Align ABC-type transporter, integral membrane subunit, component of Xylose porter (Nanavati et al. 2006). Regulated by xylose-responsive regulator XylR (characterized)
to candidate WP_061936170.1 CPter91_RS01725 ABC transporter permease
Query= TCDB::Q9WXW7 (317 letters) >NCBI__GCF_001584185.1:WP_061936170.1 Length = 327 Score = 218 bits (555), Expect = 2e-61 Identities = 123/324 (37%), Positives = 190/324 (58%), Gaps = 18/324 (5%) Query: 6 KKRTFRELGPLVALVSLAVFTAILNPRFLTAFNLQALGRQIAIFGLLAIGETFVIISGGG 65 +K ++ L +LV L + ++ + F T N ++ Q+ +L IG T VII+GG Sbjct: 5 QKDLIQKFAALGSLVVLGLVFSLTSDAFFTLNNGMSVALQVTSIAILGIGATCVIITGG- 63 Query: 66 AIDLSPGSMVALTGVMVAWLMTHGVPVWISVILILLFSIGAGAWHGLFVTKLRVPAFIIT 125 IDLS GS++AL GV+ A ++ G+PV + ++ L G +GL +T+L++P FI T Sbjct: 64 -IDLSVGSVLALAGVIAAMVVKAGMPVPVGMLCGLAVGAVCGGLNGLCITQLKLPPFIAT 122 Query: 126 LGTLTIARGMAAVITKGWPIIGLPSSFLKIGQGEFLKI----------------PIPVWI 169 LG + +ARG+A +T P+ GLP F +G G +I P PV + Sbjct: 123 LGMMLVARGVALQVTGARPVSGLPEEFGTLGNGTLFRIVKETTGPFPDVVFPGIPYPVIL 182 Query: 170 LLAVALVADFFLRKTVYGKHLRASGGNEVAARFSGVNVDRVRMIAFMVSGFLAGVVGIII 229 ++ +A+V L +T +G+H+ A G N AAR SGV V RV + +++SG LAG+ G ++ Sbjct: 183 MVVIAIVISIMLSRTQFGRHIYAVGSNAEAARLSGVKVARVTLWTYVISGTLAGLTGCVL 242 Query: 230 AARLSQGQPGVGSMYELYAIASTVIGGTSLTGGEGSVLGAIVGASIISLLWNALVLLNVS 289 +RL QP G MYEL AIAS VIGGTSL GG G++ G +G+ +I +L N L + VS Sbjct: 243 MSRLVTAQPNEGVMYELDAIASAVIGGTSLIGGIGTISGTAIGSFVIGILRNGLNMNGVS 302 Query: 290 TYWHNVVIGIVIVVAVTLDILRRR 313 ++ ++IG+VI++ V +D +R R Sbjct: 303 SFVQQIIIGLVILLTVWIDQMRNR 326 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: 318 Number of extensions: 19 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: 327 Length adjustment: 28 Effective length of query: 289 Effective length of database: 299 Effective search space: 86411 Effective search space used: 86411 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 24 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