GapMind for catabolism of small carbon sources

 

Alignments for a candidate for cbtD in Burkholderia phytofirmans PsJN

Align CbtD, component of Cellobiose and cellooligosaccharide porter (characterized)
to candidate BPHYT_RS31200 BPHYT_RS31200 peptide ABC transporter substrate-binding protein

Query= TCDB::Q97VF5
         (362 letters)



>FitnessBrowser__BFirm:BPHYT_RS31200
          Length = 325

 Score =  195 bits (495), Expect = 2e-54
 Identities = 116/303 (38%), Positives = 176/303 (58%), Gaps = 6/303 (1%)

Query: 46  LEVHNLNVIYDEGNSRIIKAVNDVSFGVEKGEILGIIGESGSGKTTLISAILRAIRPPGK 105
           L V NL   +  G + + KAV+D SF V  GEI+G++GESGSGK+    ++L  I  PG+
Sbjct: 6   LSVQNLRTHFFTG-AGVAKAVDDTSFDVAPGEIVGLVGESGSGKSITGFSVLGLIDAPGR 64

Query: 106 IISGKVIFNGMDIFSMTIDEFRKLLWKDISYVPQASQNALNPVLPISEIFYHEAISHGEA 165
           I++G+V+F G D+ ++T +  R+L    I+ + Q     LNPVL I         +H   
Sbjct: 65  IVAGRVLFKGEDLTTLTPEALRRLRGNRIAMIFQDPMMTLNPVLRIDTQMIEAVQAHTRV 124

Query: 166 DKKRVIERASELLKLVGL-DPARVLKMYPFQLSGGMKQRVMIALSLLLNPKLILMDEPTS 224
            K    +RA + L  VG+  P   L+ YP QLSGGM+QRV IA++LL +P+LI+ DEPT+
Sbjct: 125 SKHAARQRARDALASVGIPSPDERLRAYPHQLSGGMRQRVAIAIALLHDPELIIADEPTT 184

Query: 225 ALDMLNQELLLKLIKNINQEMGVTIVYVTHDILNIAQIANRLLVMYKGYVMEEGKTEEII 284
           ALD+  Q  +L  ++ +       +V+V+HD+  +A +A+R+ VMY G V+E G  +EI+
Sbjct: 185 ALDVTIQAQILAEMQKLCARSHTAMVWVSHDLAVVAGLADRICVMYAGRVVETGSVDEIL 244

Query: 285 KSPLNPYTSLLVSSIP--SLKGEVKVINVPLDEPLVSK-EKGCPFLARCSKAFGRCKEEL 341
           + P +PYT  L+ S+P  + +GE  +  +P   P   K   GC F  RC  A   C+   
Sbjct: 245 ERPRHPYTIGLIDSLPEKARRGE-SLTQIPGMAPSALKLPVGCAFAPRCVYATSLCRSAE 303

Query: 342 PEI 344
           P +
Sbjct: 304 PPV 306


Lambda     K      H
   0.319    0.138    0.391 

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: 237
Number of extensions: 5
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: 362
Length of database: 325
Length adjustment: 29
Effective length of query: 333
Effective length of database: 296
Effective search space:    98568
Effective search space used:    98568
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 (21.8 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