Align ABC-type transporter, integral membrane subunit, component of Xylose porter (Nanavati et al. 2006). Regulated by xylose-responsive regulator XylR (characterized)
to candidate PP_2456 PP_2456 D-ribose ABC transporter - permease subunit
Query= TCDB::Q9WXW7 (317 letters) >FitnessBrowser__Putida:PP_2456 Length = 331 Score = 153 bits (387), Expect = 5e-42 Identities = 106/306 (34%), Positives = 158/306 (51%), Gaps = 4/306 (1%) Query: 13 LGPLVALVSLAVFTAILNPRFLTAFNLQALGRQIAIFGLLAIGETFVIISGGGAIDLSPG 72 LG AL+++ V + L+ F + L QI +LA+G TFV+I GG IDLS G Sbjct: 27 LGLAGALLAMIVLFSFLSSHFWSYGTFSTLANQIPDLMVLAVGMTFVLIIGG--IDLSVG 84 Query: 73 SMVALTGVMVAW-LMTHGVPVWISVILILLFSIGAGAWHGLFVTKLRVPAFIITLGTLTI 131 S++AL V+ ++ G V S +L + + AG+ G R+P+FI++LG L + Sbjct: 85 SVLALAASTVSVAILGWGWGVLPSALLGMAVAALAGSITGGVTVAWRIPSFIVSLGVLEM 144 Query: 132 ARGMAAVITKGWPIIGLPSSFLKIGQGEFLKIPIPVWILLAVALVADFFLRKTVYGKHLR 191 ARG+A T + ++ + I L V ++A L +TV+G++L Sbjct: 145 ARGLAYQFTDSRTAY-IGDAYAWFSNPVAFGVSPAFIIALLVIVLAQLVLTRTVFGRYLI 203 Query: 192 ASGGNEVAARFSGVNVDRVRMIAFMVSGFLAGVVGIIIAARLSQGQPGVGSMYELYAIAS 251 G NE A R +G++ +++ F + G LAG+ + +RL P GS EL IA+ Sbjct: 204 GIGTNEEAVRLAGIDPRPYKVLVFALMGLLAGLAALFQISRLEAADPNAGSGLELQVIAA 263 Query: 252 TVIGGTSLTGGEGSVLGAIVGASIISLLWNALVLLNVSTYWHNVVIGIVIVVAVTLDILR 311 VIGGTSL GG GSV+ G IIS+L L + S ++ G VIV+AV LD R Sbjct: 264 VVIGGTSLMGGRGSVISTFFGVLIISVLAAGLAQIGASEPTKRIITGAVIVIAVVLDTYR 323 Query: 312 RRLASK 317 R A + Sbjct: 324 SRRAGR 329 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: 296 Number of extensions: 20 Number of successful extensions: 5 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: 317 Length of database: 331 Length adjustment: 28 Effective length of query: 289 Effective length of database: 303 Effective search space: 87567 Effective search space used: 87567 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