GapMind for catabolism of small carbon sources

 

Alignments for a candidate for aglK in Escherichia coli BW25113

Align ABC transporter for D-Maltose and D-Trehalose, ATPase component (characterized)
to candidate 15248 b1126 putrescine/spermidine ABC transporter ATPase protein (NCBI)

Query= reanno::Smeli:SMc03065
         (362 letters)



>FitnessBrowser__Keio:15248
          Length = 378

 Score =  239 bits (609), Expect = 1e-67
 Identities = 139/302 (46%), Positives = 185/302 (61%), Gaps = 6/302 (1%)

Query: 6   LKDIRKSYGAVDVIHGIDLDIKEGEFVVFVGPSGCGKSTLLRMIAGLEEITGGDMFIDGE 65
           L  IRK +   +VI  +DL I  GEF+  +GPSGCGK+T+LR+IAGLE +  G + +D E
Sbjct: 20  LAGIRKCFDGKEVIPQLDLTINNGEFLTLLGPSGCGKTTVLRLIAGLETVDSGRIMLDNE 79

Query: 66  RVNDVPPSKRGIAMVFQSYALYPHMTVYDNMAFGMRIARESKEEIDRRVRGAADMLQLTP 125
            +  VP   R +  VFQSYAL+PHMTV++N+AFG+R+ +    EI  RV  A  M+QL  
Sbjct: 80  DITHVPAENRYVNTVFQSYALFPHMTVFENVAFGLRMQKTPAAEITPRVMEALRMVQLET 139

Query: 126 YLDRLPKALSGGQRQRVAIGRAICRNPKVFLFDEPLSNLDAALRVATRIEIAKLSERMSD 185
           +  R P  LSGGQ+QRVAI RA+   P++ L DE LS LD  LR   + E+  L  ++  
Sbjct: 140 FAQRKPHQLSGGQQQRVAIARAVVNKPRLLLLDESLSALDYKLRKQMQNELKALQRKLG- 198

Query: 186 TTMIYVTHDQVEAMTLADRIVVLSAGHIEQVGAPLELYERPANLFVARFIGSPAMNVIPA 245
            T ++VTHDQ EA+T++DRIVV+  G IEQ G P E+YE P NLFVA FIG   +N+  A
Sbjct: 199 ITFVFVTHDQEEALTMSDRIVVMRDGRIEQDGTPREIYEEPKNLFVAGFIGE--INMFNA 256

Query: 246 T-ITATGQQTAVSLAGGKSVTLDVPTNASENGKTASFGVRPEDLRVTEA-DDFLFEGTVS 303
           T I    +Q   +   G+   + V   A E G+     +RPEDLRV E  DD   EG + 
Sbjct: 257 TVIERLDEQRVRANVEGRECNIYV-NFAVEPGQKLHVLLRPEDLRVEEINDDNHAEGLIG 315

Query: 304 IV 305
            V
Sbjct: 316 YV 317


Lambda     K      H
   0.320    0.137    0.387 

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: 299
Number of extensions: 10
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: 362
Length of database: 378
Length adjustment: 30
Effective length of query: 332
Effective length of database: 348
Effective search space:   115536
Effective search space used:   115536
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