Align PTS system glucose-specific EIICBA component; EC 2.7.1.-; EC 2.7.1.69 (characterized)
to candidate 15742 b1621 fused maltose and glucose-specific PTS enzymes: IIB component -! IIC component (NCBI)
Query= CharProtDB::CH_001857 (699 letters) >FitnessBrowser__Keio:15742 Length = 530 Score = 339 bits (870), Expect = 2e-97 Identities = 197/522 (37%), Positives = 304/522 (58%), Gaps = 19/522 (3%) Query: 5 LFGVLQKIGRALMLPVAILPAAGILLAIGNAMQNKDMIQVLHFLSNDNVQLVAGVMESAG 64 L+ Q++G+ MLPVA+L GI+L IG+++ + D+I ++ L N +Q + M G Sbjct: 11 LWEFFQQLGKTFMLPVALLSFCGIMLGIGSSLSSHDVITLIPVLGNPVLQAIFTWMSKIG 70 Query: 65 QIVFDNLPLLFAVGVAIGLANGD-GVAGIAAIIGYLVMNVSMSAVLLANGTIPSDSVERA 123 F LP++F + + +GLA + GVA A IGY VMN++++ L G +P+ A Sbjct: 71 SFAFSFLPVMFCIAIPLGLARENKGVAAFAGFIGYAVMNLAVNFWLTNKGILPTTD---A 127 Query: 124 KFFTENHPAYVNMLGIPTLATGVFGGIIVGVLAALLFNRFYTIELPQYLGFFAGKRFVPI 183 N+ ++LGI ++ TG+ G +I G++ +L RF+ I LP L FF G RFVPI Sbjct: 128 AVLKANN--IQSILGIQSIDTGILGAVIAGIIVWMLHERFHNIRLPDALAFFGGTRFVPI 185 Query: 184 VTSISALILGLIMLVIWPPIQHGLNAFSTGLVEANPTLAAFIFGVIERSLIPFGLHHIFY 243 ++S+ ++GL++ ++WP G++ ++ + +FG ER L+PFGLHHI Sbjct: 186 ISSLVMGLVGLVIPLVWPIFAMGISGLGH-MINSAGDFGPMLFGTGERLLLPFGLHHILV 244 Query: 244 SPFWY-EFFSYKSAAGEIIRGDQRIFMAQIK----DGVQLTAGTFMT-GKYPFMMFGLPA 297 + + + + G+ + G IF AQ+ G +A F++ GK P + GLP Sbjct: 245 ALIRFTDAGGTQEVCGQTVSGALTIFQAQLSCPTTHGFSESATRFLSQGKMPAFLGGLPG 304 Query: 298 AALAIYHEAKPQNKKLVAGIMGSAALTSFLTGITEPLEFSFLFVAPVLFAIHCLFAGLSF 357 AALA+YH A+P+N+ + G++ S + + G TEPLEF FLFVAPVL+ IH L GL F Sbjct: 305 AALAMYHCARPENRHKIKGLLISGLIACVVGGTTEPLEFLFLFVAPVLYVIHALLTGLGF 364 Query: 358 MVMQLLNVKIGMTFSGGLIDYFLFGILPNRTAWWLVIPVGLGL-AVIYYFGFRFAIRKFN 416 VM +L V IG T G +ID+ +FGIL + W ++PV + V+YY FRFAI +FN Sbjct: 365 TVMSVLGVTIGNT-DGNIIDFVVFGILHGLSTKWYMVPVVAAIWFVVYYVIFRFAITRFN 423 Query: 417 LKTPGRED---AAEETAAPGKTGEAGDLPYEILQAMGDQENIKHLDACITRLRVTVNDQK 473 LKTPGR+ ++ E A G G++G IL+A+G +NI LD CITRLR++V D Sbjct: 424 LKTPGRDSEVASSIEKAVAGAPGKSGYNVPAILEALGGADNIVSLDNCITRLRLSVKDMS 483 Query: 474 KVDKDRLKQLGASGVLEVG-NNIQAIFGPRSDGLKTQMQDII 514 V+ LK A GV+++ +N+Q + GP+ +K +M ++ Sbjct: 484 LVNVQALKDNRAIGVVQLNQHNLQVVIGPQVQSVKDEMAGLM 525 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: 982 Number of extensions: 63 Number of successful extensions: 10 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: 530 Length adjustment: 37 Effective length of query: 662 Effective length of database: 493 Effective search space: 326366 Effective search space used: 326366 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: 53 (25.0 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