Align TM0030, component of β-glucoside porter (Conners et al., 2005). Binds cellobiose, laminaribiose (Nanavati et al. 2006). Regulated by cellobiose-responsive repressor BglR (characterized)
to candidate GFF2862 HP15_2806 permease protein, ABC-type oligopeptide transporter
Query= TCDB::Q9WXN7 (338 letters) >FitnessBrowser__Marino:GFF2862 Length = 305 Score = 147 bits (372), Expect = 3e-40 Identities = 101/331 (30%), Positives = 163/331 (49%), Gaps = 27/331 (8%) Query: 6 MFKYLLRRFIFLLVTYIVATTIVFILPRAIPGNPLSQILSGLSRVAQANPEAIRAAERTL 65 M Y+LRR + L+ + + F L +P I A +A + + Sbjct: 1 MLNYILRRGLMALLVALTVSFGTFALFH-FATDPAQTI---------AGEDAPQEMVDDI 50 Query: 66 MEEFGLGKPWYVQYFEFITKALRGDLGTSITFYPRKVIDLIIPVIPWTLILLLPATIVAW 125 E++G +P VQY +++ AL+GD G S F+ + V++LI T++L L A V Sbjct: 51 REQYGFDRPVSVQYADWLGSALQGDFGQSY-FWKQPVVELIQEHAKVTIVLALAALGVTV 109 Query: 126 ILGNSLGALAAYKRNTWIDKGVLTTSLIVSQIPYYWLGMIFIFLFGVKLGWLPVQGAYSQ 185 ++ LG AA K N+W+D+ L+T++ IP +WLG++ I LF V PV G Sbjct: 110 LIALPLGISAALKPNSWVDRFALSTAVSAQAIPNFWLGLMLIILFAVTFPIFPVSG---- 165 Query: 186 GTIPNLSWSFFVDVLKHYIMPFASIVVSAMGGWAIGMRLMVIYELGSDYAMFSEYLGMKD 245 + +W KHY++P + S++ R ++ L SDY + G Sbjct: 166 ----DATW-------KHYVLPALVLGASSVPAVMRLTRTGLLDVLSSDYIRTARAKGFMG 214 Query: 246 KR-IFKYVFRNSLLPQITGLALSLGGVLGGALITEIVFNYPGTGYLLFRALTTLDYPLIQ 304 R I + RN+LLP ++ LA+ LG LGG+++TE VF+ G G L ++ D P +Q Sbjct: 215 YRLILQQAMRNALLPIVSVLAVQLGHKLGGSVVTESVFSMNGLGRLAVESIFNSDIPTVQ 274 Query: 305 GIFVILIASIYLANFIVDFLYALIDPRIRLG 335 + +I + + L D + A +DPRIR+G Sbjct: 275 SLILIFVLTFVLLTLAADLINAWLDPRIRMG 305 Lambda K H 0.329 0.146 0.449 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: 282 Number of extensions: 14 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: 338 Length of database: 305 Length adjustment: 28 Effective length of query: 310 Effective length of database: 277 Effective search space: 85870 Effective search space used: 85870 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 (21.8 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