GapMind for catabolism of small carbon sources

 

Alignments for a candidate for aglK' in Synechococcus elongatus PCC 7942

Align Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale)
to candidate Synpcc7942_1406 Synpcc7942_1406 ATPase

Query= uniprot:A8LLL2
         (373 letters)



>FitnessBrowser__SynE:Synpcc7942_1406
          Length = 368

 Score =  175 bits (443), Expect = 2e-48
 Identities = 110/314 (35%), Positives = 168/314 (53%), Gaps = 30/314 (9%)

Query: 19  LSNINLDIQQGELIVFVGPSGCGKSTLLRMIAGLEKITGGTLEIDG----TVVNDVPPAQ 74
           +  ++ +++ GE++  VGPSGCGK+TLLRMIAG E +  G++++ G    T    +PP  
Sbjct: 24  VDQVSFELEAGEILGLVGPSGCGKTTLLRMIAGFESLQSGSIQLAGETVATAQRSLPPET 83

Query: 75  RGIAMVFQSYALYPHMTVRENMSFALKIAKKSQAEIDAAVEAAAEKLQLGQYLDRLPKAL 134
           R + MVFQ YAL+PH+TV +N+ F L+  K S     A    A   + L     R P  L
Sbjct: 84  RSVGMVFQDYALFPHLTVLDNVCFGLRDRKGSA----AVARQALALVGLEGLERRYPHEL 139

Query: 135 SGGQRQRVAIGRSIVRDPKVYLFDEPLSNLDAALRVATRLEIAQLKEAMPESTMVYVTHD 194
           SGGQ+QRVA+ R++   P + L DEPLSNLD  +R+  R E+  +     ++T + VTHD
Sbjct: 140 SGGQQQRVALARALAPQPPLILLDEPLSNLDVQVRLRLRQELRDILR-QAQATAILVTHD 198

Query: 195 QVEAMTLATRIVVLAGGGIAQVGSPLELYEKPENEFVAQFIGSPKMNLLPGKIIGTGAQT 254
           Q EA+++  R+ V+  G   Q+G P EL++ P + FVA+F+   + N L  +  G   +T
Sbjct: 199 QEEALSICDRVAVMRLGRFEQIGQPEELFQHPASRFVAEFLS--QANFLATEYQGDAWRT 256

Query: 255 TVEMTDGGRAVSDYPSDDSLMGAAVN-----VGVRPED-MVEAAPGGDYVFEGKVAITEA 308
                     + D+ +   L G+        V VR ED ++   P G     G V   + 
Sbjct: 257 ---------VLGDFEAPGGLEGSRTGGEPPVVMVRQEDVLLHPHPEG----TGLVRDRQF 303

Query: 309 LGEVTLLYFEAPSG 322
           LG     + + P+G
Sbjct: 304 LGRDYRYFVQLPAG 317


Lambda     K      H
   0.316    0.135    0.379 

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: 341
Number of extensions: 14
Number of successful extensions: 4
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: 373
Length of database: 368
Length adjustment: 30
Effective length of query: 343
Effective length of database: 338
Effective search space:   115934
Effective search space used:   115934
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 (21.6 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