Align IIC' aka PtsC2, component of N-Acetylglucosamine (NAG) porter (PtsBC1C2)(also may facilitate xylose transport) (characterized)
to candidate 15742 b1621 fused maltose and glucose-specific PTS enzymes: IIB component -! IIC component (NCBI)
Query= TCDB::Q8GBT6 (403 letters) >FitnessBrowser__Keio:15742 Length = 530 Score = 229 bits (585), Expect = 1e-64 Identities = 145/424 (34%), Positives = 231/424 (54%), Gaps = 44/424 (10%) Query: 5 QRIGRSLMLPVAVLPAAALLVRLGNA----------DMLGRPEFPAFVTKIAGFMAAGGN 54 Q++G++ MLPVA+L +++ +G++ +LG P A T +M+ G+ Sbjct: 16 QQLGKTFMLPVALLSFCGIMLGIGSSLSSHDVITLIPVLGNPVLQAIFT----WMSKIGS 71 Query: 55 AILDNMALLFAVGIAIGFAKKSDGSTALAAVVGYLVFKNVLATF--TDKNL-----PQVA 107 + ++F + I +G A+++ G A A +GY V N+ F T+K + V Sbjct: 72 FAFSFLPVMFCIAIPLGLARENKGVAAFAGFIGYAVM-NLAVNFWLTNKGILPTTDAAVL 130 Query: 108 KAVDGKVVMVDAPVDAKVLGGVVMGLVVALLYQRFYRTKLPDWAGFFGGRRLVPILSAFA 167 KA + + ++ +D +LG V+ G++V +L++RF+ +LPD FFGG R VPI+S+ Sbjct: 131 KANNIQSILGIQSIDTGILGAVIAGIIVWMLHERFHNIRLPDALAFFGGTRFVPIISSLV 190 Query: 168 GLVIGIVFGYIWPVLGTGLHNFGEWLVGSGAVGAGIFGVANRALIPIGMHHLLNSFPWF- 226 ++G+V +WP+ G+ G + +G G +FG R L+P G+HH+L + F Sbjct: 191 MGLVGLVIPLVWPIFAMGISGLGHMINSAGDFGPMLFGTGERLLLPFGLHHILVALIRFT 250 Query: 227 QAG---EYEGK--SGDIARFLAG---------DPTAGQFMT-GFFPIMMFALPAACLAIV 271 AG E G+ SG + F A +A +F++ G P + LP A LA+ Sbjct: 251 DAGGTQEVCGQTVSGALTIFQAQLSCPTTHGFSESATRFLSQGKMPAFLGGLPGAALAMY 310 Query: 272 HCARPERRKVVGGMMFSLALTSFVTGVTEPIEFTFMFIAPVLYAIHAVLTGVSMALTWAL 331 HCARPE R + G++ S + V G TEP+EF F+F+APVLY IHA+LTG+ + L Sbjct: 311 HCARPENRHKIKGLLISGLIACVVGGTTEPLEFLFLFVAPVLYVIHALLTGLGFTVMSVL 370 Query: 332 GMKDGFGFSAGAVDFFLNLGI---ASNPWGLA-LVGVCFAALYYVVFRFAITKFNLPTPG 387 G+ G + G + F+ GI S W + +V + +YYV+FRFAIT+FNL TPG Sbjct: 371 GVT--IGNTDGNIIDFVVFGILHGLSTKWYMVPVVAAIWFVVYYVIFRFAITRFNLKTPG 428 Query: 388 RESD 391 R+S+ Sbjct: 429 RDSE 432 Lambda K H 0.328 0.143 0.441 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: 672 Number of extensions: 37 Number of successful extensions: 3 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: 403 Length of database: 530 Length adjustment: 33 Effective length of query: 370 Effective length of database: 497 Effective search space: 183890 Effective search space used: 183890 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