GapMind for catabolism of small carbon sources

 

Alignments for a candidate for aglK' in Sinorhizobium meliloti 1021

Align Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale)
to candidate SM_b20002 SM_b20002 sugar ABC transporter ATP-binding protein

Query= uniprot:A8LLL2
         (373 letters)



>FitnessBrowser__Smeli:SM_b20002
          Length = 358

 Score =  331 bits (849), Expect = 2e-95
 Identities = 182/316 (57%), Positives = 225/316 (71%), Gaps = 5/316 (1%)

Query: 1   MADLKLTGVEKAYGDVKVLSNINLDIQQGELIVFVGPSGCGKSTLLRMIAGLEKITGGTL 60
           M++L+L+ V K+YG ++V+  ++LDI+ GE +VFVGPSGCGKSTLLRMIAGLE+I+ G L
Sbjct: 1   MSELQLSDVRKSYGGLEVIKGVDLDIKSGEFVVFVGPSGCGKSTLLRMIAGLEEISSGDL 60

Query: 61  EIDGTVVNDVPPAQRGIAMVFQSYALYPHMTVRENMSFALKIAKKSQAEIDAAVEAAAEK 120
            ID   +NDV P++RGIAMVFQSYALYPHMTVRENM FAL+ A   +AEI+  V  AA  
Sbjct: 61  TIDDVRMNDVDPSKRGIAMVFQSYALYPHMTVRENMGFALRFAGVPRAEIEKRVNEAAHI 120

Query: 121 LQLGQYLDRLPKALSGGQRQRVAIGRSIVRDPKVYLFDEPLSNLDAALRVATRLEIAQLK 180
           L+LG  LDR PK LSGGQRQRVAIGR+IVR PK++LFDEPLSNLDA LRV  R+EIA+L 
Sbjct: 121 LELGALLDRKPKQLSGGQRQRVAIGRAIVRHPKIFLFDEPLSNLDAELRVHMRIEIARLH 180

Query: 181 EAMPESTMVYVTHDQVEAMTLATRIVVLAGGGIAQVGSPLELYEKPENEFVAQFIGSPKM 240
           + +  +T+VYVTHDQVEAMTLA +IVV+  G + QVGSPL+LY+ P N FVA FIGSPKM
Sbjct: 181 KQL-ATTIVYVTHDQVEAMTLADKIVVMRAGVVEQVGSPLDLYDDPANLFVAGFIGSPKM 239

Query: 241 NLLPGKIIGTGAQTTVEMTDGGRAVSDYPSDDSLMGAAVNVGVRPEDMVEAAPGGDYVFE 300
           N L G I     Q    + D G A     +  +  G AV +G+RPE   EA P      +
Sbjct: 240 NFLKGVIEIDEDQAYARLPDYGDAKIPV-TLQAAAGTAVTIGIRPEHFDEAGPA---ALD 295

Query: 301 GKVAITEALGEVTLLY 316
             + + E LG  T  Y
Sbjct: 296 LAIDMLEHLGGETFAY 311


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: 417
Number of extensions: 18
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: 373
Length of database: 358
Length adjustment: 30
Effective length of query: 343
Effective length of database: 328
Effective search space:   112504
Effective search space used:   112504
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