GapMind for catabolism of small carbon sources

 

Alignments 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)



>FitnessBrowser__Keio:16521
          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:

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