GapMind for catabolism of small carbon sources

 

Alignments for a candidate for SM_b21106 in Dechlorosoma suillum PS

Align ABC transporter for L-Fucose, ATPase component (characterized)
to candidate Dsui_2943 Dsui_2943 ABC-type spermidine/putrescine transport system, ATPase component

Query= reanno::Smeli:SM_b21106
         (365 letters)



>FitnessBrowser__PS:Dsui_2943
          Length = 356

 Score =  198 bits (504), Expect = 2e-55
 Identities = 118/299 (39%), Positives = 168/299 (56%), Gaps = 26/299 (8%)

Query: 1   MAPVTLKKLVKRYGALEVVHGIDLEVKDREFIALVGPSGCGKSTTLRMIAGLEEVSGGAI 60
           MA + L  +++RYGA  VV GI   ++      L+GPSGCGK+T LR IAG E+++ G+I
Sbjct: 1   MAHLELADVMQRYGAHTVVDGIGFHIEAGVIACLLGPSGCGKTTLLRCIAGFEDIAAGSI 60

Query: 61  EIGGRKVN----DLPPRARNISMVFQSYALYPHMTVAENMGFSLKIAGRPAEEIKTRVAE 116
            + G  V+     L P  R I MVFQ YAL+PH+TVA+N+ F LK  G   ++   RVA 
Sbjct: 61  ALDGELVSRPGFKLAPEQRRIGMVFQDYALFPHLTVADNIAFGLKTKGGERQQ---RVAA 117

Query: 117 AAAILDLAHLLERRPSQLSGGQRQRVAMGRAIVRQPDVFLFDEPLSNLDAKLRTQVRTEI 176
              ++ LA   E+ P +LSGGQ+QRVA+ RA+   P + L DEP SNLD  LR ++  E+
Sbjct: 118 MLDLVGLAGQGEKYPHELSGGQQQRVALARALAPAPRLVLLDEPFSNLDVDLRERLSLEV 177

Query: 177 KKLHARMQATMIYVTHDQVEAMTLSDRIVIMRDGHIEQVGTPEDVFRRPATKFVAGFIG- 235
           +++  +   T I VTHDQ EA  ++D I +M +G I+Q  TP +++ +PA +FVA F+G 
Sbjct: 178 REILKKAGTTAILVTHDQHEAFAMADEIGVMHEGRIQQWDTPYNLYHQPANRFVADFVGQ 237

Query: 236 ----------SPPMNMEEAVLTDGKLAFASGATLPLPPRFRSLVREGQKVTFGLRPDDV 284
                        + ME  +L  G     S            +  +G  V   LRPDDV
Sbjct: 238 GVFVPGTVLAGNRVQMELGILESGVPVECSAGC--------GVCGKGCGVDILLRPDDV 288


Lambda     K      H
   0.320    0.137    0.397 

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: 344
Number of extensions: 14
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: 365
Length of database: 356
Length adjustment: 29
Effective length of query: 336
Effective length of database: 327
Effective search space:   109872
Effective search space used:   109872
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 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