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 GFF2183 PS417_11135 peptide ABC transporter
Query= TCDB::Q9WXN7 (338 letters) >FitnessBrowser__WCS417:GFF2183 Length = 313 Score = 159 bits (402), Expect = 9e-44 Identities = 96/330 (29%), Positives = 172/330 (52%), Gaps = 18/330 (5%) Query: 6 MFKYLLRRFIFLLVTYIVATTIVFILPRAIPGNPLSQILSGLSRVAQANPEAIRAAERTL 65 M +++L++ + T ++ + +VF L R IPG+P +L + A+P+++ TL Sbjct: 1 MLRFILQKLAMAVPTLLLISVMVFALIRLIPGDPALLMLGDM-----ADPQSLADMRHTL 55 Query: 66 MEEFGLGKPWYVQYFEFITKALRGDLGTSITFYPRKVIDLIIPVIPWTLILLLPATIVAW 125 GL Q+ + L DLG SI+ + V+ LI+ + ++L A + A Sbjct: 56 ----GLDHSLVTQFLIWFKAVLSFDLGFSIST-KQAVLPLILDRFSVSATIVLVAVLFAT 110 Query: 126 ILGNSLGALAAYKRNTWIDKGVLTTSLIVSQIPYYWLGMIFIFLFGVKLGWLPVQGAYSQ 185 ++ +G +AA+K+N+ +D G+++ + ++ IP +WLG++ + FG++LGWLPV G S Sbjct: 111 LIAVPIGLIAAWKQNSALDLGLVSIATLLLSIPSFWLGLLLLHAFGIQLGWLPVVGYVSF 170 Query: 186 GTIPNLSWSFFVDVLKHYIMPFASIVVSAMGGWAIGMRLMVIYELGSDYAMFSEYLGMKD 245 P W + + ++P ++ + +G R I L +Y + G+ + Sbjct: 171 SQAP---WQ----AMSYMVLPVVTLTLVEVGAITRMARASTIEVLRLEYIAHARAKGLSE 223 Query: 246 KRI-FKYVFRNSLLPQITGLALSLGGVLGGALITEIVFNYPGTGYLLFRALTTLDYPLIQ 304 + + +K+ N+ P T + L LG +LGG + E VF PG G L+ A+ DYP++Q Sbjct: 224 RAVLWKHALPNAFAPTWTLVGLILGNLLGGIAVLETVFTLPGIGRLMVDAIFARDYPVLQ 283 Query: 305 GIFVILIASIYLANFIVDFLYALIDPRIRL 334 G +++ L N VD LY L DPR++L Sbjct: 284 GCLLLITFIYVLVNLCVDLLYPLFDPRVKL 313 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: 291 Number of extensions: 21 Number of successful extensions: 4 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: 313 Length adjustment: 28 Effective length of query: 310 Effective length of database: 285 Effective search space: 88350 Effective search space used: 88350 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