GapMind for catabolism of small carbon sources

 

Alignments for a candidate for malK_Bb in Escherichia coli BW25113

Align ABC-type maltose transport, ATP binding protein (characterized, see rationale)
to candidate 15248 b1126 putrescine/spermidine ABC transporter ATPase protein (NCBI)

Query= uniprot:Q6MNM2
         (347 letters)



>FitnessBrowser__Keio:15248
          Length = 378

 Score =  247 bits (630), Expect = 4e-70
 Identities = 125/247 (50%), Positives = 169/247 (68%), Gaps = 2/247 (0%)

Query: 4   IQFSNIKKSFGSADVLKGIDLDIAPGEFLVLVGPSGCGKSTLLRTLAGLESADSGTISID 63
           +Q + I+K F   +V+  +DL I  GEFL L+GPSGCGK+T+LR +AGLE+ DSG I +D
Sbjct: 18  VQLAGIRKCFDGKEVIPQLDLTINNGEFLTLLGPSGCGKTTVLRLIAGLETVDSGRIMLD 77

Query: 64  GKKINDIEPQNRDIAMVFQSYALYPHMTVAENMGFGLKLKNLAAAEITKRVNEISELLQI 123
            + I  +  +NR +  VFQSYAL+PHMTV EN+ FGL+++   AAEIT RV E   ++Q+
Sbjct: 78  NEDITHVPAENRYVNTVFQSYALFPHMTVFENVAFGLRMQKTPAAEITPRVMEALRMVQL 137

Query: 124 KHLLDRKPKELSGGQRQRVALGRALSRQTPVILFDEPLSNLDAHLRSQMRLEIKRLHHNS 183
           +    RKP +LSGGQ+QRVA+ RA+  +  ++L DE LS LD  LR QM+ E+K L    
Sbjct: 138 ETFAQRKPHQLSGGQQQRVAIARAVVNKPRLLLLDESLSALDYKLRKQMQNELKALQRKL 197

Query: 184 KSTMIYVTHDQMEATTLGDRIAVLKDGVIEQIGTPSEIYHRPKNTFIATFIGSPEMNFLE 243
             T ++VTHDQ EA T+ DRI V++DG IEQ GTP EIY  PKN F+A FIG  E+N   
Sbjct: 198 GITFVFVTHDQEEALTMSDRIVVMRDGRIEQDGTPREIYEEPKNLFVAGFIG--EINMFN 255

Query: 244 GAVLEKI 250
             V+E++
Sbjct: 256 ATVIERL 262


Lambda     K      H
   0.318    0.136    0.383 

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: 273
Number of extensions: 7
Number of successful extensions: 1
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: 347
Length of database: 378
Length adjustment: 29
Effective length of query: 318
Effective length of database: 349
Effective search space:   110982
Effective search space used:   110982
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 (21.7 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