GapMind for catabolism of small carbon sources

 

Aligments 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)



>lcl|FitnessBrowser__BFirm:BPHYT_RS22760 BPHYT_RS22760 sugar ABC
           transporter ATP-binding protein
          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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 on GapMind for carbon sources, or view the source code.

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