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 PfGW456L13_5058 Dipeptide transport ATP-binding protein DppF (TC 3.A.1.5.2)
Query= TCDB::Q9X272 (328 letters) >FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_5058 Length = 326 Score = 264 bits (674), Expect = 3e-75 Identities = 133/323 (41%), Positives = 201/323 (62%), Gaps = 8/323 (2%) Query: 10 MKPLLQTVDLKKYFP------QGKRILKAVDGISIEIKEGETLGLVGESGCGKSTLGRTI 63 M +L DL +++ +G ++A++G+S E++ G+TL +VGESGCGKSTL R + Sbjct: 1 MAVVLTARDLTRHYEVSRGLFKGHATVRALNGVSFELEAGKTLAVVGESGCGKSTLARAL 60 Query: 64 LKLLRPDGGKIFFEGKDITNLNDKEMKPYRKKMQIIFQDPLGSLNPQMTVGRIIEDPLII 123 + P G + G+++ + + K RK +Q++FQ P SLNP+ VG + +PL+I Sbjct: 61 TLIEEPSSGSLKIAGQEVAGADKAQRKQLRKDVQMVFQSPYASLNPRQKVGDQLAEPLLI 120 Query: 124 HKIGTKKERRKRVEELLDMVGIGREFINSFPHEFSGGQQQRIGIARALALNPKFIVCDEP 183 + + ERR++V+ ++ VG+ E +PH FSGGQ+QRI +ARA+ L PK +V DEP Sbjct: 121 NTNLSAAERREKVQAMMKQVGLRPEHYQRYPHMFSGGQRQRIALARAMMLQPKVLVADEP 180 Query: 184 VSALDVSIQAQIIDLLEEIQQKMGISYLFIAHNLAVVEHISHKVAVMYLGKIVEYGDVDK 243 SALDVSIQAQ+++L ++QQ+ +Y+FI+HNLAVV H++ V VMYLG+ VE G + Sbjct: 181 TSALDVSIQAQVLNLFMDLQQEFNTAYVFISHNLAVVRHVADHVMVMYLGRPVEMGTKED 240 Query: 244 IFLNPIHPYTRALLKSVPKIPWDGQKQRFYSLKGELPSPIDLPKGCRFQTRCTEKKAICF 303 I+ P+HPYT+ALL + P I D K + + GELP+P++ P GC F RC C Sbjct: 241 IYSRPLHPYTQALLSATPAIHPDPDKPKI-KIVGELPNPLNPPSGCAFHKRCPYATERCS 299 Query: 304 EKEPELTEVEKNHFVSCHLVRSY 326 +EP L + V+CH + Sbjct: 300 TEEPALRLIAGRQ-VACHYAEQF 321 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: 341 Number of extensions: 17 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: 328 Length of database: 326 Length adjustment: 28 Effective length of query: 300 Effective length of database: 298 Effective search space: 89400 Effective search space used: 89400 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