GapMind for catabolism of small carbon sources

 

Aligments for a candidate for gtsD in Escherichia coli BW25113

Align Sugar ABC transporter ATP-binding protein (characterized, see rationale)
to candidate 16521 b2422 sulfate/thiosulfate transporter subunit (NCBI)

Query= uniprot:A0A165KQ08
         (355 letters)



>lcl|FitnessBrowser__Keio:16521 b2422 sulfate/thiosulfate
           transporter subunit (NCBI)
          Length = 365

 Score =  221 bits (563), Expect = 2e-62
 Identities = 134/362 (37%), Positives = 203/362 (56%), Gaps = 21/362 (5%)

Query: 4   SLDIAGINKRFGKGDKSVEVLRKVDIHVAPGEFLILVGPSGCGKSTLLNIIAGLDEPTEG 63
           S++IA I K FG+     +VL  + + +  G+ + L+GPSG GK+TLL IIAGL+  T G
Sbjct: 2   SIEIANIKKSFGR----TQVLNDISLDIPSGQMVALLGPSGSGKTTLLRIIAGLEHQTSG 57

Query: 64  EIRIGGKNVVGMPPRDRDIAMVFQSYALYPTLSVADNIGFALEMRKMPKPER------QK 117
            IR  G +V  +  RDR +  VFQ YAL+  ++V DNI F L +  +P+ ER      + 
Sbjct: 58  HIRFHGTDVSRLHARDRKVGFVFQHYALFRHMTVFDNIAFGLTV--LPRRERPNAAAIKA 115

Query: 118 RIDEVAAMLQISHLLDRRPSQLSGGQRQRVAMGRALARQPQLFLFDEPLSNLDAKLRVEM 177
           ++ ++  M+Q++HL DR P+QLSGGQ+QRVA+ RALA +PQ+ L DEP   LDA++R E+
Sbjct: 116 KVTKLLEMVQLAHLADRYPAQLSGGQKQRVALARALAVEPQILLLDEPFGALDAQVRKEL 175

Query: 178 RAEIKRLHQASGITSVYVTHDQVEAMTLGSRIAVMKGGVVQQLGTPDEIYNRPANTYVAT 237
           R  +++LH+    TSV+VTHDQ EA  +  R+ VM  G ++Q   PD+++  PA  +V  
Sbjct: 176 RRWLRQLHEELKFTSVFVTHDQEEATEVADRVVVMSQGNIEQADAPDQVWREPATRFVLE 235

Query: 238 FIGSPTMNLLRGAVTGGQFGIQGAALNLAPPPSSANEVLLGVRPEHLVMQE----TAPWR 293
           F+G   +N L+G + GGQF +      L   P+    V L +RP  + +       +P  
Sbjct: 236 FMGE--VNRLQGTIRGGQFHVGAHRWPLGYTPAYQGPVDLFLRPWEVDISRRTSLDSPLP 293

Query: 294 GRVSVVEPTGPDTYVMVDTAA---GSVTLRTDAQTRVQPGEHVGLALAPAHAHWFDAQSE 350
            +V    P G  T ++V         +T+        Q GE + + L  A  +  D + E
Sbjct: 294 VQVLEASPKGHYTQLVVQPLGWYNEPLTVVMHGDDAPQRGERLFVGLQHARLYNGDERIE 353

Query: 351 ER 352
            R
Sbjct: 354 TR 355


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: 314
Number of extensions: 11
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: 365
Length adjustment: 29
Effective length of query: 326
Effective length of database: 336
Effective search space:   109536
Effective search space used:   109536
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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint on GapMind for carbon sources, or view the source code.

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