Align IIC' aka PtsC2, component of N-Acetylglucosamine (NAG) porter (PtsBC1C2)(also may facilitate xylose transport) (characterized)
to candidate BWI76_RS11130 BWI76_RS11130 PTS glucose transporter subunit IIBC
Query= TCDB::Q8GBT6 (403 letters) >FitnessBrowser__Koxy:BWI76_RS11130 Length = 477 Score = 336 bits (862), Expect = 8e-97 Identities = 177/398 (44%), Positives = 249/398 (62%), Gaps = 19/398 (4%) Query: 2 AVLQRIGRSLMLPVAVLPAAALLVRLGNADMLGRPEFPAFVTKIAGFMAAGGNAILDNMA 61 A LQ++G+SLMLPV+VLP A +L+ +G+A+ PA V+ + MA G ++ NM Sbjct: 7 ANLQKVGKSLMLPVSVLPIAGILLGVGSANFSW---LPAVVSHV---MAEAGGSVFANMP 60 Query: 62 LLFAVGIAIGFAKKSDGSTALAAVVGYLVFKNVLATFTDKNLPQVAKAVDGKVVMVDAPV 121 L+FA+G+A+GF +DG +ALA+VV Y + ++ L A+ + K + Sbjct: 61 LIFAIGVALGFTN-NDGVSALASVVAYGIMVKTMSVVAPLVLHLPAEEIAAKHL-----A 114 Query: 122 DAKVLGGVVMGLVVALLYQRFYRTKLPDWAGFFGGRRLVPILSAFAGLVIGIVFGYIWPV 181 D VLGG++ G + A ++ RFYR KLP++ GFF G+R VPI+S A + G++ +IWP Sbjct: 115 DTGVLGGIISGAIAAYMFNRFYRIKLPEYLGFFAGKRFVPIISGLAAIFTGVILSFIWPP 174 Query: 182 LGTGLHNFGEWLVGSGAVGA-GIFGVANRALIPIGMHHLLNSFPWFQAGEYEGKSG---- 236 +GT + F +W V A GI+G R L+P G+HH+ N Q GEY +G Sbjct: 175 IGTAIQTFSQWAAYQNPVVAFGIYGFIERCLVPFGLHHIWNVPFQMQIGEYTNAAGQVFH 234 Query: 237 -DIARFLAGDPTAGQFMTGFFPIMMFALPAACLAIVHCARPERRKVVGGMMFSLALTSFV 295 DI R++AGDPTAG+ GF M+ LPAA +AI H A+PE R VGG+M S ALTSF+ Sbjct: 235 GDIPRYMAGDPTAGKLSGGFL-FKMYGLPAAAIAIWHSAKPENRAKVGGIMISAALTSFL 293 Query: 296 TGVTEPIEFTFMFIAPVLYAIHAVLTGVSMALTWALGMKDGFGFSAGAVDFFLNLGIASN 355 TG+TEPIEF+FMF+AP+LY IHA+L G++ + LGM+DG FS G +DF + G +S Sbjct: 294 TGITEPIEFSFMFVAPILYIIHAILAGLAFPICILLGMRDGTSFSHGLIDFIVLSGNSSK 353 Query: 356 PWGLALVGVCFAALYYVVFRFAITKFNLPTPGRESDEE 393 W +VG+C+A +YYVVFR I +L TPGRE E Sbjct: 354 LWLFPIVGICYAIVYYVVFRVLIKALDLKTPGREDATE 391 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: 605 Number of extensions: 37 Number of successful extensions: 8 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: 477 Length adjustment: 32 Effective length of query: 371 Effective length of database: 445 Effective search space: 165095 Effective search space used: 165095 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