Align ABC-type transporter, integral membrane subunit, component of Xylose porter (Nanavati et al. 2006). Regulated by xylose-responsive regulator XylR (characterized)
to candidate GFF2276 PGA1_c23080 ribose transport system permease protein RbsC
Query= TCDB::Q9WXW7 (317 letters) >FitnessBrowser__Phaeo:GFF2276 Length = 324 Score = 162 bits (409), Expect = 1e-44 Identities = 106/315 (33%), Positives = 172/315 (54%), Gaps = 13/315 (4%) Query: 9 TFRELGPLVA----LVSLAVFT---AILNPRFLTAFNLQALGRQIAIFGLLAIGETFVII 61 T +++G L+A L++ A+F I NP+FLT N + + R AI G++A+G TFV+I Sbjct: 5 TKQDIGKLLAKQGILIAFALFIIGFTIANPKFLTLDNFENVVRSSAILGVMALGVTFVVI 64 Query: 62 SGGGAIDLSPGSMVALTGVMVAWLMTHGVPVWISVILILLFSIGAGAWHGLFVTKLRVPA 121 SG +DLS GSM++ + ++V L P +++ + ++ GA G V L++ + Sbjct: 65 SGN--LDLSVGSMMSFSTIVVLDLHDKLGPT-LAIPAMFAMTLCLGALIGFLVGYLKLNS 121 Query: 122 FIITLGTLTIARGMAAVIT--KGWPIIGLPSSFLKI-GQGEFLKIPIPVWILLAVALVAD 178 I+TLG L+ G+ + K I ++ I GQG L I P+ I +A+A + Sbjct: 122 LIVTLGMLSAIHGLTLTYSGGKNMDIADKEGTWFAIFGQGNILGIQTPILIFIALAALLG 181 Query: 179 FFLRKTVYGKHLRASGGNEVAARFSGVNVDRVRMIAFMVSGFLAGVVGIIIAARLSQGQP 238 L KT +G+ + A GGN AA FSG+ RV + +++S G+I A+R Q Sbjct: 182 IILAKTPFGRKVYAVGGNGTAATFSGIRRARVVFLCYIMSALCVATAGLIQASRSMGSQN 241 Query: 239 GVGSMYELYAIASTVIGGTSLTGGEGSVLGAIVGASIISLLWNALVLLNVSTYWHNVVIG 298 VG EL +A+ ++GG SL GG G++ ++G I+ + N L+L+ + VV Sbjct: 242 TVGQGLELEVLAAVILGGASLLGGSGTIFKTVIGVLILGFIQNGLLLVGLDFSVQYVVTW 301 Query: 299 IVIVVAVTLDILRRR 313 I+I++AV LDI +R Sbjct: 302 IIIILAVWLDIAAKR 316 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: 295 Number of extensions: 21 Number of successful extensions: 3 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: 324 Length adjustment: 28 Effective length of query: 289 Effective length of database: 296 Effective search space: 85544 Effective search space used: 85544 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