Align PTS system glucose-specific EIICBA component; EC 2.7.1.-; EC 2.7.1.69 (characterized)
to candidate 5210198 Shew_2641 PTS system, glucose-like IIB subunint (RefSeq)
Query= CharProtDB::CH_001857 (699 letters) >FitnessBrowser__PV4:5210198 Length = 490 Score = 310 bits (795), Expect = 8e-89 Identities = 186/506 (36%), Positives = 283/506 (55%), Gaps = 47/506 (9%) Query: 6 FGVLQKIGRALMLPVAILPAAGILLAIGNAMQNKDMIQVLHFLSNDNVQLVAGVMESAGQ 65 F Q++ +AL+LP+AILPAAG+++ + + F+S D +A +M + G Sbjct: 24 FKFAQRLSQALLLPIAILPAAGVMIGLAT--------NPIPFISAD----LATLMWTVGN 71 Query: 66 IVFDNLPLLFAVGVAIGLANGDGVAGIAAIIGYLVMNVSMSAVLLANGTIPSDSVERAKF 125 +VF +P+LFAV +AIG G+A +A+ GY V S+SA+ AK Sbjct: 72 LVFSMMPMLFAVTIAIGFCRDQGIAAFSAVFGYGVFFSSLSAL--------------AKI 117 Query: 126 FTENHPAYVNMLGIPTLATGVFGGIIVGVLAALLFNRFYTIELPQYLGFFAGKRFVPIVT 185 + H +LG T+ TG+ GG++VG L+ I LP FF G+R P++ Sbjct: 118 Y---HLPTEMILGQATIDTGIAGGMMVGAFTCLVVKHSERIRLPAVFSFFEGRRSAPLLM 174 Query: 186 SISALILGLIMLVIWPPIQHGLNAFSTGLVEANPTLAAFIFGVIERSLIPFGLHHIFYSP 245 A++L + L++WP + + + S V P A ++G++ER LIP GLHHI+ +P Sbjct: 175 LPMAILLAYLFLLLWPLLSNWIEQISNWAVYQEPASAFAVYGMVERLLIPLGLHHIWNAP 234 Query: 246 FWYEFFSYKSAAGEIIRGDQRIFMAQIKDGVQLTAGTFMTGKYPFMMFGLPAAALAIYHE 305 F+ E Y + E +RG+ ++A L G Y M+GLPAAALAI+ Sbjct: 235 FYLEMGQYFNG-DEWVRGEVARYLAGDPQAGNLAGG------YLIKMWGLPAAALAIWRC 287 Query: 306 AKPQNKKLVAGIMGSAALTSFLTGITEPLEFSFLFVAPVLFAIHCLFAGLSFMVMQLLNV 365 A + VAGIM SAA +LTG+TEP+EF+F+FVAP+LF +H L G+++ V L++ Sbjct: 288 ADKHERNRVAGIMLSAATACWLTGVTEPIEFAFMFVAPLLFILHALMTGIAYAVTISLDI 347 Query: 366 KIGMTFSGGLIDYFLFGILPNRTAWWLVIPVGLGLAVIYYFGFRFAIRKFNLKTPGREDA 425 + FS GL+D+ L W+L++ G AVIYY FR AI FNLKTPGR +A Sbjct: 348 HHSVVFSHGLVDFSLLLGQSRNVEWFLIL--GPLTAVIYYLVFRGAILAFNLKTPGRMEA 405 Query: 426 AEETAAPGKTGEAGDLPYEILQAMGDQENIKHLDACITRLRVTVNDQKKVDKDRLKQLGA 485 +G+ L ++ A+G Q+NI L AC+TRLR++V + VDK +L +LGA Sbjct: 406 G--------SGQRAGL-ISMITALGGQDNINELTACLTRLRISVKHAELVDKAQLNKLGA 456 Query: 486 SGVLEVGNNIQAIFGPRSDGLKTQMQ 511 GV+ VGN +Q ++G +++ ++ +Q Sbjct: 457 KGVVLVGNGVQLVYGTKAESIRRLLQ 482 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: 765 Number of extensions: 33 Number of successful extensions: 5 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: 490 Length adjustment: 37 Effective length of query: 662 Effective length of database: 453 Effective search space: 299886 Effective search space used: 299886 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