GapMind for catabolism of small carbon sources

 

Alignments for a candidate for glcV in Pedobacter sp. GW460-11-11-14-LB5

Align monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized)
to candidate CA265_RS04175 CA265_RS04175 phosphonate ABC transporter ATP-binding protein

Query= BRENDA::Q97UY8
         (353 letters)



>FitnessBrowser__Pedo557:CA265_RS04175
          Length = 232

 Score =  139 bits (349), Expect = 9e-38
 Identities = 84/220 (38%), Positives = 129/220 (58%), Gaps = 5/220 (2%)

Query: 4   IIVKNVSKVFKKGKV--VALDNVNINIENGERFGILGPSGAGKTTFMRIIAGLDVPSTGE 61
           I ++N+ KV+K  +V   AL+ +N+++  GE   I+GPSG GK+T + ++  LD P  G 
Sbjct: 2   IKIENLEKVYKTEEVETTALNGINLHVAAGEFVSIMGPSGCGKSTLLNVMGLLDKPENGS 61

Query: 62  LYF-DDRLVASNGKLIVPPEDRKIGMVFQTWALYPNLTAFENIAFPLTNMKMSKEEIRKR 120
             F D  L+  N +       R +G VFQ + L   LT FENI  PL   K+   E +K 
Sbjct: 62  YKFIDTELLTLNDRERSNFRKRNMGFVFQNFNLIDELTVFENIELPLIYNKIPAGERKKL 121

Query: 121 VEEVAKILDIHHVLNHFPRELSGGQQQRVALARALVKDPSLLLLDEPFSNLDARMRDSAR 180
           V E+ + ++I +   HFP++LSGGQQQRVA+ARALV  P L+L DEP  NLD+   +   
Sbjct: 122 VNEIIERMNIVNRSGHFPQQLSGGQQQRVAVARALVTKPKLVLADEPTGNLDSSHGNEVM 181

Query: 181 ALVKEVQSRLGVTLLVVSHDPADIFAIADRVGVLVKGKLV 220
            L+ E+ +  G T+++V+H   D  + ++R+  L  G ++
Sbjct: 182 ELLCEL-NETGTTIVMVTHSSHDA-SFSNRIINLKDGHVI 219


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: 197
Number of extensions: 11
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: 232
Length adjustment: 26
Effective length of query: 327
Effective length of database: 206
Effective search space:    67362
Effective search space used:    67362
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: 47 (22.7 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