GapMind for catabolism of small carbon sources

 

Alignments for a candidate for glcV in Escherichia coli BW25113

Align monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized)
to candidate 18063 b4035 fused maltose transport subunit, ATP-binding component of ABC superfamily/regulatory protein (NCBI)

Query= BRENDA::Q97UY8
         (353 letters)



>FitnessBrowser__Keio:18063
          Length = 371

 Score =  203 bits (517), Expect = 5e-57
 Identities = 123/332 (37%), Positives = 195/332 (58%), Gaps = 31/332 (9%)

Query: 1   MVRIIVKNVSKVFKKGKVVALDNVNINIENGERFGILGPSGAGKTTFMRIIAGLDVPSTG 60
           M  + ++NV+K +  G+VV   ++N++I  GE    +GPSG GK+T +R+IAGL+  ++G
Sbjct: 1   MASVQLQNVTKAW--GEVVVSKDINLDIHEGEFVVFVGPSGCGKSTLLRMIAGLETITSG 58

Query: 61  ELYFDDRLVASNGKLIVPPEDRKIGMVFQTWALYPNLTAFENIAFPLTNMKMSKEEIRKR 120
           +L+  ++ +        PP +R +GMVFQ++ALYP+L+  EN++F L      KE I +R
Sbjct: 59  DLFIGEKRMNDT-----PPAERGVGMVFQSYALYPHLSVAENMSFGLKLAGAKKEVINQR 113

Query: 121 VEEVAKILDIHHVLNHFPRELSGGQQQRVALARALVKDPSLLLLDEPFSNLDARMRDSAR 180
           V +VA++L + H+L+  P+ LSGGQ+QRVA+ R LV +PS+ LLDEP SNLDA +R   R
Sbjct: 114 VNQVAEVLQLAHLLDRKPKALSGGQRQRVAIGRTLVAEPSVFLLDEPLSNLDAALRVQMR 173

Query: 181 ALVKEVQSRLGVTLLVVSHDPADIFAIADRVGVLVKGKLVQVGKPEDLYDNPVSIQVASL 240
             +  +  RLG T++ V+HD  +   +AD++ VL  G++ QVGKP +LY  P    VA  
Sbjct: 174 IEISRLHKRLGRTMIYVTHDQVEAMTLADKIVVLDAGRVAQVGKPLELYHYPADRFVAGF 233

Query: 241 IG--EINELEGKVTNEGVVIGSLRFP---------------VSVSSDRAIIGIRPEDVKL 283
           IG  ++N L  KVT   +    +  P               V V ++ + +GIRPE    
Sbjct: 234 IGSPKMNFLPVKVTATAIDQVQVELPMPNRQQVWLPVESRDVQVGANMS-LGIRPE---- 288

Query: 284 SKDVIKDDSWILVGKGKVKVIGYQGGLFRITI 315
              ++  D   ++ +G+V+V+   G   +I I
Sbjct: 289 --HLLPSDIADVILEGEVQVVEQLGNETQIHI 318


Lambda     K      H
   0.319    0.139    0.390 

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: 283
Number of extensions: 10
Number of successful extensions: 2
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: 353
Length of database: 371
Length adjustment: 29
Effective length of query: 324
Effective length of database: 342
Effective search space:   110808
Effective search space used:   110808
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 (21.7 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