Alignments for a candidate for ptsG-crr in Paraburkholderia bryophila 376MFSha3.1

GapMind for catabolism of small carbon sources

Alignments for a candidate for ptsG-crr in Paraburkholderia bryophila 376MFSha3.1

Align PTS system glucose-specific EIICBA component; EIICBA-Glc; EII-Glc; EIICBA-Glc 1; EC 2.7.1.199 (characterized)
to candidate H281DRAFT_01853 H281DRAFT_01853 PTS system D-glucose-specific IIB component, Glc family /PTS system D-glucose-specific IIC component, Glc family

Query= SwissProt::Q57071
         (675 letters)



>FitnessBrowser__Burk376:H281DRAFT_01853
          Length = 596

 Score =  454 bits (1168), Expect = e-132
 Identities = 251/535 (46%), Positives = 353/535 (65%), Gaps = 41/535 (7%)

Query: 1   MWKKFFGQLQRIGKALMLPVAILPAAGLLLALGNA-FQGDALQSLMPFIKAEGFQNVAKM 59
           ++K  FG LQ++GK+LMLPVA+LP AGLLL LG   F G      +P I       V  +
Sbjct: 1   VFKHAFGVLQKVGKSLMLPVAVLPVAGLLLGLGATDFHG-----YVPAI-------VLAL 48

Query: 60  MEGAGGIIFDNLAIIFALGVAIGLASGDGVAAIAAFVGFIVLNKTMGMFL---GVTPEKA 116
           M+ AG +IF NL +IFA+GVA+G    DGV+ IAA +G++V+  T+G+     G+ P+  
Sbjct: 49  MKNAGDVIFANLPLIFAIGVALGFTENDGVSGIAATIGYLVMTATLGVIAKVEGIEPDM- 107

Query: 117 ADAATGFANVLGIPTLQTGVFGGIIIGALAAWCYNKFYNISLPSYLGFFAGKRFVPIMMA 176
                    ++GIP++QTGVFGGI+ G LAAW +N++Y I+LP+YLGFFAGKRFVPI+ A
Sbjct: 108 ---------IMGIPSIQTGVFGGILAGGLAAWMFNRYYRIALPAYLGFFAGKRFVPIVTA 158

Query: 177 TCSFILAFPMAIIWPSIQGGLNAFSEGLLASNTGLAVFLFGFIKRLLIPFGLHHIFHAPF 236
             S +L   ++++WP I   + AFS+    S+   A  ++GF++RLLIPFGLHHI++ PF
Sbjct: 159 IGSIVLGAILSVVWPPIGSAIKAFSQWAAVSDPRTAATVYGFVERLLIPFGLHHIWNVPF 218

Query: 237 WFEFGSYKN-AAGQIIHGDQRIFIEQIRDNVPLTAGKFMQGEFPVMMFGLPAAALAIYQT 295
           +FE GS+ +   G+++HGD   F    R     TAG  + G F   MFGLPAAA+AI+  
Sbjct: 219 FFEAGSFLDPTTGKVVHGDITRFFAGDR-----TAG-ILAGAFLFKMFGLPAAAIAIWHC 272

Query: 296 AKKENKKVVAGLMLSGALTSFLTGITEPLEFSFLFVAPLLFFIHAVLDGLSFLILYLLDL 355
           AK ENK  V G+M+S ALTSFLTGITEP+EF+FLFVAP+L+ IHA L   +  +   L +
Sbjct: 273 AKPENKVAVGGMMVSAALTSFLTGITEPIEFAFLFVAPVLYLIHACLAASAQFVANTLGM 332

Query: 356 HLGYTFSGGFIDFFLLGILPNK-TQWWLVIPVGLVYAAIYYIIFRFLIVKFNFKTPGRED 414
            +G+TFS G IDF +  ++ NK T  W V  +G +YA IYY +FRF+I +F+ KTPGRED
Sbjct: 333 RMGFTFSQGGIDFLMFNLIGNKSTHAWYVFILGPIYAVIYYGVFRFVITRFDLKTPGRED 392

Query: 415 KEVKSSNVAASEL---PFKVLDAMGGKANIKHLDACITRLRVEVNDKAKVDVQELKDLGA 471
             V+++ V+ + +     +++ A GG++NI  LDACITRLR+ V + A V+  +LK LGA
Sbjct: 393 DTVETAKVSTAGVGGRSRELVLAFGGRSNIDSLDACITRLRISVKNPALVNEGKLKALGA 452

Query: 472 SGVLEVGNNMQAIFGPKSDQIKHDMQQIMDGKITSPEETTVTEEGDKETAEIAAA 526
           +GV+ VGN +QAIFGP S+ +K DM + +    T+  E  +  +G K  AE AA+
Sbjct: 453 AGVVRVGNGVQAIFGPLSENMKTDMHEYLK---TAGSEADLAADG-KAVAEAAAS 503



 Score = 36.6 bits (83), Expect = 3e-06
 Identities = 23/61 (37%), Positives = 32/61 (52%), Gaps = 1/61 (1%)

Query: 420 SNVAASELPFKVLDAMGGKANIKHLDA-CITRLRVEVNDKAKVDVQELKDLGASGVLEVG 478
           S    +E   K+  A+GG ANI+ LDA   TRLRV + D +++D   LK  G      + 
Sbjct: 517 STTQQAERVEKIRAALGGVANIQKLDALAATRLRVGLRDASQLDTAALKAAGVPATQTLT 576

Query: 479 N 479
           N
Sbjct: 577 N 577


Lambda     K      H
   0.324    0.143    0.421 

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: 1065
Number of extensions: 60
Number of successful extensions: 7
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 2
Length of query: 675
Length of database: 596
Length adjustment: 38
Effective length of query: 637
Effective length of database: 558
Effective search space:   355446
Effective search space used:   355446
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (22.0 bits)
S2: 54 (25.4 bits)

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

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Protein sequences (fasta format)
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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:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

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:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

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:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

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
the source code
instructions for running GapMind on your computer

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

GapMind for catabolism of small carbon sources