Align TM1750, component of Probable mannose/mannoside porter. Induced by beta-mannan (Conners et al., 2005). Regulated by mannose-responsive regulator manR (characterized)
to candidate GFF668 PGA1_c06820 dipeptide transport ATP-binding protein DppF
Query= TCDB::Q9X272 (328 letters) >FitnessBrowser__Phaeo:GFF668 Length = 321 Score = 241 bits (615), Expect = 2e-68 Identities = 131/297 (44%), Positives = 185/297 (62%), Gaps = 8/297 (2%) Query: 27 KRILKAVDGISIEIKEGETLGLVGESGCGKSTLGRTILKLLRPDGGKIFFEGKDITNLND 86 K L AV +S +IKE LVGESG GKST+G+ ++ LL G + G D+ D Sbjct: 30 KSHLTAVSDVSFDIKEKTVYSLVGESGSGKSTIGKMVVGLLENSSGAVKVSGVDLNRETD 89 Query: 87 K-EMKPYRKKMQIIFQDPLGSLNPQMTVGRIIEDPLIIHKIGTKKERRKRVEELLDMVGI 145 + R +Q+IFQDP S+NP+ V II +P + K G KE +R LL+ VG+ Sbjct: 90 AVAITKARDAIQMIFQDPYASMNPRWRVRDIIAEP-VAAKGGETKELAER---LLEQVGL 145 Query: 146 GREFINSFPHEFSGGQQQRIGIARALALNPKFIVCDEPVSALDVSIQAQIIDLLEEIQQK 205 E + FPHEFSGGQ+QRI IAR+LA P+ IVCDEP SALDVS+QAQ+++L+ +++ Sbjct: 146 SAEDADKFPHEFSGGQRQRICIARSLASQPRLIVCDEPTSALDVSVQAQVLNLMSDLKDD 205 Query: 206 MGISYLFIAHNLAVVEHISHKVAVMYLGKIVEYGDVDKIFLNPIHPYTRALLKSVPKIPW 265 +G++YLFI+H+L VV HIS ++ V+YLG++VE D +F P HPYT+ LL + PK+ Sbjct: 206 LGLTYLFISHDLTVVRHISDRIGVLYLGRLVEEAAPDDLFEAPKHPYTQMLLAAAPKM-- 263 Query: 266 DGQKQRFYSLKGELPSPIDLPKGCRFQTRCTEKKAICFEKEPELTEVEKNHFVSCHL 322 D + +GE+P PI+ P GC F RC A C + P++ + + V+CHL Sbjct: 264 DAFGREVEPPQGEIPDPINPPSGCAFHPRCPIATAQCSQVRPQMRNINGSR-VACHL 319 Lambda K H 0.321 0.142 0.417 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: 292 Number of extensions: 9 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: 328 Length of database: 321 Length adjustment: 28 Effective length of query: 300 Effective length of database: 293 Effective search space: 87900 Effective search space used: 87900 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 (21.8 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