Align TM0027, 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 AZOBR_RS30440 AZOBR_RS30440 hypothetical protein
Query= TCDB::Q9WXN4 (268 letters) >FitnessBrowser__azobra:AZOBR_RS30440 Length = 682 Score = 165 bits (417), Expect = 3e-45 Identities = 89/237 (37%), Positives = 140/237 (59%), Gaps = 5/237 (2%) Query: 25 AVKNVSFEVKEKEIVSLVGESGSGKTTTAKMILRLLPPTSGEIYFEGKDIWKDIKDRESL 84 AV +VSF ++ E++ +VGESGSGK+T + +L L+ PT+G + F+G D K K+ Sbjct: 372 AVDDVSFTIQRGEVLGVVGESGSGKSTIGRSLLALIEPTAGTVLFDGADFVKQAKEGNR- 430 Query: 85 VEFRRKVHAVFQDPFASYNPFYPVERTLWQAISLLENKPSNKKEALELIKESLFRVGIDP 144 + RR+ VFQ+ AS NP V + + + L + + E E+I L RVG+ P Sbjct: 431 -DLRRRAQLVFQNSAASLNPRKTVGAAMERPLVLAGRQ--GEAERREMIAALLTRVGL-P 486 Query: 145 KDVLGKYPHQISGGQKQRIMIARCWILRPLLIVADEPTSMIDASSRGGIIKLLEELREEQ 204 +YPH++SGG++QR+ IAR P +V DE S +D S + I+ LL +LR+E Sbjct: 487 AAYADRYPHELSGGERQRVNIARALATDPEFVVCDEAVSALDVSVQANILNLLADLRDEL 546 Query: 205 GTSIIFITHDLGLAYYVSDNIFVMKNGEIVERGHPDKVVLEPTHEYTKLLVGSIPKL 261 G S +FITHD+ + +++D + V+ G I E G +V+ P H YT+ L+ ++P+L Sbjct: 547 GLSYLFITHDIAVVSHIADRVLVVYGGTICEEGPIGRVLRPPYHPYTEALLSAVPRL 603 Score = 162 bits (411), Expect = 1e-44 Identities = 103/265 (38%), Positives = 153/265 (57%), Gaps = 15/265 (5%) Query: 4 LVVKNLTKIFSLGFFSKR-RIEAVKNVSFEVKEKEIVSLVGESGSGKTTTAKMILRLLPP 62 L V+NLT + + S R + A +VSF ++ E++ LVGESGSGK+T A IL LL Sbjct: 2 LEVRNLT----INYASPRGTLRAASDVSFAIRPGEVMGLVGESGSGKSTVAMAILDLLGE 57 Query: 63 TS----GEIYFEGKDIWK-DIKDRESLVEFRRKVHAVFQDPFASYNPFYPVERTLWQAIS 117 GEI FEG D+ + R SL R + AVFQDPF S NP V R + A Sbjct: 58 AGRIDGGEILFEGTDLRRLSAAHRRSLRGDR--IAAVFQDPFTSLNPALTVGRQI--AEP 113 Query: 118 LLENKPSNKKEALELIKESLFRVGI-DPKDVLGKYPHQISGGQKQRIMIARCWILRPLLI 176 L+++K ++A ++E L VGI +P+ + YPHQ+SGG +QR++IA P L+ Sbjct: 114 LVQHKGFTPRQAAPRVEELLAEVGIREPRRIAQSYPHQLSGGMQQRVLIATALGCDPKLL 173 Query: 177 VADEPTSMIDASSRGGIIKLLEELREEQGTSIIFITHDLGLAYYVSDNIFVMKNGEIVER 236 + DEPT+ +D + II+LL L E S +F++H+LG+ + +++ V+ E+VE Sbjct: 174 ILDEPTTALDVTVEARIIELLAGLCESHHLSALFVSHNLGIVNRICNSVCVLYGSEVVET 233 Query: 237 GHPDKVVLEPTHEYTKLLVGSIPKL 261 G V+ P H YTK LV ++P++ Sbjct: 234 GRTRDVLARPVHPYTKGLVAALPRI 258 Lambda K H 0.319 0.139 0.397 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: 400 Number of extensions: 19 Number of successful extensions: 6 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 268 Length of database: 682 Length adjustment: 32 Effective length of query: 236 Effective length of database: 650 Effective search space: 153400 Effective search space used: 153400 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 51 (24.3 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