GapMind for catabolism of small carbon sources

 

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

Align ABC-type maltose transporter (EC 7.5.2.1) (characterized)
to candidate 200449 SO1271 polyamine ABC transporter, ATP-binding protein (NCBI ptt file)

Query= BRENDA::Q8NMV1
         (376 letters)



>FitnessBrowser__MR1:200449
          Length = 378

 Score =  212 bits (540), Expect = 1e-59
 Identities = 119/285 (41%), Positives = 171/285 (60%), Gaps = 17/285 (5%)

Query: 21  VKKFNLEIADGEFLVLVGPSGCGKSTTLRMLAGLENVTDGAIFIGDKDVTHVAPRDRDIA 80
           V   +L I  GE   L+G SG GKST LRMLAG E  T G I++  +D+T + P +R I 
Sbjct: 36  VDDVSLTINKGEIFALLGGSGSGKSTLLRMLAGFERPTSGRIYLDGEDITDLPPYERPIN 95

Query: 81  MVFQNYALYPHMTVGENMGFALKIAGKSQDEINKRVDEAAATLGLTEFLERKPKALSGGQ 140
           M+FQ+YAL+PHMTV +N+ F LK     + EI +RV E    + + ++ +RKP  LSGGQ
Sbjct: 96  MMFQSYALFPHMTVAQNIAFGLKQDKLPKAEIEQRVQEMLKLVHMEQYGKRKPHQLSGGQ 155

Query: 141 RQRVAMGRAIVRNPQVFLMDEPLSNLDAKLRVQTRTQIAALQRKLGVTTVYVTHDQTEAL 200
           RQRVA+ R++ + P++ L+DEP+  LD KLR Q + ++  +  ++GVT V VTHDQ EA+
Sbjct: 156 RQRVALARSLAKRPKLLLLDEPMGALDKKLRTQMQLEVVEILERVGVTCVMVTHDQEEAM 215

Query: 201 TMGDRIAVLKDGYLQQVGAPRELYDRPANVFVAGFIGSPAMNLGTFSVKDGDATSGHARI 260
           TM  RI+++ DG++ Q G+P ++Y+ P +  +A FIGS  +  G   V + D    H  I
Sbjct: 216 TMAGRISIMSDGWIAQTGSPMDIYESPNSRMIAEFIGSVNLFSGEIEVDEVD----HLII 271

Query: 261 KLSPETLA--------AMTPEDNGRITIGFRPEALEII---PEGE 294
           K  P  LA          T  ++ R+ +  RPE   I    PEGE
Sbjct: 272 K--PNDLARSFYVGYGVTTSLEDKRVWLAVRPEKTIISREQPEGE 314


Lambda     K      H
   0.316    0.135    0.380 

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: 339
Number of extensions: 13
Number of successful extensions: 1
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: 376
Length of database: 378
Length adjustment: 30
Effective length of query: 346
Effective length of database: 348
Effective search space:   120408
Effective search space used:   120408
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 (21.6 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