Align PTS system glucose-specific EIICBA component; EC 2.7.1.-; EC 2.7.1.69 (characterized)
to candidate WP_083848942.1 C683_RS02545 PTS transporter subunit EIIC
Query= CharProtDB::CH_001857 (699 letters) >NCBI__GCF_000313915.1:WP_083848942.1 Length = 553 Score = 265 bits (678), Expect = 3e-75 Identities = 180/567 (31%), Positives = 288/567 (50%), Gaps = 79/567 (13%) Query: 6 FGVLQKIGRALMLPVAILPAAGILLAIGNAMQNKDMIQVLHFLSNDNVQLVAGVMESAGQ 65 F QK G+ALM+ +A++PAAG++++IG + M QV ++ + GV E+ G Sbjct: 7 FEFWQKFGKALMVVIAVMPAAGLMISIGKLIA---MAQVSLAVT------IGGVTENIGW 57 Query: 66 IVFDNLPLLFAVGVAIGLANGDGVAGIAAIIGYLVMNVSMSAV------LLANGTIPSDS 119 + NLP+LFA+ + A A+ + ++++N AV +LAN + Sbjct: 58 AIIGNLPILFALAIGGSWAKERAGGAFASGLAFILINRITGAVFGVTKEMLANPEATVHT 117 Query: 120 VERAKFFTENHPAYVNMLGIPTLATGVFGGIIVGVLAALLFNRFYTI-ELPQYLGFFAGK 178 + K + + ++L P L GVF GII G A+++N++Y +LP L FF GK Sbjct: 118 IFGQKILVNGY--FTSVLEAPALNMGVFVGIIAGFAGAIIYNKYYNFRKLPNCLSFFNGK 175 Query: 179 RFVPIVTSISALILGLIMLVIWPPIQHGLNAFSTGLVEAN---PTLAAFIFGVIERSLIP 235 RFVP V + ++I+ L++ V WP Q G+N F + ++ P A FI+G +ER L+P Sbjct: 176 RFVPFVVILWSVIIALLLSVFWPFAQTGINEFGKWIAQSGDSAPFWAPFIYGTLERLLLP 235 Query: 236 FGLHHIFYSPFWYEFFSYK------SAAGEIIRGDQRIFMAQIKDGVQLTAGTFMTGKYP 289 FGLHH+ P Y + AG+ + G +++A + D + L MT + Sbjct: 236 FGLHHMLTIPMNYTDLGGTYHILTGAQAGQAVLGQDPLWLAWVTDLINLKEKGDMTQYHQ 295 Query: 290 FM------------MFG----LPAAALAIYHEAKPQNKKLVAGIMGSAALTSFLTGITEP 333 + M G L A+Y +P+ KK+ I SAAL FLTG+TEP Sbjct: 296 LLESIRPARFKVGQMIGSSGILMGVTFAMYRNVEPKRKKVYKQIFLSAALAVFLTGVTEP 355 Query: 334 LEFSFLFVAPVLFAIHCLFAGLSFMVMQLLNVKIGMTFSGGLIDYFLFGILPNRTAWWLV 393 LEF F+F L+ ++ L G++F + ++++++ FG + T + Sbjct: 356 LEFMFMFAGIPLYVVYALLQGVAFGLADIIDLRL-----------HAFGNIELLTRLPMS 404 Query: 394 IPVGLGLAVI------------YYFGFRFAIRKFNLKTPGR----------EDAAEETAA 431 I GLG+ +I YF F I+KF++ TPGR A++ T A Sbjct: 405 IKAGLGMDIINFIITCIVFFFLAYFVANFMIKKFHIATPGRLGNYIEGNDDSSASDTTTA 464 Query: 432 PGKT--GEAGDLPYEILQAMGDQENIKHLDACITRLRVTVNDQKKV-DKDRLKQLGASGV 488 T EA + I+Q +G +ENI +DAC+TRLRVTV D KV D++ K+ GA G+ Sbjct: 465 TSSTKPSEANNQVMNIIQLLGGKENIVDVDACMTRLRVTVKDTTKVADEEAWKKEGAMGL 524 Query: 489 LEVGNNIQAIFGPRSDGLKTQMQDIIA 515 + N +QA++GP++D LK+ + D ++ Sbjct: 525 IHKNNGVQAVYGPKADVLKSDINDYLS 551 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: 913 Number of extensions: 64 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: 553 Length adjustment: 37 Effective length of query: 662 Effective length of database: 516 Effective search space: 341592 Effective search space used: 341592 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: 54 (25.4 bits)
This GapMind analysis is from Sep 24 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