Align Putative beta-xyloside ABC transporter, permease component, component of Glucose porter. Also bind xylose (Boucher and Noll 2011). Induced by glucose (Frock et al. 2012). Directly regulated by glucose-responsive regulator GluR (characterized)
to candidate WP_061936170.1 CPter91_RS01725 ABC transporter permease
Query= TCDB::G4FGN4 (313 letters) >NCBI__GCF_001584185.1:WP_061936170.1 Length = 327 Score = 246 bits (629), Expect = 4e-70 Identities = 138/311 (44%), Positives = 194/311 (62%), Gaps = 17/311 (5%) Query: 17 LIAIVVFLGVTTREFLTVENIFTVILNVSFIAIMSFGMTMVIITSGIDLSVGSILGAASV 76 L+ + + +T+ F T+ N +V L V+ IAI+ G T VIIT GIDLSVGS+L A V Sbjct: 18 LVVLGLVFSLTSDAFFTLNNGMSVALQVTSIAILGIGATCVIITGGIDLSVGSVLALAGV 77 Query: 77 VMGLLMDEKGLSPFLSVVIGLAVGVGFGLANGLLITKARLAPFISTLGMLSVGRGLAYVM 136 + +++ + G+ + ++ GLAVG G NGL IT+ +L PFI+TLGM+ V RG+A + Sbjct: 78 IAAMVV-KAGMPVPVGMLCGLAVGAVCGGLNGLCITQLKLPPFIATLGMMLVARGVALQV 136 Query: 137 SGGWPISPFPESFTVHGQGMV--------GP--------VPVPVIYMAVIGVIAHIFLKY 180 +G P+S PE F G G + GP +P PVI M VI ++ I L Sbjct: 137 TGARPVSGLPEEFGTLGNGTLFRIVKETTGPFPDVVFPGIPYPVILMVVIAIVISIMLSR 196 Query: 181 TVTGRRIYAIGGNMEASKLVGIKTDRILILVYTINGFLAAFAGFLLTAWLGVAQPNAGQG 240 T GR IYA+G N EA++L G+K R+ + Y I+G LA G +L + L AQPN G Sbjct: 197 TQFGRHIYAVGSNAEAARLSGVKVARVTLWTYVISGTLAGLTGCVLMSRLVTAQPNEGVM 256 Query: 241 YELDVIAATVIGGTSLSGGEGTILGAFLGAVIMGVLRNGMILLGVSSFWQQVVIGIVIII 300 YELD IA+ VIGGTSL GG GTI G +G+ ++G+LRNG+ + GVSSF QQ++IG+VI++ Sbjct: 257 YELDAIASAVIGGTSLIGGIGTISGTAIGSFVIGILRNGLNMNGVSSFVQQIIIGLVILL 316 Query: 301 AIAIDQIRRAK 311 + IDQ+R + Sbjct: 317 TVWIDQMRNRR 327 Lambda K H 0.328 0.145 0.421 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: 337 Number of extensions: 18 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: 313 Length of database: 327 Length adjustment: 28 Effective length of query: 285 Effective length of database: 299 Effective search space: 85215 Effective search space used: 85215 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