGR+IVR P  FLFDEPLSNLDAALR N R+EI  LH
Sbjct: 121 LNLTAYLQRTPKALSGGQRQRVAIGRSIVRSPKVFLFDEPLSNLDAALRGNTRVEIASLH 180

Query: 181 QSLETTMIYVTHDQVEAMTMADKIVVLNAGRIEQVGSPLTLYRNPANLFVAGFIGSPKMN 240
           + L  T +YVTHDQVEAMT+AD++VVL  G IEQVG+PL LY  P N FVA FIG P+MN
Sbjct: 181 RELGATTVYVTHDQVEAMTLADRVVVLRDGIIEQVGTPLELYDQPINRFVARFIGMPQMN 240

Query: 241 LIEGPEAAKHGA--TTIGIRPEHIDL-SREAGAWEGEVGVSEHLGSDTFLHVH---VAGM 294
           +       +  A    +GIRPEH+ + S E G   G+V + E LG++T +HV    V   
Sbjct: 241 VAPASLFGQFPAQVAEVGIRPEHLQMVSPEDGLLAGKVVLVEALGNETLVHVRPDKVQLE 300

Query: 295 PTLTVRTGGEFGVHHGDRVWLTPQADK-IHRFGADGKAL 332
             L VR  G   VH GDRV L     K IH F   G  L
Sbjct: 301 EPLIVRLYGRTTVHVGDRVGLKWDDSKHIHYFDTKGMRL 339


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: 382
Number of extensions: 16
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: 348
Length adjustment: 28
Effective length of query: 304
Effective length of database: 320
Effective search space:    97280
Effective search space used:    97280
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