Align IIC' aka PtsC2, component of N-Acetylglucosamine (NAG) porter (PtsBC1C2)(also may facilitate xylose transport) (characterized)
to candidate 200788 SO1623 PTS system, glucose-specific IIBC component (NCBI ptt file)
Query= TCDB::Q8GBT6 (403 letters) >FitnessBrowser__MR1:200788 Length = 499 Score = 233 bits (595), Expect = 7e-66 Identities = 144/391 (36%), Positives = 213/391 (54%), Gaps = 22/391 (5%) Query: 5 QRIGRSLMLPVAVLPAAALLVRLGNADMLGRPEFPAFVTKIAGFMAAGGNAILDNMALLF 64 QR+ ++L++P+A+LPAA +++ L + + PE + M A G I M +LF Sbjct: 29 QRLSQALLIPIAILPAAGVMLGLTVSPIPFMPEV------LNVLMLAVGKLIFAIMPILF 82 Query: 65 AVGIAIGFAKKSDGSTALAAVVGYLVFKNVLATFTDK-NLPQVAKAVDGKVVMVDAPVDA 123 AV +AIGF + G A AV GY V LA D LP ++V+ +D Sbjct: 83 AVAVAIGFCR-DQGIAAFTAVFGYGVMTATLAALADLYQLPT-------QLVLGMETLDT 134 Query: 124 KVLGGVVMGLVVALLYQRFYRTKLPDWAGFFGGRRLVPILSAFAGLVIGIVFGYIWPVLG 183 + GG+++G V + +LP FF GRR +L + +G V +IWP L Sbjct: 135 GIAGGMLIGGVTCFAVRWSQYIRLPAIFSFFEGRRSASLLIIPLAMGLGYVLAHIWPSLS 194 Query: 184 TGLHNFGEWLV-GSGAVGAGIFGVANRALIPIGMHHLLNSFPWFQAGEYEGKS-----GD 237 + +W V A+ G++G R LIP+G+HH+ N+ + + G+Y+ + G+ Sbjct: 195 LLIERVSDWAVYQKPAIAFGVYGALERLLIPLGLHHIWNAPFYLEVGQYQLQDAEVVRGE 254 Query: 238 IARFLAGDPTAGQFMTGFFPIMMFALPAACLAIVHCARPERRKVVGGMMFSLALTSFVTG 297 +AR+LAGDP AG G+ I M+ LPAA LAI CA R V G+M S A S++TG Sbjct: 255 VARYLAGDPQAGNLAGGYL-IKMWGLPAAALAIWRCADNSERNRVAGIMLSAAAASWLTG 313 Query: 298 VTEPIEFTFMFIAPVLYAIHAVLTGVSMALTWALGMKDGFGFSAGAVDFFLNLGIASNPW 357 VTEPIEF FMF+AP+L+ IH +L+G++ + L + FS G VDF L ++ N Sbjct: 314 VTEPIEFAFMFVAPLLFLIHVMLSGLAYFVCIMLDIHHSIVFSHGLVDFTLLFSLSRNTG 373 Query: 358 GLALVGVCFAALYYVVFRFAITKFNLPTPGR 388 A++G A +YY++FR +I FNL TPGR Sbjct: 374 WFAVLGPLTAVIYYILFRGSILAFNLKTPGR 404 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: 540 Number of extensions: 25 Number of successful extensions: 6 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: 499 Length adjustment: 33 Effective length of query: 370 Effective length of database: 466 Effective search space: 172420 Effective search space used: 172420 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