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 Pf6N2E2_3314 Dipeptide transport ATP-binding protein DppF (TC 3.A.1.5.2)
Query= TCDB::Q9X272 (328 letters) >FitnessBrowser__pseudo6_N2E2:Pf6N2E2_3314 Length = 326 Score = 271 bits (692), Expect = 2e-77 Identities = 135/323 (41%), Positives = 204/323 (63%), Gaps = 8/323 (2%) Query: 10 MKPLLQTVDLKKYFP------QGKRILKAVDGISIEIKEGETLGLVGESGCGKSTLGRTI 63 M +L DL +++ +G ++A++G+S E++ G+TL +VGESGCGKSTL R + Sbjct: 1 MAVVLTARDLTRHYEVSRGMFKGHATVRALNGVSFELEAGKTLAVVGESGCGKSTLARAL 60 Query: 64 LKLLRPDGGKIFFEGKDITNLNDKEMKPYRKKMQIIFQDPLGSLNPQMTVGRIIEDPLII 123 + P G + G+++ N E K RK +Q++FQ P SLNP+ +G + +PL+I Sbjct: 61 TLIEEPSAGSLKIAGQEVAGANKAERKQLRKDVQMVFQSPYASLNPRQKIGDQLAEPLLI 120 Query: 124 HKIGTKKERRKRVEELLDMVGIGREFINSFPHEFSGGQQQRIGIARALALNPKFIVCDEP 183 + + ERR++V+ ++ VG+ E +PH FSGGQ+QRI +ARA+ L PK +V DEP Sbjct: 121 NTKLSATERREKVQAMMKQVGLRPEHYQRYPHMFSGGQRQRIALARAMMLQPKVLVADEP 180 Query: 184 VSALDVSIQAQIIDLLEEIQQKMGISYLFIAHNLAVVEHISHKVAVMYLGKIVEYGDVDK 243 SALDVSIQAQ+++L ++QQ+ +Y+FI+HNLAVV+H++ V VMYLG+ VE G + Sbjct: 181 TSALDVSIQAQVLNLFMDLQQEFNTAYVFISHNLAVVQHVADDVMVMYLGRPVEMGPNES 240 Query: 244 IFLNPIHPYTRALLKSVPKIPWDGQKQRFYSLKGELPSPIDLPKGCRFQTRCTEKKAICF 303 I+ P+HPYT+ALL + P I D K + + GELP+P++ P GC F RC C Sbjct: 241 IYSRPLHPYTQALLSATPTIHPDPNKPKI-KIVGELPNPLNPPSGCAFHKRCPYATERCK 299 Query: 304 EKEPELTEVEKNHFVSCHLVRSY 326 +EP L ++ N V+CH + Sbjct: 300 TEEPALRPLD-NRLVACHYAERF 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: 331 Number of extensions: 12 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