GapMind for catabolism of small carbon sources

 

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

Align MalK, component of Maltose/Maltotriose/maltodextrin (up to 7 glucose units) transporters MalXFGK (MsmK (3.A.1.1.28) can probably substitute for MalK; Webb et al., 2008) (characterized)
to candidate 202699 SO3602 sulfate ABC transporter, ATP-binding protein (NCBI ptt file)

Query= TCDB::Q8DT25
         (377 letters)



>FitnessBrowser__MR1:202699
          Length = 376

 Score =  196 bits (497), Expect = 1e-54
 Identities = 107/269 (39%), Positives = 165/269 (61%), Gaps = 18/269 (6%)

Query: 3   TLKLDNIYKRYPNAKHYSVENFNLDIHDKEFIVFVGPSGCGKSTTLRMIAGLEDITEGNL 62
           +++L NI K++   +  ++   NLDI + E I  +GPSG GK+T LR+IAGLE    G++
Sbjct: 2   SIRLTNISKKF--GQFQALSPLNLDIQEGEMIGLLGPSGSGKTTLLRIIAGLEGADSGHI 59

Query: 63  YIDDKLMNDASPKDRDIAMVFQNYALYPHMSVYENMAFGLKLRKYKKD----DINKRVHE 118
           +  ++ +     +DR +  VFQNYAL+ HM+V +N+AFGL++   K+     +I KRV  
Sbjct: 60  HFGNRDVTQVHVRDRRVGFVFQNYALFRHMTVADNVAFGLEVIPKKQRPSAAEIQKRVSH 119

Query: 119 AAEILGLTEFLERKPADLSGGQRQRVAMGRAIVRDAKVFLMDEPLSNLDAKLRVAMRAEI 178
             E++ L    +R P  LSGGQ+QR+A+ RA+    +V L+DEP   LDAK+R  +R  +
Sbjct: 120 LLEMVQLGHLAQRYPEQLSGGQKQRIALARALATQPEVLLLDEPFGALDAKVRKELRRWL 179

Query: 179 AKIHRRIGATTIYVTHDQTEAMTLADRIVIMSATPNPDKTGSIGRIEQIGTPQELYNEPA 238
             +H  +  T+++VTHDQ EA+ L+DR+V+MS           G IEQ+ TP ELY +P 
Sbjct: 180 RSLHDELKFTSVFVTHDQDEALELSDRVVVMSN----------GNIEQVNTPIELYAQPN 229

Query: 239 NKFVAGFIGSPAMNFFEVTVEKERLVNQD 267
           ++FV  F+G+  +N FE   ++ R  N D
Sbjct: 230 SRFVFDFLGN--VNRFEANWQQNRWTNGD 256


Lambda     K      H
   0.318    0.135    0.379 

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: 320
Number of extensions: 12
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: 376
Length adjustment: 30
Effective length of query: 347
Effective length of database: 346
Effective search space:   120062
Effective search space used:   120062
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: 50 (23.9 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