Align PTS system lactose-specific EIICB component; EIICB-Lac; EII-Lac; EC 2.7.1.207 (characterized)
to candidate BWI76_RS22405 BWI76_RS22405 PTS cellobiose transporter subunit IIC
Query= SwissProt::P23531 (568 letters) >FitnessBrowser__Koxy:BWI76_RS22405 Length = 440 Score = 246 bits (627), Expect = 2e-69 Identities = 143/437 (32%), Positives = 229/437 (52%), Gaps = 20/437 (4%) Query: 3 KLIELIE-KGKPFFEKISRNIYLRAIRDGFIAGMPVILFSSIFILIAYVP----NAWGF- 56 KLI +IE K P I + Y+ +IRDGFI +P ++ S ++ + P WGF Sbjct: 7 KLIAVIEQKITPMAGAIGQQKYVTSIRDGFITALPFMIVGSFLLVFIFPPFSPDTTWGFA 66 Query: 57 ----HWSKDIETFLMTPYSYSMGILAFFVGGTTAKALTDSKNRDLPATNQINFLSTMLAS 112 +S D LM P+++SMG++ F+ A +L N D L+ + S Sbjct: 67 RAWLQFSLDHRDALMLPFNFSMGVMTLFIAVGIAASLAKHHNLDS--------LTAGMLS 118 Query: 113 MVGFLLMAAEPAKEGGFLTAFMGTKGLLTAFIAAFVTVNVYKVCVKNNVTIRMPEDVPPN 172 ++ FLL+AA P K+G TA+ +G+ TA + A + +Y ++N+TIR+P +VP Sbjct: 119 LMSFLLVAA-PLKDGQISTAYFSGQGIFTAILVAIYSTELYAFLKRHNITIRLPPEVPAG 177 Query: 173 ISQVFKDLIPFTVSVVLLYGLELLVKGTLGVTVAESIGTLIAPLFSAADGYLGITLIFGA 232 +++ F+ LIP V+ L+ L L ++ LG+ + E+I +L+ PL +A+D I L Sbjct: 178 VARSFEILIPVLAIVLTLHPLNLFIEAQLGMIIPEAIMSLVKPLVAASDTLPAILLSVLV 237 Query: 233 YAFFWFVGIHGPSIVEPAIAAITYANIDVNLHLIQAGQHADKVITSGTQMFIATMGGTGA 292 WF GIHG IV + AN+ +N + AG + G +GG G+ Sbjct: 238 CQVLWFAGIHGALIVTGIMNPFWMANLSINQAAMAAGTAIPHIYVQGFWDHYLLIGGVGS 297 Query: 293 TLIVPFLFMWICKSDRNRAIGRASVVPTFFGVNEPILFGAPIVLNPIFFVPFIFAPIVNV 352 TL + L + K+ R IGR VVP F +NEPILFGAPI++NP+FF+PF+ P++N Sbjct: 298 TLPLA-LMLLRSKAVHLRTIGRMGVVPGVFNINEPILFGAPIIMNPLFFLPFVLVPMINA 356 Query: 353 WIFKFFVDTLNMNSFSANLPWVTPGPLGIVLGTNFQVLSFILAGLLVVVDTIIYYPFVKV 412 + F + ++ + PW TP P+G N+ I+ + + ++Y PF+K Sbjct: 357 TLAYFALKLDLVSRVVSMTPWTTPAPIGASWAANWSFSPVIMCLICMATAMVMYLPFLKA 416 Query: 413 YDEQILEEERSGKTNDA 429 Y++Q+LE+E + A Sbjct: 417 YEKQLLEQEHANAAAQA 433 Lambda K H 0.324 0.140 0.414 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: 570 Number of extensions: 32 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: 568 Length of database: 440 Length adjustment: 34 Effective length of query: 534 Effective length of database: 406 Effective search space: 216804 Effective search space used: 216804 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