Align PTS lactose transporter subunit IIC, component of PTS-type lactose transporter, IIC-IIB-IIA (characterized)
to candidate BWI76_RS14945 BWI76_RS14945 PTS system, cellobiose-specific IIC component
Query= TCDB::U5MFA1 (445 letters) >FitnessBrowser__Koxy:BWI76_RS14945 Length = 439 Score = 243 bits (619), Expect = 1e-68 Identities = 140/413 (33%), Positives = 238/413 (57%), Gaps = 12/413 (2%) Query: 22 RYIMAIKSAFITLMPVIIVGAFSVLISNMVLDPKNGLASFSSLSFLAALKPITSALNYAT 81 R++ AI+ A+++ MP IIVG+ ++IS+ P F + +F A+ I A Sbjct: 23 RHLGAIRGAYVSFMPFIIVGSILLVISSF---PNQSYQQFMASTFGASWSAIIEIPFNAV 79 Query: 82 LNFLNIGAVFLIGIELGRINGIKSLFPGLLAVICFICVTPTTVEMMVDGQMHVVKDVLLR 141 + +++ FL+ L G + G+L+++ F+ +TP +++ +G + V+ Sbjct: 80 FSTMSLFISFLVAYRLAEHYGDDRISCGILSLVGFLILTPF-IKVAENGGITVIPV---- 134 Query: 142 QFSDTRSLFLGMFIAILSVEIYCWLEGRKGLKIKMPDTVPPNVSASFSALIPAIITTTAI 201 ++ T+ LF+ M ++L E++CWL+ RK L IKMPD VPP V SF+ALIPA++ I Sbjct: 135 EWIGTKGLFVAMIGSLLWTELFCWLK-RKKLVIKMPDGVPPAVQESFAALIPALLVMILI 193 Query: 202 ATFGFLFHQLTGMYLYDAVYQVVQQPLERVVQSLPGILLLMFVAQLFWVIGIHGNQMIKP 261 F ++ +Y+VV P+ S G L+ +F + W +GI+ MI Sbjct: 194 LAIRIGFEHTHYATIHQFIYEVVASPVRHYGTSYFGALMTVFSITILWSVGINSGSMING 253 Query: 262 IREPLLLGAITVNMSAFEQGKEVPNIITMPFWDVYMSIGGSGLTIGLLIAVMIATRRKEM 321 I PL + T N++A + G P+IIT F+D+ +GG+G T+ L+IA++I R K M Sbjct: 254 IIRPLWMENQTDNIAAIQAGVTPPHIITEQFFDMIW-MGGAGATLSLVIAMLIFARSKNM 312 Query: 322 KEIAKLSIGPGLFNINEPVIFGMPIMLNPILAIPFIITPLVTGSIGYFATLTG-FAGKAV 380 +E+A+L G +FNINEP++FG+P+++NPI+ IPF + PLV ++ Y A G A Sbjct: 313 REVARLGAGASIFNINEPILFGLPVIMNPIMLIPFNLVPLVLVTVQYAAMKIGAVAVTTG 372 Query: 381 VMVPWTTPPLINAWLSTAGSMGAVVTQLICIVVAVLIYLPFVKIATRRADAAQ 433 V +PWT PP+I+ ++ T G + V Q++ +++ ++YLPF++I ++ AA+ Sbjct: 373 VFIPWTLPPVISGFIVT-GHLSGSVMQILNLLIGAMLYLPFMRIVDKQYRAAE 424 Lambda K H 0.328 0.142 0.419 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: 501 Number of extensions: 27 Number of successful extensions: 7 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: 445 Length of database: 439 Length adjustment: 32 Effective length of query: 413 Effective length of database: 407 Effective search space: 168091 Effective search space used: 168091 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.1 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.7 bits) S2: 51 (24.3 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