Align PTS system glucose-specific EIICBA component; EC 2.7.1.-; EC 2.7.1.69 (characterized)
to candidate BWI76_RS16295 BWI76_RS16295 bifunctional PTS system maltose and glucose-specific transporter subunits IICB
Query= CharProtDB::CH_001857 (699 letters) >FitnessBrowser__Koxy:BWI76_RS16295 Length = 530 Score = 351 bits (900), Expect = e-101 Identities = 206/518 (39%), Positives = 304/518 (58%), Gaps = 19/518 (3%) Query: 5 LFGVLQKIGRALMLPVAILPAAGILLAIGNAMQNKDMIQVLHFLSNDNVQLVAGVMESAG 64 L+ Q++G+ MLPVA+L GI+L IG+++ + D++ +L +L +Q V M G Sbjct: 11 LWEFFQQLGKTFMLPVALLSFCGIMLGIGSSLSSHDVLTLLPWLDVPLLQAVFIWMGKVG 70 Query: 65 QIVFDNLPLLFAVGVAIGLANGD-GVAGIAAIIGYLVMNVSMSAVLLANGTIPSDSVERA 123 F LP++F + + +GLA + GVA A +GY VMN++++ L A G +P+ A Sbjct: 71 SFAFSFLPVMFCIAIPLGLARENKGVAAFAGFVGYAVMNLAVNFWLTAKGILPTTD---A 127 Query: 124 KFFTENHPAYVNMLGIPTLATGVFGGIIVGVLAALLFNRFYTIELPQYLGFFAGKRFVPI 183 N+ N++GI ++ TG+ G +I G++ +L RF+ I LP L FF G RFVPI Sbjct: 128 AVLKANN--IQNIIGIQSIDTGILGAVIAGIIVWMLHERFHNIRLPDALAFFGGTRFVPI 185 Query: 184 VTSISALILGLIMLVIWPPIQHGLNAFSTGLVEANPTLAAFIFGVIERSLIPFGLHHIFY 243 +T++ ++GL++ +IWP G+NA ++ + IFG ER L+PFGLHHI Sbjct: 186 ITTVVLGLVGLVIPLIWPVFAMGINALGQ-VINSAGDFGPMIFGTGERLLLPFGLHHILV 244 Query: 244 SPFWY-EFFSYKSAAGEIIRGDQRIFMAQIK----DGVQLTAGTFMT-GKYPFMMFGLPA 297 + + E G + G IF AQ+ G +A F++ GK P + GLP Sbjct: 245 ALIRFTEAGGTMDVCGHSVSGALTIFQAQLSCPTTHGFSESATRFLSQGKMPAFLGGLPG 304 Query: 298 AALAIYHEAKPQNKKLVAGIMGSAALTSFLTGITEPLEFSFLFVAPVLFAIHCLFAGLSF 357 AALA+YH A+P+N+ + G++ S + + G TEPLEF FLFVAPVL+ IH L GL F Sbjct: 305 AALAMYHCARPENRHKIKGLLISGVIACVVGGTTEPLEFLFLFVAPVLYVIHALLTGLGF 364 Query: 358 MVMQLLNVKIGMTFSGGLIDYFLFGILPNRTAWWLVIPVGLGLAVIYYFG-FRFAIRKFN 416 +M +L V IG T G +ID+ +FGIL + W ++PV + Y+G FRFAI +FN Sbjct: 365 TMMAILGVTIGNT-DGNVIDFVVFGILHGLSTKWYLVPVVAAIWFAVYYGIFRFAITRFN 423 Query: 417 LKTPGRE---DAAEETAAPGKTGEAGDLPYEILQAMGDQENIKHLDACITRLRVTVNDQK 473 LKTPGR+ ++A E A G TG++G IL A+G ENI LD CITRLR++VND Sbjct: 424 LKTPGRDIETNSAFEKAVTGVTGKSGYNVPAILAALGGAENIVSLDNCITRLRLSVNDMS 483 Query: 474 KVDKDRLKQLGASGVLEVG-NNIQAIFGPRSDGLKTQM 510 KVD LK A GV+++ +N+Q + GP+ +K +M Sbjct: 484 KVDSAALKANRAIGVVQLNQHNLQVVIGPQVQSVKDEM 521 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: 971 Number of extensions: 64 Number of successful extensions: 9 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