GapMind for catabolism of small carbon sources

 

Alignments for a candidate for malK in Shewanella oneidensis MR-1

Align MsmK aka SMU.882, component of The raffinose/stachyose transporter, MsmEFGK (MalK (3.A.1.1.27) can probably substitute for MsmK; Webb et al., 2008). This system may also transport melibiose, isomaltotriose and sucrose as well as isomaltosaccharides (characterized)
to candidate 203725 SO4655 sulfate ABC transporter, ATP-binding protein (NCBI ptt file)

Query= TCDB::Q00752
         (377 letters)



>FitnessBrowser__MR1:203725
          Length = 354

 Score =  203 bits (516), Expect = 7e-57
 Identities = 105/265 (39%), Positives = 166/265 (62%), Gaps = 18/265 (6%)

Query: 2   VELNLNHIYKKYPNSSHYSVEDFDLDIKNKEFIVFVGPSGCGKSTTLRMVAGLEDITKGE 61
           + +++  + K + N    +V+  +L+IK  E    +GPSG GK+T LR++AGLE    G 
Sbjct: 1   MSIHIQQVNKHFGN--FVAVDSVNLEIKTGELTALLGPSGSGKTTLLRIIAGLEQADSGI 58

Query: 62  LKIDGEVVNDKAPKDRDIAMVFQNYALYPHMSVYDNMAFGLKLR----HYSKEAIDKRVK 117
           +K +GE +  +   +R +  VFQ+YAL+ HM+V++N+A+GL +R      SK  I ++V 
Sbjct: 59  VKFNGEDITTQHVSERGVGFVFQHYALFKHMTVFENVAYGLTVRPRKTRPSKAEIAEKVH 118

Query: 118 EAAQILGLTEFLERKPADLSGGQRQRVAMGRAIVRDAKVFLMDEPLSNLDAKLRVSMRAE 177
              +++ L    +R P+ LSGGQRQR+A+ RA+  + KV L+DEP   LDAK+R  +R  
Sbjct: 119 SLLKLVQLDWTADRYPSQLSGGQRQRIALARALAVEPKVLLLDEPFGALDAKVRAELRRW 178

Query: 178 IAKIHRRIGATTIYVTHDQTEAMTLADRIVIMSSTKNEDGSGTIGRVEQVGTPQELYNRP 237
           + ++H  I  TT++VTHDQ EA+ +AD+IV+M+           GR+EQ GTP+E+Y+ P
Sbjct: 179 LRRLHDEINVTTVFVTHDQEEALEVADKIVVMNK----------GRIEQQGTPEEVYDTP 228

Query: 238 ANKFVAGFIGSPAMNFFDVTIKDGH 262
           +N FV  F+G+  +N F   +K GH
Sbjct: 229 SNPFVYEFLGN--VNLFHARVKHGH 251


Lambda     K      H
   0.318    0.135    0.375 

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: 290
Number of extensions: 11
Number of successful extensions: 3
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: 377
Length of database: 354
Length adjustment: 30
Effective length of query: 347
Effective length of database: 324
Effective search space:   112428
Effective search space used:   112428
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 49 (23.5 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