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 Pf1N1B4_1127 Dipeptide transport ATP-binding protein DppF (TC 3.A.1.5.2)
Query= TCDB::Q9X272 (328 letters) >FitnessBrowser__pseudo1_N1B4:Pf1N1B4_1127 Length = 326 Score = 265 bits (676), Expect = 2e-75 Identities = 130/302 (43%), Positives = 194/302 (64%), Gaps = 2/302 (0%) Query: 25 QGKRILKAVDGISIEIKEGETLGLVGESGCGKSTLGRTILKLLRPDGGKIFFEGKDITNL 84 +G ++A++G+S E++ G+TL +VGESGCGKSTL R + + P G + G+++ Sbjct: 22 KGHATVRALNGVSFELEAGKTLAVVGESGCGKSTLARALTLIEEPSSGSLKIAGQEVAGA 81 Query: 85 NDKEMKPYRKKMQIIFQDPLGSLNPQMTVGRIIEDPLIIHKIGTKKERRKRVEELLDMVG 144 + + K RK +Q++FQ P SLNP+ VG + +PL+I+ + ERR++V+ ++ VG Sbjct: 82 DKAQRKQLRKDVQMVFQSPYASLNPRQKVGDQLAEPLLINTNLSASERREKVQAMMKQVG 141 Query: 145 IGREFINSFPHEFSGGQQQRIGIARALALNPKFIVCDEPVSALDVSIQAQIIDLLEEIQQ 204 + E +PH FSGGQ+QRI +ARA+ L PK +V DEP SALDVSIQAQ+++L ++QQ Sbjct: 142 LRPEHYQRYPHMFSGGQRQRIALARAMMLQPKVLVADEPTSALDVSIQAQVLNLFMDLQQ 201 Query: 205 KMGISYLFIAHNLAVVEHISHKVAVMYLGKIVEYGDVDKIFLNPIHPYTRALLKSVPKIP 264 + +Y+FI+HNLAVV H++ V VMYLG+ VE G + I+ P+HPYT+ALL + P I Sbjct: 202 EFNTAYVFISHNLAVVRHVADHVMVMYLGRPVEMGPKEDIYTRPLHPYTQALLSATPTIH 261 Query: 265 WDGQKQRFYSLKGELPSPIDLPKGCRFQTRCTEKKAICFEKEPELTEVEKNHFVSCHLVR 324 D K + + GELP+P++ P GC F RC C +EP L V+ V+CH Sbjct: 262 PDPTKPKI-KIVGELPNPLNPPSGCAFHKRCPYATDRCTTEEPLLRLVDTRQ-VACHYAE 319 Query: 325 SY 326 + Sbjct: 320 QF 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: 340 Number of extensions: 16 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 Apr 09 2024. 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