Align ABC-type transporter, integral membrane subunit, component of Xylose porter (Nanavati et al. 2006). Regulated by xylose-responsive regulator XylR (characterized)
to candidate CCNA_00904 CCNA_00904 inositol ABC transport system, permease protein IatP
Query= TCDB::Q9WXW7 (317 letters) >FitnessBrowser__Caulo:CCNA_00904 Length = 332 Score = 219 bits (559), Expect = 5e-62 Identities = 128/298 (42%), Positives = 181/298 (60%), Gaps = 8/298 (2%) Query: 16 LVALVSLAVFTAILNPRFLTAFNLQALGRQIAIFGLLAIGETFVIISGGGAIDLSPGSMV 75 L L+ +AVF A N RFLTA N + +++I+G++A+G TFVI+ GG ID++ GS++ Sbjct: 30 LFLLLLVAVFGAA-NERFLTARNALNILSEVSIYGIIAVGMTFVILIGG--IDVAVGSLL 86 Query: 76 ALTGVMVAWLMT----HGVPVWISVILI-LLFSIGAGAWHGLFVTKLRVPAFIITLGTLT 130 A + A+++T G W+ +L+ L + G G VT L VPAFI+TLG +T Sbjct: 87 AFASIAAAYVVTAVVGDGPATWLIALLVSTLIGLAGGYVQGKAVTWLHVPAFIVTLGGMT 146 Query: 131 IARGMAAVITKGWPIIGLPSSFLKIGQGEFLKIPIPVWILLAVALVADFFLRKTVYGKHL 190 + RG ++ G PI G ++ G GE L +P+PV I VA LR T YG+ + Sbjct: 147 VWRGATLLLNDGGPISGFNDAYRWWGSGEILFLPVPVVIFALVAAAGHVALRYTRYGRQV 206 Query: 191 RASGGNEVAARFSGVNVDRVRMIAFMVSGFLAGVVGIIIAARLSQGQPGVGSMYELYAIA 250 A GGN AAR SGVNVD + + + G LAG+ G +++ARL + G+ YEL IA Sbjct: 207 YAVGGNAEAARLSGVNVDFITTSVYAIIGALAGLSGFLLSARLGSAEAVAGTGYELRVIA 266 Query: 251 STVIGGTSLTGGEGSVLGAIVGASIISLLWNALVLLNVSTYWHNVVIGIVIVVAVTLD 308 S VIGG SLTGG G V G ++GA +I +L N LV+L+V++Y VVIG++IV AV D Sbjct: 267 SVVIGGASLTGGSGGVGGTVLGALLIGVLSNGLVMLHVTSYVQQVVIGLIIVAAVAFD 324 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: 382 Number of extensions: 27 Number of successful extensions: 3 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 1 Length of query: 317 Length of database: 332 Length adjustment: 28 Effective length of query: 289 Effective length of database: 304 Effective search space: 87856 Effective search space used: 87856 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 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