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_1562 N515DRAFT_1562 sulfate transport system ATP-binding protein

Query= uniprot:A0A165KQ08
         (355 letters)



>FitnessBrowser__Dyella79:N515DRAFT_1562
          Length = 384

 Score =  221 bits (562), Expect = 3e-62
 Identities = 124/308 (40%), Positives = 187/308 (60%), Gaps = 13/308 (4%)

Query: 4   SLDIAGINKRFGKGDKSVEVLRKVDIHVAPGEFLILVGPSGCGKSTLLNIIAGLDEPTEG 63
           SL I  + +R+G    +   L    + +A GEF+ L+GPSG GKS+LL I+AGLD+P  G
Sbjct: 2   SLSIRQLTRRYG----AFAALDDFSLDIAEGEFVALLGPSGSGKSSLLRILAGLDDPDRG 57

Query: 64  EIRIGGKNVVGMPPRDRDIAMVFQSYALYPTLSVADNIGFALEMR-KMPKPERQK---RI 119
           ++   G +++ +P + RDI +VFQ YAL+P ++VADNI F L +R +  +P R+    R+
Sbjct: 58  DVLRDGTDLLALPAQRRDIGLVFQHYALFPHMTVADNIAFGLRVRPRARRPSRRDIAARV 117

Query: 120 DEVAAMLQISHLLDRRPSQLSGGQRQRVAMGRALARQPQLFLFDEPLSNLDAKLRVEMRA 179
           +++   +Q+  L  R P+QLSGGQRQRVA+ RALA +P L L DEP   LDA++R  +R 
Sbjct: 118 EDLLRRVQLEELGRRYPTQLSGGQRQRVALARALAVEPSLLLLDEPFGALDAQVRGTLRV 177

Query: 180 EIKRLHQASGITSVYVTHDQVEAMTLGSRIAVMKGGVVQQLGTPDEIYNRPANTYVATFI 239
            ++ L ++ G+T+V VTHDQ EA+ L  R+ VM  G ++Q+G P EIY  PA  +V  F+
Sbjct: 178 WLRDLQRSLGLTTVLVTHDQDEALELADRVVVMNRGRIEQVGAPSEIYREPATPFVHGFV 237

Query: 240 GSPTMNLLRGAVTGGQFGIQGAAL-NLAPPPSSANEVLLGVRPEHLVM--QETAPWRGRV 296
           G    N +RG V   +  + G +     P   +  E+   +RPEHL +  +    W GR+
Sbjct: 238 G--RANRIRGHVERDRLHLGGHSFQGELPGDLAGREIEAWLRPEHLALASRGLGGWTGRL 295

Query: 297 SVVEPTGP 304
             ++  GP
Sbjct: 296 QHLDLAGP 303


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: 365
Number of extensions: 15
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: 355
Length of database: 384
Length adjustment: 30
Effective length of query: 325
Effective length of database: 354
Effective search space:   115050
Effective search space used:   115050
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