GapMind for catabolism of small carbon sources

 

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

Align PTS system glucose-specific EIICBA component; EC 2.7.1.-; EC 2.7.1.69 (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= CharProtDB::CH_001857
         (699 letters)



>FitnessBrowser__Burk376:H281DRAFT_01853
          Length = 596

 Score =  456 bits (1173), Expect = e-132
 Identities = 250/516 (48%), Positives = 335/516 (64%), Gaps = 37/516 (7%)

Query: 1   MFKALFGVLQKIGRALMLPVAILPAAGILLAIGNAMQNKDMIQVLHFLSNDNVQLVAGVM 60
           +FK  FGVLQK+G++LMLPVA+LP AG+LL +G A      +  +          V  +M
Sbjct: 1   VFKHAFGVLQKVGKSLMLPVAVLPVAGLLLGLG-ATDFHGYVPAI----------VLALM 49

Query: 61  ESAGQIVFDNLPLLFAVGVAIGLANGDGVAGIAAIIGYLVMNVSMSAVLLANGTIPSDSV 120
           ++AG ++F NLPL+FA+GVA+G    DGV+GIAA IGYLVM  ++  +    G  P    
Sbjct: 50  KNAGDVIFANLPLIFAIGVALGFTENDGVSGIAATIGYLVMTATLGVIAKVEGIEPD--- 106

Query: 121 ERAKFFTENHPAYVNMLGIPTLATGVFGGIIVGVLAALLFNRFYTIELPQYLGFFAGKRF 180
                          ++GIP++ TGVFGGI+ G LAA +FNR+Y I LP YLGFFAGKRF
Sbjct: 107 --------------MIMGIPSIQTGVFGGILAGGLAAWMFNRYYRIALPAYLGFFAGKRF 152

Query: 181 VPIVTSISALILGLIMLVIWPPIQHGLNAFSTGLVEANPTLAAFIFGVIERSLIPFGLHH 240
           VPIVT+I +++LG I+ V+WPPI   + AFS     ++P  AA ++G +ER LIPFGLHH
Sbjct: 153 VPIVTAIGSIVLGAILSVVWPPIGSAIKAFSQWAAVSDPRTAATVYGFVERLLIPFGLHH 212

Query: 241 IFYSPFWYEFFSY-KSAAGEIIRGDQRIFMAQIKDGVQLTAGTFMTGKYPFMMFGLPAAA 299
           I+  PF++E  S+     G+++ GD   F A  +     TAG  + G + F MFGLPAAA
Sbjct: 213 IWNVPFFFEAGSFLDPTTGKVVHGDITRFFAGDR-----TAG-ILAGAFLFKMFGLPAAA 266

Query: 300 LAIYHEAKPQNKKLVAGIMGSAALTSFLTGITEPLEFSFLFVAPVLFAIHCLFAGLSFMV 359
           +AI+H AKP+NK  V G+M SAALTSFLTGITEP+EF+FLFVAPVL+ IH   A  +  V
Sbjct: 267 IAIWHCAKPENKVAVGGMMVSAALTSFLTGITEPIEFAFLFVAPVLYLIHACLAASAQFV 326

Query: 360 MQLLNVKIGMTFSGGLIDYFLFGILPNR-TAWWLVIPVGLGLAVIYYFGFRFAIRKFNLK 418
              L +++G TFS G ID+ +F ++ N+ T  W V  +G   AVIYY  FRF I +F+LK
Sbjct: 327 ANTLGMRMGFTFSQGGIDFLMFNLIGNKSTHAWYVFILGPIYAVIYYGVFRFVITRFDLK 386

Query: 419 TPGREDAAEETAAPGKTGEAGDLPYEILQAMGDQENIKHLDACITRLRVTVNDQKKVDKD 478
           TPGRED   ETA     G  G    E++ A G + NI  LDACITRLR++V +   V++ 
Sbjct: 387 TPGREDDTVETAKVSTAG-VGGRSRELVLAFGGRSNIDSLDACITRLRISVKNPALVNEG 445

Query: 479 RLKQLGASGVLEVGNNIQAIFGPRSDGLKTQMQDII 514
           +LK LGA+GV+ VGN +QAIFGP S+ +KT M + +
Sbjct: 446 KLKALGAAGVVRVGNGVQAIFGPLSENMKTDMHEYL 481


Lambda     K      H
   0.323    0.141    0.412 

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: 1113
Number of extensions: 51
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: 699
Length of database: 596
Length adjustment: 38
Effective length of query: 661
Effective length of database: 558
Effective search space:   368838
Effective search space used:   368838
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.5 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 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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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