Align ABC-type transporter, integral membrane subunit, component of Xylose porter (Nanavati et al. 2006). Regulated by xylose-responsive regulator XylR (characterized)
to candidate N515DRAFT_2415 N515DRAFT_2415 simple sugar transport system permease protein
Query= TCDB::Q9WXW7 (317 letters) >FitnessBrowser__Dyella79:N515DRAFT_2415 Length = 337 Score = 141 bits (355), Expect = 3e-38 Identities = 99/307 (32%), Positives = 162/307 (52%), Gaps = 14/307 (4%) Query: 16 LVALVSLAVFTAILNPRFLTAFNLQALGRQIAIFGLLAIGETFVIISGGGAIDLSPGSMV 75 LV V++A +L FLT L A ++A+G TFVI++GG IDLS G++V Sbjct: 31 LVLFVAMAGAGGVLYHGFLTPQVFLNLLIDNAFLCIVAVGMTFVILAGG--IDLSVGAVV 88 Query: 76 ALTGVMVAWLMT-HGVPVWISVILILLFSIGAGAWHGLFVTKLRVPAFIITLGTLTIARG 134 A + V++A L+ HG P ++ L+L G GA G+ + + R+ F++TL + +ARG Sbjct: 89 AFSTVLLAELVQRHGWPPLAAIALVLAVGTGFGAGMGVLIQRFRLQPFVVTLAGMFLARG 148 Query: 135 MAAVIT-------KGWPIIGLPSSFLKIGQGEFLKIPIPVWILLAVALVADFFLRKTVYG 187 +A +I+ + W + + + L +G G L + + LAV + +G Sbjct: 149 VATLISVDSIDIDQPW-LASVANLRLPLGGGSMLSVG--ALVALAVVAAGALLAGASSFG 205 Query: 188 KHLRASGGNEVAARFSGVNVDRVRMIAFMVSGFLAGVVGIIIAARLSQGQPGVGSMYELY 247 + + A GG+E +AR G+ VD + + +SGF A + G++ + G EL Sbjct: 206 RTVYAIGGSESSARLMGLPVDATVVRVYALSGFCAALAGVVYTLYMLSGYSQHALGLELD 265 Query: 248 AIASTVIGGTSLTGGEGSVLGAIVGASIISLLWNALVL-LNVSTYWHNVVIGIVIVVAVT 306 AIA+ VIGGT L GG G VLG ++G ++ L+ +V +S++W +VIG +++ Sbjct: 266 AIAAVVIGGTVLAGGSGYVLGTLLGVLVLGLIQTLIVFDGELSSWWTRIVIGALLLAFCL 325 Query: 307 LDILRRR 313 L L RR Sbjct: 326 LQRLFRR 332 Score = 26.2 bits (56), Expect = 0.001 Identities = 52/218 (23%), Positives = 88/218 (40%), Gaps = 37/218 (16%) Query: 69 LSPGSMVALTGVMVAWLMTHGVPVWISVILILLFSIGAGA--WHGLFVTKLRVPAFIITL 126 ++P + A G W VP+ ++++L + + GAG +HG ++ + I Sbjct: 4 VAPAATSAAAGRRPWWRRRAQVPLLVTLVLFVAMA-GAGGVLYHGFLTPQVFLNLLIDNA 62 Query: 127 GTLTIARGMAAVITKGW--PIIGLPSSFLKIGQGEFLKIPIPVW-ILLAVALVADFFLRK 183 +A GM VI G +G +F + E + W L A+ALV Sbjct: 63 FLCIVAVGMTFVILAGGIDLSVGAVVAFSTVLLAEL--VQRHGWPPLAAIALV---LAVG 117 Query: 184 TVYGKHLRASGGNEVAARFSGVNVDRVRMIAFMVS---GFLA-GVVGIIIAARLSQGQPG 239 T +G + GV + R R+ F+V+ FLA GV +I + QP Sbjct: 118 TGFGAGM-------------GVLIQRFRLQPFVVTLAGMFLARGVATLISVDSIDIDQPW 164 Query: 240 VGSMYELYAIASTVIGGTSLTGGEGSVLGAIVGASIIS 277 + S+ L L GG +GA+V ++++ Sbjct: 165 LASVANL---------RLPLGGGSMLSVGALVALAVVA 193 Lambda K H 0.328 0.143 0.424 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: 360 Number of extensions: 33 Number of successful extensions: 5 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: 317 Length of database: 337 Length adjustment: 28 Effective length of query: 289 Effective length of database: 309 Effective search space: 89301 Effective search space used: 89301 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: 48 (23.1 bits)
This GapMind analysis is from Apr 09 2024. 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