Align PTS system lactose-specific EIICB component; EIICB-Lac; EII-Lac; EC 2.7.1.207 (characterized)
to candidate BWI76_RS04045 BWI76_RS04045 PTS system lactose/cellobiose-specific transporter subunit IIC
Query= SwissProt::P11162 (570 letters) >FitnessBrowser__Koxy:BWI76_RS04045 Length = 447 Score = 243 bits (620), Expect = 1e-68 Identities = 142/433 (32%), Positives = 230/433 (53%), Gaps = 15/433 (3%) Query: 14 PFFEKLSRNIYLRAIRDGFISAMPVILFSSIFLLIAYVP----NIFGFK--W---DKGME 64 P ++S ++ AIRDGFISAMP ++ S L+ AY P +GF W K E Sbjct: 21 PVAGRISSQRHVMAIRDGFISAMPFMIVGSFLLVFAYPPFSPDTTWGFARAWLDLAKEFE 80 Query: 65 AILMKPYNYTMGLVAFLVAGTTAKSLTDSFNRKLESTNQINFISTMQAAMCGFLFLASDP 124 ++ P++ TMG+++ + A +L + E T+Q++ ++ FL +A+ P Sbjct: 81 GRILTPFDMTMGIMSIYICAAIAYNL----GKHYEKTDQLDPFMCAMLSIMAFLLVAA-P 135 Query: 125 AKDGGFLSAFMGTKGLLTAFLSAFVTVIVYNFCVKRNITIKMPKEVPPNISQVFKDLIPF 184 +G +G G+ TA L A V + F NI I++P +VPP I F LIP Sbjct: 136 KTNGNLPVDSLGGTGIFTAILVAVYCVEMMRFLKAHNIGIRLPDQVPPMIKNSFDLLIPV 195 Query: 185 SAVIIILYALDLVIRNSFKSNVAEGILKLFEPLFTAADGWIGVTIIFGAFALFWFVGIHG 244 V++ LY L L+I++ F + + I+ +F+PL +AAD + + L WF GIHG Sbjct: 196 LVVVLTLYPLSLLIQHHFDMLIPQAIMAIFKPLVSAADSLPAILLAVLVGHLLWFAGIHG 255 Query: 245 PSIVEPAIAAITYANIEANFKLLQAGEHADKIITSGTQMFIVTFGGTGATLVVPFMFMWM 304 +IV + N+ N + L G I F + GG+GAT+ + F ++ Sbjct: 256 AAIVSGMLQMFWLTNLGMNQQALAQGAPLPHIFMEAFWTFFIVIGGSGATMGLVFCYL-R 314 Query: 305 TKSKRNKAIGRASVVPTFFGVNEPILFGAPLVLNPVFFIPFVLAPIVNVWIFKLFVEVLG 364 ++S ++IGR SVVP+ F +NEP++FG P+V+NPVFFIPF+LAP+VN + +++ Sbjct: 315 SRSAHLRSIGRLSVVPSLFNINEPVIFGTPIVMNPVFFIPFLLAPMVNAVLAWAAMKMDL 374 Query: 365 MNSFSVNLPWTTPGPLGIIMGTGFGLWSFVLAITLIVVDIIIYYPFLKVYDSEILDEEEG 424 + +PWT P P+G G+ + +L + L V IIY+PF KVY+ ++L +E Sbjct: 375 IGRVISVVPWTAPAPIGGAWALGWDFRAAILVVVLACVSAIIYFPFFKVYEKQLLAQEAE 434 Query: 425 RKESNSDLKEKVA 437 + ++ ++ A Sbjct: 435 EAQRIAEESQQTA 447 Lambda K H 0.324 0.140 0.410 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: 637 Number of extensions: 29 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: 570 Length of database: 447 Length adjustment: 34 Effective length of query: 536 Effective length of database: 413 Effective search space: 221368 Effective search space used: 221368 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.0 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.5 bits) S2: 52 (24.6 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