GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gtsD in Shewanella amazonensis SB2B

Align Sugar ABC transporter ATP-binding protein (characterized, see rationale)
to candidate 6936480 Sama_0668 iron(III) ABC transporter, ATP-binding protein (RefSeq)

Query= uniprot:A0A165KQ08
         (355 letters)



>FitnessBrowser__SB2B:6936480
          Length = 341

 Score =  191 bits (484), Expect = 3e-53
 Identities = 113/299 (37%), Positives = 175/299 (58%), Gaps = 13/299 (4%)

Query: 3   SSLDIAGINKRFGKGDKSVEVLRKVDIHVAPGEFLILVGPSGCGKSTLLNIIAGLDEPTE 62
           S+L I G++  +    +  +VLR +++ +  GE   L+GPSGCGK+TLL  IAGL + + 
Sbjct: 2   STLSIQGLHSDY----RGEQVLRGLNLTLTQGEITALLGPSGCGKTTLLRTIAGLQDISA 57

Query: 63  GEIRIGGKNVVG----MPPRDRDIAMVFQSYALYPTLSVADNIGFALEMRKMPKPERQKR 118
           G I I GK V      + P  R I M+FQ YAL+P L+VADNI F +  R++ K  R  R
Sbjct: 58  GSIAINGKTVSADGCFVAPEKRSIGMIFQDYALFPHLTVADNILFGV--RQLDKQSRSVR 115

Query: 119 IDEVAAMLQISHLLDRRPSQLSGGQRQRVAMGRALARQPQLFLFDEPLSNLDAKLRVEMR 178
           ++E+ +++++  L  R P +LSGGQ+QRV++ RALA +P L L DEP SN+DA++R  + 
Sbjct: 116 LEEMLSLVKLEGLGKRYPHELSGGQQQRVSIARALAYEPDLLLLDEPFSNIDAQVRRALM 175

Query: 179 AEIKRLHQASGITSVYVTHDQVEAMTLGSRIAVMKGGVVQQLGTPDEIYNRPANTYVATF 238
            EI+ + +A  +++V+VTH + EA      +A+ + G + Q G P+ +Y  P   YVA F
Sbjct: 176 LEIRAILKARNVSAVFVTHSKDEAFAFADTLALFEAGRIVQHGIPETLYQSPNTPYVADF 235

Query: 239 IGSPTMNLLRGAVTGGQFGIQGAALNLAPPPSSANEV-LLGVRPEHLVMQETAPWRGRV 296
           +G+   N L   +  GQ      A  L     +A+E     +RPE L+++  A   G +
Sbjct: 236 LGA--SNYLDVRLEAGQLISTLGAFPLPQDFKAASETGRWLLRPEQLLIEARADGAGEI 292


Lambda     K      H
   0.318    0.135    0.388 

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: 263
Number of extensions: 9
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: 355
Length of database: 341
Length adjustment: 29
Effective length of query: 326
Effective length of database: 312
Effective search space:   101712
Effective search space used:   101712
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