Align PTS system, galactitol-specific, IIC component, component of Pentitol [arabitol (arabinitol, lyxitol)/xylitol] PTS permease, IICBA (encoded within an operon that also encodes a polyol-P dehydrogenase, a ribose-5-P isomerase, a ribulose 5-P-3-epimerase, and a BlgG-type PTS antiterminator) (Saklani-Jusforgues et al., 2001; Kentache T et al., 2016, in press) (characterized)
to candidate BWI76_RS24890 BWI76_RS24890 PTS system galactitol-specific transporter subunit IIC
Query= TCDB::Q71WA6 (423 letters) >FitnessBrowser__Koxy:BWI76_RS24890 Length = 457 Score = 355 bits (911), Expect = e-102 Identities = 167/407 (41%), Positives = 271/407 (66%), Gaps = 2/407 (0%) Query: 8 VQYVLNLGPTVILPIMIFFIALIFRVPAKKALRSAITIGIGFVGINLVISLLSSNLGPAA 67 ++Y+L+LGPTV+LPI+I + I + +S + IGIGFVGI LVI L+ ++GPAA Sbjct: 6 MRYILDLGPTVMLPIVIIIFSKILGMKLGDCFKSGLHIGIGFVGIGLVIGLMLDSIGPAA 65 Query: 68 QQMVERFGLNLTIIDAGWPAAAAASWASPVAAILIPICLVVNLALIFFKVTKTLDIDIWN 127 + M E F +NL +ID GWP ++ +WAS +A + IPI + VN+ ++ ++T+ +++DIWN Sbjct: 66 KAMAEHFQINLHVIDIGWPGSSPMTWASQIALVAIPIAIAVNIFMLVTRMTRVVNVDIWN 125 Query: 128 YWHFIAAGATGYIVTGGNWWFAILCAIIYEVAVLWMADRTQPMVEEFYGLKGISLPTGST 187 WH GA +I TG ++W IL +++ V + D +F+GL+GI++P GS+ Sbjct: 126 IWHMTFTGAMLHIATG-SYWIGILGVVVHAAFVYKLGDWFAKDTRDFFGLEGIAIPHGSS 184 Query: 188 AAFGFIGIPVGWLIAKIPGIKNIHVDPETIQKRFGIFGEPMMMGLILGIAIGILAGYDVG 247 A G I + V +I KIPG+ IH + IQKRFG FGEP+ +G ++G+ IG LAGYD+ Sbjct: 185 AYLGPIAVLVDTIIEKIPGLNRIHFSADDIQKRFGPFGEPVTVGFVMGLVIGALAGYDLK 244 Query: 248 AVAQLGMSMGAVMFLMPRMVKILMEGLIPISESAREFMKSRFKGRELYIGLDAALSIGHP 307 + QL + AVM LMPR++K +M+GL PI++ AR+ ++++F G++ IGLD AL +GH Sbjct: 245 GILQLAVKTAAVMLLMPRVIKPIMDGLNPIAKQARKRLQAKFGGQDFLIGLDPALLLGHT 304 Query: 308 ANISTGLILVPITLFLAVIIPGNKVLPFGDLATIPFYVSFVVASRKGNILHSVLAGTVVI 367 + +S LI +P+++ +AV++PGN+VLPFGDLATI F+V+ VA +GN+ ++++G +++ Sbjct: 305 SVVSASLIFIPLSILIAVLVPGNQVLPFGDLATIGFFVAMAVAVHQGNLFRTLISGIILM 364 Query: 368 ALALLMATDFGLVHTEMMKGVYEFPKGATQVSTLDMGGNFFNWVILK 414 + L +AT +HT++ G V+++D GG+ W++++ Sbjct: 365 GITLWIATQTIGLHTQLAANAGALKAGGL-VASMDQGGSPITWLLIQ 410 Score = 31.2 bits (69), Expect = 7e-05 Identities = 43/192 (22%), Positives = 74/192 (38%), Gaps = 9/192 (4%) Query: 25 FFIALIFRVPAKKALRSAITIGIGFVGINL----VISLLSSNLGPAAQQMVERFGLNLTI 80 F + L+ A L+ + + + + L VI + L P A+Q +R Sbjct: 229 FVMGLVIGALAGYDLKGILQLAVKTAAVMLLMPRVIKPIMDGLNPIAKQARKRLQAKFGG 288 Query: 81 ID--AGWPAAAAASWASPVAAILIPICLVVNLALIFFKVTKTLDIDIWNYWHFIAAGATG 138 D G A S V+A LI I L + +A++ D+ F+A Sbjct: 289 QDFLIGLDPALLLGHTSVVSASLIFIPLSILIAVLVPGNQVLPFGDLATIGFFVAMAVA- 347 Query: 139 YIVTGGNWWFAILCAIIYEVAVLWMADRTQPMVEEFYGLKGISLPTGSTAAFGFIGIPVG 198 V GN + ++ II LW+A +T + + G G A+ G P+ Sbjct: 348 --VHQGNLFRTLISGIILMGITLWIATQTIGLHTQLAANAGALKAGGLVASMDQGGSPIT 405 Query: 199 WLIAKIPGIKNI 210 WL+ ++ +N+ Sbjct: 406 WLLIQLFTWQNV 417 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: 554 Number of extensions: 33 Number of successful extensions: 4 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 423 Length of database: 457 Length adjustment: 32 Effective length of query: 391 Effective length of database: 425 Effective search space: 166175 Effective search space used: 166175 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