GapMind for catabolism of small carbon sources

 

Alignments for a candidate for glcV in Pseudomonas stutzeri RCH2

Align monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized)
to candidate GFF857 Psest_0871 ABC-type sugar transport systems, ATPase components

Query= BRENDA::Q97UY8
         (353 letters)



>FitnessBrowser__psRCH2:GFF857
          Length = 371

 Score =  194 bits (494), Expect = 2e-54
 Identities = 124/369 (33%), Positives = 204/369 (55%), Gaps = 29/369 (7%)

Query: 1   MVRIIVKNVSKVFKKGKVVALDNVNINIENGERFGILGPSGAGKTTFMRIIAGLDVPSTG 60
           M  + ++++ K +    +    +++++IE+GE    +GPSG GK+T +R+IAGL+  ++G
Sbjct: 1   MASVTLRDICKSYDGTPITR--HIDLDIEDGEFVVFVGPSGCGKSTLLRLIAGLEDITSG 58

Query: 61  ELYFDDRLVASNGKLIVPPEDRKIGMVFQTWALYPNLTAFENIAFPLTNMKMSKEEIRKR 120
           +L  D++ V       +PP+DR +GMVFQ++ALYP++T  EN+AF L    + K EI++R
Sbjct: 59  DLLIDNQRVND-----LPPKDRSVGMVFQSYALYPHMTVAENMAFGLKLASVDKREIKRR 113

Query: 121 VEEVAKILDIHHVLNHFPRELSGGQQQRVALARALVKDPSLLLLDEPFSNLDARMRDSAR 180
           VE VA+IL +  +L   P++LSGGQ+QRVA+ R +V++P + L DEP SNLDA +R   R
Sbjct: 114 VEAVAEILQLDKLLERKPKDLSGGQRQRVAIGRTMVREPKVFLFDEPLSNLDAFLRVQMR 173

Query: 181 ALVKEVQSRLGVTLLVVSHDPADIFAIADRVGVLVKGKLVQVGKPEDLYDNPVSIQVASL 240
             +  +  R+  T++ V+HD  +   +AD++ VL  G++ QVG+P  LY  P +  VA  
Sbjct: 174 IEIARLHQRIRSTMIYVTHDQVEAMTLADKIVVLNAGEIAQVGQPLHLYHYPKNRFVAGF 233

Query: 241 IG--EINELEGKVTN---EGVVIG-----SLRFPVSVSS----DRAIIGIRPEDVKLSKD 286
           +G  ++N +E +  +   E V I       L  PV  S+    D   +GIRPE       
Sbjct: 234 LGSPQMNFVEVRAISASPETVTIELPSGYPLTLPVDGSAVSPGDPLTLGIRPE------H 287

Query: 287 VIKDDSWILVGKGKVKVIGYQG--GLFRITITPLDSEEEIFTYSDHPIHSGEEVLVYVRK 344
            +  D       G++ V    G   L  +T+  L     +    +  +  GE     ++ 
Sbjct: 288 FVMPDEADFTFHGQITVAERLGQYNLLYLTLERLQDVITLCVDGNLRVTEGETFAAGLKA 347

Query: 345 DKIKVFEKN 353
           DK  +F +N
Sbjct: 348 DKCHLFREN 356


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: 282
Number of extensions: 12
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