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.
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