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 203725 SO4655 sulfate ABC transporter, ATP-binding protein (NCBI ptt file)

Query= BRENDA::Q8NMV1
         (376 letters)



>FitnessBrowser__MR1:203725
          Length = 354

 Score =  201 bits (511), Expect = 3e-56
 Identities = 120/295 (40%), Positives = 172/295 (58%), Gaps = 13/295 (4%)

Query: 21  VKKFNLEIADGEFLVLVGPSGCGKSTTLRMLAGLENVTDGAIFIGDKDVTHVAPRDRDIA 80
           V   NLEI  GE   L+GPSG GK+T LR++AGLE    G +    +D+T     +R + 
Sbjct: 18  VDSVNLEIKTGELTALLGPSGSGKTTLLRIIAGLEQADSGIVKFNGEDITTQHVSERGVG 77

Query: 81  MVFQNYALYPHMTVGENMGFALKIAGK----SQDEINKRVDEAAATLGLTEFLERKPKAL 136
            VFQ+YAL+ HMTV EN+ + L +  +    S+ EI ++V      + L    +R P  L
Sbjct: 78  FVFQHYALFKHMTVFENVAYGLTVRPRKTRPSKAEIAEKVHSLLKLVQLDWTADRYPSQL 137

Query: 137 SGGQRQRVAMGRAIVRNPQVFLMDEPLSNLDAKLRVQTRTQIAALQRKLGVTTVYVTHDQ 196
           SGGQRQR+A+ RA+   P+V L+DEP   LDAK+R + R  +  L  ++ VTTV+VTHDQ
Sbjct: 138 SGGQRQRIALARALAVEPKVLLLDEPFGALDAKVRAELRRWLRRLHDEINVTTVFVTHDQ 197

Query: 197 TEALTMGDRIAVLKDGYLQQVGAPRELYDRPANVFVAGFIGSPAMNLGTFSVKDGDATSG 256
            EAL + D+I V+  G ++Q G P E+YD P+N FV  F+G+  +NL    VK G +T G
Sbjct: 198 EEALEVADKIVVMNKGRIEQQGTPEEVYDTPSNPFVYEFLGN--VNLFHARVKHGHSTIG 255

Query: 257 HARIKLSPETLAAMTPEDNGRITIGFRPEALEIIPEGESTDLSIPIKLDFVEELG 311
           +  I  SPE   A   E  G   +  RP  +E++   + T+ +I + LD V  +G
Sbjct: 256 NIHIP-SPE--HAGGEEQQGLAYV--RPHEIEVLT--QPTENAIKVNLDLVTIVG 303


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: 326
Number of extensions: 17
Number of successful extensions: 2
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: 354
Length adjustment: 30
Effective length of query: 346
Effective length of database: 324
Effective search space:   112104
Effective search space used:   112104
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: 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