GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gntC in Paraburkholderia bryophila 376MFSha3.1

Align TRAP dicarboxylate transport system, periplasmic component (DctP-like) (characterized, see rationale)
to candidate H281DRAFT_03359 H281DRAFT_03359 tripartite ATP-independent transporter solute receptor, DctP family

Query= uniprot:G8AR24
         (337 letters)



>FitnessBrowser__Burk376:H281DRAFT_03359
          Length = 342

 Score =  144 bits (363), Expect = 3e-39
 Identities = 89/298 (29%), Positives = 155/298 (52%), Gaps = 7/298 (2%)

Query: 5   RSVLLATGLAAAI-----LAPVAASAQDIKPRLIRFGYGLSESSNQGRAVKFFVEDMAKR 59
           R+ L   G AA       L P  A AQ  + +L ++   L+ S       K   + + K 
Sbjct: 7   RTFLQTLGAAAVATTGTGLFPSLACAQTAQFKL-KYANNLALSHPLNVRAKEAADAIRKE 65

Query: 60  SGGKLKVKGFADASLGSDIQMQNALIGGAQEMMVGSTATLVGIVKDFAVFDLPFLFNNEQ 119
           +GG++ ++ F +  +G+D  M + +  GA + +      L  +V   A+  + F F +  
Sbjct: 66  TGGRVDLQIFPNGQMGTDTDMLSQVRSGAIDFLTQGGVVLSTLVPVSAINGIGFAFKDYN 125

Query: 120 EADAVFDGPFGQKLAAKLNDKGLVGLVY-WENGFRNLTNSKRPVEKVEDLKGIKLRVMQN 178
           +  A  DG  G  +   ++  GL+ +   W+NGFR+LT+S +PV    DLKG+K+RV  +
Sbjct: 126 QVWAAMDGDLGSYIRRAVSKVGLIAMEKPWDNGFRHLTSSVKPVLSPTDLKGLKIRVPVS 185

Query: 179 PVYIDMFNGFGANAVPLSFSELFTAMETGTVDGQENPVTTIQSSKFYEVQKYLTISKHVY 238
           P++  MF    A+   ++FSE ++A++T  VD +ENP+  I++ +FYEVQKY +++ H++
Sbjct: 186 PLWTSMFKALDASPTSINFSEAYSALQTKVVDAEENPLALIETGRFYEVQKYCSLTGHIW 245

Query: 239 SPWIVLASKRWYDGLSADERKIINEAAVASRDFERKDSREASKQSIAYLKDKGMQINE 296
             +  LA+ R +  L  D + I+ +   A+   ER D    S   +  L+  GM  N+
Sbjct: 246 DGFWFLANARSWGNLPPDLQTIVAKHLNAAAVAERADVAALSTSLVETLRSHGMAFNK 303


Lambda     K      H
   0.317    0.134    0.372 

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: 242
Number of extensions: 9
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: 337
Length of database: 342
Length adjustment: 28
Effective length of query: 309
Effective length of database: 314
Effective search space:    97026
Effective search space used:    97026
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