GapMind for catabolism of small carbon sources

 

Aligments for a candidate for mtlK in Shewanella oneidensis MR-1

Align SmoK aka POLK, component of Hexitol (glucitol; mannitol) porter (characterized)
to candidate 203725 SO4655 sulfate ABC transporter, ATP-binding protein (NCBI ptt file)

Query= TCDB::P54933
         (332 letters)



>lcl|FitnessBrowser__MR1:203725 SO4655 sulfate ABC transporter,
           ATP-binding protein (NCBI ptt file)
          Length = 354

 Score =  218 bits (554), Expect = 2e-61
 Identities = 120/274 (43%), Positives = 164/274 (59%), Gaps = 12/274 (4%)

Query: 4   ITLRNVQKRFGEAVVIPSLDLDIEDGEFVVFVGPSGCGKSTLLRLIAGLEDVSDGQIMID 63
           I ++ V K FG  V + S++L+I+ GE    +GPSG GK+TLLR+IAGLE    G +  +
Sbjct: 3   IHIQQVNKHFGNFVAVDSVNLEIKTGELTALLGPSGSGKTTLLRIIAGLEQADSGIVKFN 62

Query: 64  GRDATEMPPAKRGLAMVFQSYALYPHMTVKKNIAFPL----RMAKMEPQEIERRVSNAAK 119
           G D T    ++RG+  VFQ YAL+ HMTV +N+A+ L    R  +    EI  +V +  K
Sbjct: 63  GEDITTQHVSERGVGFVFQHYALFKHMTVFENVAYGLTVRPRKTRPSKAEIAEKVHSLLK 122

Query: 120 ILNLTNYLDRRPGQLSGGQRQRVAIGRAIVREPAAFLFDEPLSNLDAALRVNMRLEITEL 179
           ++ L    DR P QLSGGQRQR+A+ RA+  EP   L DEP   LDA +R  +R  +  L
Sbjct: 123 LVQLDWTADRYPSQLSGGQRQRIALARALAVEPKVLLLDEPFGALDAKVRAELRRWLRRL 182

Query: 180 HQSLETTMIYVTHDQVEAMTMADKIVVLNAGRIEQVGSPLTLYRNPANLFVAGFIGSPKM 239
           H  +  T ++VTHDQ EA+ +ADKIVV+N GRIEQ G+P  +Y  P+N FV  F+G+  +
Sbjct: 183 HDEINVTTVFVTHDQEEALEVADKIVVMNKGRIEQQGTPEEVYDTPSNPFVYEFLGN--V 240

Query: 240 NLIEGPEAAKHGATTIG----IRPEHIDLSREAG 269
           NL       KHG +TIG      PEH     + G
Sbjct: 241 NLFHA--RVKHGHSTIGNIHIPSPEHAGGEEQQG 272


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: 308
Number of extensions: 13
Number of successful extensions: 3
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 1
Length of query: 332
Length of database: 354
Length adjustment: 29
Effective length of query: 303
Effective length of database: 325
Effective search space:    98475
Effective search space used:    98475
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 Sep 17 2021. The underlying query database was built on Sep 17 2021.

Links

Downloads

Related tools

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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 on GapMind for carbon sources, or view the source code.

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