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 SMc00787 SMc00787 peptide ABC transporter permease
Query= TCDB::Q9WXN7 (338 letters) >FitnessBrowser__Smeli:SMc00787 Length = 334 Score = 164 bits (416), Expect = 2e-45 Identities = 110/344 (31%), Positives = 178/344 (51%), Gaps = 27/344 (7%) Query: 6 MFKYLLRRFIFLLVTYIVATTIVFILPRAIPGNPLSQILSGLSRVAQANPEAIRAAER-- 63 MF++LL R L+ T+I + I F R +PG+P++ +LSG E + + ER Sbjct: 1 MFRFLLGRLAVLIPTFIGVSIIAFSFIRLLPGDPVA-LLSG---------ERVMSPERHA 50 Query: 64 TLMEEFGLGKPWYVQYFEFITKALRGDLGTSITFYPRKVIDLIIPVIPWTLILLLPATIV 123 + + G +P +QY +++ L+GD GTSI + VID + + P T+ L L A I Sbjct: 51 EISHQLGFDRPIVMQYLDYLWGVLQGDFGTSIVT-KKPVIDQFMELFPATVELSLCAIIF 109 Query: 124 AWILGNSLGALAAYKRNTWIDKGVLTTSLIVSQIPYYWLGMIFIFLFGVKLGWLPVQGAY 183 A ++G G +AA KR + D+ ++ T+LI +P +W G++ I + L W PV G Sbjct: 110 AVVVGIPAGVVAAVKRGSIFDQIIMGTALIGFSMPIFWWGLLLIIVVSGILQWTPVSGRI 169 Query: 184 S-QGTIPNLSWSFFVDVL------------KHYIMPFASIVVSAMGGWAIGMRLMVIYEL 230 S P+++ VD L H I+P + + A R ++ L Sbjct: 170 SLMFFFPSVTGFMLVDSLLSGQEGAFQSAFNHLILPTIVLGTIPLAVIARQTRSAMLEVL 229 Query: 231 GSDYAMFSEYLGMKDKRIFK-YVFRNSLLPQITGLALSLGGVLGGALITEIVFNYPGTGY 289 DY + G+ R+ + RN+++P +T + L +G +L GA++TE +F++PG G Sbjct: 230 SEDYVRTARAKGLSTFRVVGIHALRNAMIPVVTTIGLQIGVMLAGAILTETIFSWPGIGK 289 Query: 290 LLFRALTTLDYPLIQGIFVILIASIYLANFIVDFLYALIDPRIR 333 + ++ DY +IQG +I+ A I L N VD LY LI+PRIR Sbjct: 290 WMVDSVFRRDYAVIQGGLLIIAAVIMLVNLAVDLLYGLINPRIR 333 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: 311 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: 334 Length adjustment: 28 Effective length of query: 310 Effective length of database: 306 Effective search space: 94860 Effective search space used: 94860 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