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 Synpcc7942_0822 Synpcc7942_0822 permease protein of oligopeptide ABC
Query= TCDB::Q9WXN7 (338 letters) >FitnessBrowser__SynE:Synpcc7942_0822 Length = 341 Score = 177 bits (449), Expect = 3e-49 Identities = 107/346 (30%), Positives = 177/346 (51%), Gaps = 24/346 (6%) Query: 3 SKSMFKYLLRRFIFLLVTYIVATTIVFILPRAIPGNPLSQILSGLSRVAQANPEAIRAAE 62 ++ + +YLL R + L + T++F+L RA PG+P+ IL P+A AA Sbjct: 4 ARDLGRYLLARLLLLPLMLWTIATLIFLLLRATPGDPIDAILG---------PKAPAAAR 54 Query: 63 RTLMEEFGLGKPWYVQYFEFITKALRGDLGTSITFYPRKVIDLIIPVIPWTLILLLPATI 122 L + GL +P + QYF+++ + L+GDLG S++ + V +I P T L + + Sbjct: 55 LALRSQLGLDRPLWQQYFDYLGQLLKGDLGQSLSSQGQSVRQIIGEYFPATAELAIASLA 114 Query: 123 VAWILGNSLGALAAYKRNTWIDKGVLTTSLIVSQIPYYWLGMIFIFLFGVKLGWLPV--- 179 +A +G LG +AA K N+ + ++ +P +W M+ LF V LGW PV Sbjct: 115 IAIAIGLGLGLMAAAKPNSRRETASRLFGILTYALPTFWAAMLAQLLFAVDLGWFPVGTR 174 Query: 180 -----------QGAYSQGTIPNLSWSFFVDVLKHYIMPFASIVVSAMGGWAIGMRLMVIY 228 G Y + W L++ +P ++ + G + +R+ + Sbjct: 175 YPVTLDPPLGPTGLYVLDALLKADWRAAGLALRYLALPALTLGLLLSGVFERLVRVNLGQ 234 Query: 229 ELGSDYAMFSEYLGMKDKRIF-KYVFRNSLLPQITGLALSLGGVLGGALITEIVFNYPGT 287 L +DY G+ ++R+ + RN+L+P +T L L+L +LGGAL+TE+ F++PG Sbjct: 235 SLQADYIDAGRSRGLSERRLLLNHALRNALIPVVTLLGLTLASLLGGALLTEVAFSWPGL 294 Query: 288 GYLLFRALTTLDYPLIQGIFVILIASIYLANFIVDFLYALIDPRIR 333 L+ A++ DY +QGI V + LA+ +VDF+ ALIDPRIR Sbjct: 295 ANRLYEAISLRDYSTVQGIIVFFGCLVVLASIVVDFINALIDPRIR 340 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: 314 Number of extensions: 17 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: 341 Length adjustment: 28 Effective length of query: 310 Effective length of database: 313 Effective search space: 97030 Effective search space used: 97030 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: 49 (23.5 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