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_0947 Synpcc7942_0947 ATPase

Query= uniprot:A8LLL2
         (373 letters)



>FitnessBrowser__SynE:Synpcc7942_0947
          Length = 355

 Score =  249 bits (636), Expect = 8e-71
 Identities = 154/357 (43%), Positives = 212/357 (59%), Gaps = 21/357 (5%)

Query: 4   LKLTGVEKAYG-DVKVLSNINLDIQQGELIVFVGPSGCGKSTLLRMIAGLEKITGGTLEI 62
           L+L  + KAY   V  ++N++L +Q GE +  +GPSGCGKST LR+IAGL++ T G++ +
Sbjct: 6   LELRQLRKAYSPSVVPVANLSLQLQPGEFLTLLGPSGCGKSTTLRLIAGLDQPTSGSIWL 65

Query: 63  DGTVVNDVPPAQRGIAMVFQSYALYPHMTVRENMSFALKIAKKSQAEIDAAVEAAAEKLQ 122
               +  +PP  R +AMVFQSYALYPH+ VR+N++  L+I + S AEI+  ++  A  L+
Sbjct: 66  GDREITTLPPGDRDMAMVFQSYALYPHLNVRQNLTLGLQIRRTSAAEIEQRLQQVAHNLE 125

Query: 123 LGQYLDRLPKALSGGQRQRVAIGRSIVRDPKVYLFDEPLSNLDAALRVATRLEIAQLKEA 182
           L   LDR P  LSGGQRQRVA+GR++VR P V+L DEPLSNLDA LR   R ++  L  +
Sbjct: 126 LDHLLDRRPAQLSGGQRQRVALGRALVRQPSVFLLDEPLSNLDALLREQVRAQMKAL-FS 184

Query: 183 MPESTMVYVTHDQVEAMTLATRIVVLAGGGIAQVGSPLELYEKPENEFVAQFIGSPKMNL 242
              S +VYVTHDQ EA++L+ RI +L GG + Q+ SP  +Y+ P N FVA FIGSP+MNL
Sbjct: 185 QQASPVVYVTHDQTEALSLSHRIAILNGGHLQQLDSPDRIYQAPANAFVAGFIGSPRMNL 244

Query: 243 LPGKIIGTGAQTTVEMTDGGRAVSDYPSDDSLMG-AAVNVGVRPEDMVEAAPGGDYVFEG 301
           LP  I    A        G RA+   P    L   + V  G+RPE +  A P  +     
Sbjct: 245 LPLPIHSGQAWL------GSRAL---PIPSHLAARSQVLWGLRPEHLKLATPEVERAIPV 295

Query: 302 KVAITEALGEVTLLYFEAPSGEDPTIGKL----QGIHKDLKGQVTRLTAEPAKVHVF 354
           ++ +TE LG   LL     +  +  +  L    Q I  DL     ++T EP   H F
Sbjct: 296 QLHLTENLGMQRLLTVAIAANPEVRLRLLMPSDQPIPTDL-----QVTFEPESQHWF 347


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: 16
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: 355
Length adjustment: 29
Effective length of query: 344
Effective length of database: 326
Effective search space:   112144
Effective search space used:   112144
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.

Links

Downloads

Related tools

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