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.
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:
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