GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gtsD in Dyella japonica UNC79MFTsu3.2

Align Sugar ABC transporter ATP-binding protein (characterized, see rationale)
to candidate N515DRAFT_2392 N515DRAFT_2392 putative ABC transport system ATP-binding protein

Query= uniprot:A0A165KQ08
         (355 letters)



>FitnessBrowser__Dyella79:N515DRAFT_2392
          Length = 254

 Score =  124 bits (311), Expect = 3e-33
 Identities = 75/225 (33%), Positives = 120/225 (53%), Gaps = 8/225 (3%)

Query: 2   ASSLDIAGINKRFGKGDKSVEVLRKVDIHVAPGEFLILVGPSGCGKSTLLNIIAGLDEPT 61
           A+ + +  + K F   +     L  V + +A GE++ + GPSGCGK+TLL+I+  LD  T
Sbjct: 5   ANVITLRDLRKVFQTDEVETHALSDVHLSIARGEYVSISGPSGCGKTTLLSILGLLDTAT 64

Query: 62  EGEIRIGGKNVVGMPP------RDRDIAMVFQSYALYPTLSVADNIGFALEMRK-MPKPE 114
            G   + G +V  +        R+ +I  +FQ++ L   LSV +N+   L  R  +   E
Sbjct: 65  SGSFVLNGHDVATLNAAQRARIRNAEIGFIFQAFNLIGDLSVQENVELPLTYRSSIGAAE 124

Query: 115 RQKRIDEVAAMLQISHLLDRRPSQLSGGQRQRVAMGRALARQPQLFLFDEPLSNLDAKLR 174
           R+ R+ E    + ++H +   P+QLSGGQ+QRVA+ RAL  +P + L DEP  NLD++  
Sbjct: 125 RRARVQEALERVGMAHRMRHYPAQLSGGQQQRVAVARALVGRPAILLADEPTGNLDSRNG 184

Query: 175 VEMRAEIKRLHQASGITSVYVTHDQVEAMTLGSRIAVMKGGVVQQ 219
             + + +  LH+  G T   VTHD   A     ++ +  G VV +
Sbjct: 185 EAVMSLLDELHK-GGATICMVTHDARYAELAQRKVRLFDGRVVDE 228


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: 220
Number of extensions: 10
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: 254
Length adjustment: 27
Effective length of query: 328
Effective length of database: 227
Effective search space:    74456
Effective search space used:    74456
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: 48 (23.1 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