Align IIC' aka PtsC2, component of N-Acetylglucosamine (NAG) porter (PtsBC1C2)(also may facilitate xylose transport) (characterized)
to candidate 7025672 Shewana3_2822 PTS system, glucose-like IIB subunint (RefSeq)
Query= TCDB::Q8GBT6 (403 letters) >FitnessBrowser__ANA3:7025672 Length = 452 Score = 219 bits (558), Expect = 1e-61 Identities = 139/383 (36%), Positives = 205/383 (53%), Gaps = 23/383 (6%) Query: 18 LPAAALLVRLGNADMLGRPEFPAFVTKIAGFMAAGGNAILDNMALLFAVGIAIGFAKKSD 77 +PAA +++ L + + P P +T + M A G I M +LFAV +AIGF + Sbjct: 1 MPAAGVMLGLTVSPI---PFMPEVLTVL---MLAVGKLIFAIMPILFAVAVAIGFCR-DQ 53 Query: 78 GSTALAAVVGYLVFKNVLATFTDK-NLPQVAKAVDGKVVMVDAPVDAKVLGGVVMGLVVA 136 G A AV GY V LA D LP ++++ +D + GG+++G V Sbjct: 54 GIAAFTAVFGYGVMTATLAALADLYQLPT-------QLLLGMETLDTGIAGGMLIGGVTC 106 Query: 137 LLYQRFYRTKLPDWAGFFGGRRLVPILSAFAGLVIGIVFGYIWPVLGTGLHNFGEWLV-G 195 + +LP FF GRR +L + +G + ++WP L + +W V Sbjct: 107 FAVRWSQYIRLPAIFSFFEGRRSASLLIIPLAMGLGYILAHVWPPLSLLIERVSDWAVYQ 166 Query: 196 SGAVGAGIFGVANRALIPIGMHHLLNSFPWFQAGEYEGKS-----GDIARFLAGDPTAGQ 250 A+ G++G R LIP+G+HH+ N+ + + G+Y+ ++ G++AR+LAGDP AG Sbjct: 167 KPAIAFGVYGALERLLIPLGLHHIWNAPFYLEVGQYQLQNSEVVRGEVARYLAGDPQAGN 226 Query: 251 FMTGFFPIMMFALPAACLAIVHCARPERRKVVGGMMFSLALTSFVTGVTEPIEFTFMFIA 310 G+ I M+ LPAA LAI CA P R V G+M S A S++TGVTEPIEF FMF+A Sbjct: 227 LAGGYL-IKMWGLPAAALAIWRCAEPSERNRVAGIMLSAAAASWLTGVTEPIEFAFMFVA 285 Query: 311 PVLYAIHAVLTGVSMALTWALGMKDGFGFSAGAVDFFLNLGIASNPWGLALVGVCFAALY 370 P L+ IH +L+G++ + L + FS G VDF L ++ N +G A +Y Sbjct: 286 PFLFLIHVLLSGLAYFVCIMLDIHHSIVFSHGLVDFTLLFSLSRNTGWFVFLGPLTAVIY 345 Query: 371 YVVFRFAITKFNLPTPGR-ESDE 392 Y++FR +I FNL TPGR E DE Sbjct: 346 YLLFRGSILAFNLKTPGRLEPDE 368 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: 482 Number of extensions: 25 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: 403 Length of database: 452 Length adjustment: 32 Effective length of query: 371 Effective length of database: 420 Effective search space: 155820 Effective search space used: 155820 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