Align PTS system glucose-specific EIICBA component; EC 2.7.1.-; EC 2.7.1.69 (characterized)
to candidate 7025672 Shewana3_2822 PTS system, glucose-like IIB subunint (RefSeq)
Query= CharProtDB::CH_001857 (699 letters) >FitnessBrowser__ANA3:7025672 Length = 452 Score = 297 bits (760), Expect = 8e-85 Identities = 178/496 (35%), Positives = 277/496 (55%), Gaps = 44/496 (8%) Query: 23 LPAAGILLAIGNAMQNKDMIQVLHFLSNDNVQLVAGVMESAGQIVFDNLPLLFAVGVAIG 82 +PAAG++L + + + F+ +++ +M + G+++F +P+LFAV VAIG Sbjct: 1 MPAAGVMLGL--------TVSPIPFMP----EVLTVLMLAVGKLIFAIMPILFAVAVAIG 48 Query: 83 LANGDGVAGIAAIIGYLVMNVSMSAVLLANGTIPSDSVERAKFFTENHPAYVNMLGIPTL 142 G+A A+ GY VM +++A L +P+ +LG+ TL Sbjct: 49 FCRDQGIAAFTAVFGYGVMTATLAA-LADLYQLPTQL----------------LLGMETL 91 Query: 143 ATGVFGGIIVGVLAALLFNRFYTIELPQYLGFFAGKRFVPIVTSISALILGLIMLVIWPP 202 TG+ GG+++G + I LP FF G+R ++ A+ LG I+ +WPP Sbjct: 92 DTGIAGGMLIGGVTCFAVRWSQYIRLPAIFSFFEGRRSASLLIIPLAMGLGYILAHVWPP 151 Query: 203 IQHGLNAFSTGLVEANPTLAAFIFGVIERSLIPFGLHHIFYSPFWYEFFSYKSAAGEIIR 262 + + S V P +A ++G +ER LIP GLHHI+ +PF+ E Y+ E++R Sbjct: 152 LSLLIERVSDWAVYQKPAIAFGVYGALERLLIPLGLHHIWNAPFYLEVGQYQLQNSEVVR 211 Query: 263 GDQRIFMAQIKDGVQLTAGTFMTGKYPFMMFGLPAAALAIYHEAKPQNKKLVAGIMGSAA 322 G+ ++A L G Y M+GLPAAALAI+ A+P + VAGIM SAA Sbjct: 212 GEVARYLAGDPQAGNLAGG------YLIKMWGLPAAALAIWRCAEPSERNRVAGIMLSAA 265 Query: 323 LTSFLTGITEPLEFSFLFVAPVLFAIHCLFAGLSFMVMQLLNVKIGMTFSGGLIDYFLFG 382 S+LTG+TEP+EF+F+FVAP LF IH L +GL++ V +L++ + FS GL+D+ L Sbjct: 266 AASWLTGVTEPIEFAFMFVAPFLFLIHVLLSGLAYFVCIMLDIHHSIVFSHGLVDFTLLF 325 Query: 383 ILPNRTAWWLVIPVGLGLAVIYYFGFRFAIRKFNLKTPGREDAAEETAAPGKTGEAGDLP 442 L T W++ + G AVIYY FR +I FNLKTPGR + P + A + Sbjct: 326 SLSRNTGWFVFL--GPLTAVIYYLLFRGSILAFNLKTPGRLE-------PDEPHGAKESL 376 Query: 443 YEILQAMGDQENIKHLDACITRLRVTVNDQKKVDKDRLKQLGASGVLEVGNNIQAIFGPR 502 I+ A+G +ENI L+AC+TRLR++V+ + V+K RL QLGA GV+ +G +Q ++G + Sbjct: 377 RAIIAALGGRENIVELNACLTRLRLSVHSPELVNKVRLSQLGAKGVIVMGKGVQVVYGTK 436 Query: 503 SDGLKTQMQDIIAGRK 518 ++ L+ +Q + R+ Sbjct: 437 AETLRKVLQRYLDTRR 452 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: 750 Number of extensions: 32 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: 452 Length adjustment: 36 Effective length of query: 663 Effective length of database: 416 Effective search space: 275808 Effective search space used: 275808 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