GapMind for catabolism of small carbon sources

 

Alignments for a candidate for glcV in Echinicola vietnamensis KMM 6221, DSM 17526

Align monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized)
to candidate Echvi_1022 Echvi_1022 ABC-type spermidine/putrescine transport systems, ATPase components

Query= BRENDA::Q97UY8
         (353 letters)



>FitnessBrowser__Cola:Echvi_1022
          Length = 345

 Score =  182 bits (461), Expect = 1e-50
 Identities = 102/280 (36%), Positives = 160/280 (57%), Gaps = 7/280 (2%)

Query: 9   VSKVFKKGKVVALDNVNINIENGERFGILGPSGAGKTTFMRIIAGLDVPSTGELYFDDRL 68
           +SK F + K  A+ ++++ IE G    I+G +G+GKTT +++IAGL+ P  GE+ F  + 
Sbjct: 9   ISKKFPQTKQFAVKDIHMEIEEGSVQAIVGENGSGKTTLLKLIAGLEHPDKGEIVFSGQT 68

Query: 69  VASNGKLIVPPEDRKIGMVFQTWALYPNLTAFENIAFPLTNMKMSKEEIRKRVEEVAKIL 128
           +  NGK  +P   R++G++FQ +AL+P +T  EN+   L     +  +I      +A + 
Sbjct: 69  IV-NGKSALPANQREVGVIFQEYALFPQMTLLENVREALHQESRNARQIAMDSLALAGLE 127

Query: 129 DIHHVLNHFPRELSGGQQQRVALARALVKDPSLLLLDEPFSNLDARMRDSARALVKEVQS 188
           D     + +P +LS GQ+QR ALARAL   P LLLLD+PF +LD R ++     ++++  
Sbjct: 128 DS---FSAYPHQLSSGQRQRAALARALASRPKLLLLDDPFRSLDTRFKNEISEDIRDIVK 184

Query: 189 RLGVTLLVVSHDPADIFAIADRVGVLVKGKLVQVGKPEDLYDNPVSIQVASLIGEINELE 248
             G+T +V SH   D  ++AD + +L KG L QVG P ++Y  P +  VA+  G+ NEL 
Sbjct: 185 ATGITAIVASHHAKDALSLADSIAILHKGILQQVGTPVEIYKKPANAYVANFFGKRNELL 244

Query: 249 GKVTNEGVV--IGSLRFPVSVS-SDRAIIGIRPEDVKLSK 285
              T +G     G +  P S S +D+  I  R ED K+ K
Sbjct: 245 ATPTEDGFYAGFGFIPHPDSASYTDKVKILFRSEDAKIKK 284


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: 289
Number of extensions: 12
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: 353
Length of database: 345
Length adjustment: 29
Effective length of query: 324
Effective length of database: 316
Effective search space:   102384
Effective search space used:   102384
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