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 3609626 Dshi_3009 binding-protein-dependent transport systems inner membrane component (RefSeq)
Query= TCDB::Q9WXN6 (280 letters) >FitnessBrowser__Dino:3609626 Length = 314 Score = 149 bits (376), Expect = 8e-41 Identities = 85/280 (30%), Positives = 150/280 (53%), Gaps = 12/280 (4%) Query: 12 NKKFIIGFSIFLFFLFLGIFGPMFYRVD------------PTEMTWDYEQPPSSAHPLGT 59 N + + G I L + GI G M + D P Q + +PLGT Sbjct: 34 NPRLLWGSGILLVIILGGIIGRMLWDTDLVFTGSTPLKLPPLGFENLRRQEGIADYPLGT 93 Query: 60 DTYGRDVLAQLLHGIRSSLYIGFLAAIISLVIGTIIGSFSAVKRGIVDDVLMGITNIVLT 119 D GRD+LA L+ G ++L IG +A++I + +G +G + G VDD + ++++++T Sbjct: 94 DGAGRDMLAMLIIGTPNTLMIGAIASVIGMSLGIFLGFTAGFVGGRVDDTIRVLSDVMIT 153 Query: 120 TPSILIAILIASYLKVRSVEMVAVILGLFQWPWFARAIRAQLMSVMSREYVYLSVMAGYS 179 P +LI ++ + S+ M+A ++ F W R IRAQ++S+ YV ++ ++G S Sbjct: 154 IPPLLILVVFQASFGDVSLVMMAFLIAGFMWQSPTRLIRAQVLSMKRSGYVQMAQLSGAS 213 Query: 180 DLRLVIEDLIPTIATYAFMSFVLFINGGIMGEAGLSLIGLGPTQGISLGIMLQWAVLMEA 239 ++ +++P + Y F SF+ + I+ GL ++GLGP + +LG ++ A+ A Sbjct: 214 TFHIMFREMLPNLIPYLFGSFIANVTTAIVTAVGLEVLGLGPQRIPTLGRVIYDAINSGA 273 Query: 240 VRRGLWWWFVPPGLAIVAVTASLLVISTAMDEVFNPRLRE 279 + + LWWW+ P + + +LL+I+ +DEV NPRLR+ Sbjct: 274 LIQNLWWWWGLPTALLATMFIALLLINLGLDEVSNPRLRK 313 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: 11 Number of successful extensions: 2 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: 314 Length adjustment: 26 Effective length of query: 254 Effective length of database: 288 Effective search space: 73152 Effective search space used: 73152 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