Align TM0029, 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_0445 Synpcc7942_0445 ABC-type dipeptide/oligopeptide/nickel transport systems permease components-like
Query= TCDB::Q9WXN6 (280 letters) >FitnessBrowser__SynE:Synpcc7942_0445 Length = 351 Score = 121 bits (304), Expect = 2e-32 Identities = 77/234 (32%), Positives = 121/234 (51%), Gaps = 11/234 (4%) Query: 51 PSSAHPLGTDTYGRDVLAQLLHGIRSSLYIGFLAAIISLVIGTIIGSFSAVKRGIVDDVL 110 P H LGTD GRD ++LL+G R SL +G + I++ +G ++G + G VD ++ Sbjct: 120 PGKLHLLGTDDQGRDQFSRLLYGSRISLSVGLVGVILTFPLGILVGGIAGYWGGWVDALI 179 Query: 111 MGITNIVLTTPSILIAILIASYLK--VRSVE---MVAVILGLFQWPWFARAIRAQLMSVM 165 M + +++T PS+ + + +A+ L + S E ++ I L W AR IR Q++S+ Sbjct: 180 MRLVEVLMTIPSLYLLVALAAVLPPGLSSAERFLLIVAITSLINWAGLARVIRGQVLSLR 239 Query: 166 SREYVYLSVMAGYSDLRLVIEDLIPTIATYAFMSFVLFINGGIMGEAGLSLIGLGPTQ-G 224 REYV S + G S L L+I ++P TY ++ L + I+ E+ LSL+GLG Q Sbjct: 240 EREYVQASQVMGASRLYLLIRHILPQTLTYVIIAATLAVPSFIVAESVLSLVGLGIQQPD 299 Query: 225 ISLGIMLQWAVLMEAVRRGLW--WWFVPPGLAIVAVTASLLVISTAMDEVFNPR 276 S G ML A + W W PP L IV + V+ + + +PR Sbjct: 300 PSWGNMLSLATNASMLLLNPWLIW---PPALLIVVAVLAFNVVGDGLRDRLDPR 350 Lambda K H 0.330 0.144 0.441 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: 236 Number of extensions: 13 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: 280 Length of database: 351 Length adjustment: 27 Effective length of query: 253 Effective length of database: 324 Effective search space: 81972 Effective search space used: 81972 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