GapMind for catabolism of small carbon sources

 

Alignments for a candidate for malK in Burkholderia phytofirmans PsJN

Align Maltose/maltodextrin import ATP-binding protein MalK; EC 7.5.2.1 (characterized)
to candidate BPHYT_RS22760 BPHYT_RS22760 sugar ABC transporter ATP-binding protein

Query= SwissProt::P19566
         (369 letters)



>FitnessBrowser__BFirm:BPHYT_RS22760
          Length = 384

 Score =  379 bits (973), Expect = e-110
 Identities = 208/378 (55%), Positives = 265/378 (70%), Gaps = 16/378 (4%)

Query: 1   MASVQLRNVTKAWGD-VVVSKDINLDIHDGEFVVFVGPSGCGKSTLLRMIAGLETITSGD 59
           MAS+ LR V KA+G+   V +D++L+I + EF VF+GPSGCGKSTLLRMIAGLE +T GD
Sbjct: 1   MASISLRGVQKAYGEGAPVIRDVDLEIGENEFCVFLGPSGCGKSTLLRMIAGLEDLTDGD 60

Query: 60  LFIGETRMNDIPPAERGVGMVFQSYALYPHLSVAENMSFGLKLAGAKKEVMNQRVNQVAE 119
           L IG   MND+P A+RGV MVFQSYAL+PH+SV ENM+FGLKLA   K+ ++++V + A 
Sbjct: 61  LSIGGKLMNDVPAAQRGVAMVFQSYALFPHMSVFENMAFGLKLAKTPKDEVDRKVREAAR 120

Query: 120 VLQLAHLLERKPKALSGGQRQRVAIGRTLVAEPRVFLLDEPLSNLDAALRVQMRIEISRL 179
           +LQL  LLERKPKALSGGQRQRVAIGR +V EP VFL DEPLSNLDA LR Q RIEI+RL
Sbjct: 121 ILQLEALLERKPKALSGGQRQRVAIGRAIVREPGVFLFDEPLSNLDATLRGQTRIEIARL 180

Query: 180 HKRLGR-TMIYVTHDQVEAMTLADKIVVLDAGR-------VAQVGKPLELYHYPADRFVA 231
           HK+  + +++YVTHDQ+EAMTLADKIV+L AG+       +AQ+G PLELYH P  RFVA
Sbjct: 181 HKQFAKASVVYVTHDQIEAMTLADKIVLLHAGKDTERYGSIAQIGAPLELYHRPKSRFVA 240

Query: 232 GFIGSPKMNFLPVKVTATAIEQVQVELPNRQQ-IWLPVESRGVQVGANMSLGIRPEHLL- 289
           GFIGSP+MNFLP +V +   + V + L + Q+ + +PV   G+Q    ++LG+RPEHL  
Sbjct: 241 GFIGSPRMNFLPGRVASLDAQGVTITLDHTQETVRVPVNGAGLQTSQAVTLGVRPEHLEF 300

Query: 290 --PSDIA--DVTLEGEVQVVEQLGHETQIHIQIPAIRQNLVYRQNDVVLVEEGATFAIGL 345
             PS +A  D  L   V +VEQLG  + +H+  P     LV +      +  G   ++ +
Sbjct: 301 VDPSSVAPDDAVLTRTVSLVEQLGEHSYVHLDQPG-GAALVAKAPGNTRLAPGERASLRV 359

Query: 346 PPERCHLFREDGSACRRL 363
           P   CHLF EDG A   L
Sbjct: 360 PRAACHLFTEDGFAAASL 377


Lambda     K      H
   0.321    0.138    0.396 

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: 401
Number of extensions: 14
Number of successful extensions: 7
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: 369
Length of database: 384
Length adjustment: 30
Effective length of query: 339
Effective length of database: 354
Effective search space:   120006
Effective search space used:   120006
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: 50 (23.9 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