Align PTS system lactose-specific EIICB component; EIICB-Lac; EII-Lac; EC 2.7.1.207 (characterized)
to candidate BWI76_RS27750 BWI76_RS27750 PTS lactose/cellobiose family transporter subunit IIC
Query= SwissProt::P24400 (577 letters) >FitnessBrowser__Koxy:BWI76_RS27750 Length = 441 Score = 235 bits (600), Expect = 2e-66 Identities = 138/440 (31%), Positives = 226/440 (51%), Gaps = 24/440 (5%) Query: 8 LKPVFEAIAANKYISAIRDGFIACMPIIIFSSIFMMVAYVP------NAWGFYWPD---N 58 + P+ + KY+ AIRDGF A +P +I S ++ + P N + W D Sbjct: 16 ITPLAGRLGQQKYVIAIRDGFTAALPFMIIGSFMLVFIFPPFSPDTTNGFARGWLDFSQQ 75 Query: 59 VTNTLMVAYNYSMGLLALFVAGTTAKNLTDSKNLELPKTNQINPVAVIVASEISFVILSI 118 LM+ +N SMG++ F++ +L + Q++PV + + ++F++++ Sbjct: 76 YREQLMLPFNLSMGVMTFFISVGIGASLG--------RQFQLDPVMSGLLAFMAFLLVAA 127 Query: 119 LPLKTGVDLTYMGTQGLICAYIVGLIVPNIYYVCIKNNVTIKLPEQVPGNIAQSFKDLIP 178 + Y+ QG+ A I + +Y +NN+TI+LP++VP +A+SF+ LIP Sbjct: 128 PYADGKISTQYLSGQGIFTALITAIYSTRVYAWLKQNNITIRLPKEVPTGVARSFEILIP 187 Query: 179 MGLSVTAFWLFGVGFKAATGTVLPRWIIQVLSPLFQASDSYLGLALIAGAMAFFWFCGVQ 238 + + + + +A TG +LP+ I+ +L PL ASDS + L FWF G+ Sbjct: 188 VLVVIATLHPLNLFIEAQTGMILPQAIMHLLEPLVSASDSLPAILLSVLMCQIFWFAGIH 247 Query: 239 GPSIVQPAVVPIMIANTAANLQQYQAGQHVSHVLAMNTMDYVMNFGGTGATLVVPFIMLF 298 G IV + P +AN +AN AG + HV D+ + GG G+TL + F++L Sbjct: 248 GSLIVTGIMNPFWMANLSANQAALAAGAALPHVYLQGFWDHYLLIGGVGSTLPLAFLLL- 306 Query: 299 AARSAQLKAVGKAAFVPCTFGVNEPVLFGMPIIMNPMLFIPFLATPIVNVCLFKFFVSVL 358 +R L+ +GK VP F +NEP+LFG PIIMNPM+FIPF+ P++N L + Sbjct: 307 RSRVTHLRTIGKMGIVPSFFNINEPILFGAPIIMNPMMFIPFVFVPMINAVLAYGATRLG 366 Query: 359 GMNSMMYTMPWTVPGPIGILISTGFAPLAFVFVLLTLVLDVAIYFPFIRVYDSTLLAEEK 418 ++ ++ PWT P PIG + + V L+ +V+ IY PF+R Y+ +L+ E Sbjct: 367 WLSQVVSLTPWTTPAPIGASWAANWTLSPVVMCLICMVMSALIYLPFLRAYERSLMKTE- 425 Query: 419 AKEEVIEDDGMAVLASDTVS 438 +E AV ++TVS Sbjct: 426 -----VEKAKAAVPVAETVS 440 Lambda K H 0.324 0.138 0.411 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: 632 Number of extensions: 35 Number of successful extensions: 4 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: 577 Length of database: 441 Length adjustment: 34 Effective length of query: 543 Effective length of database: 407 Effective search space: 221001 Effective search space used: 221001 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