Align TM1749, 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::Q9X271 (324 letters) >FitnessBrowser__pseudo1_N1B4:Pf1N1B4_1127 Length = 326 Score = 232 bits (591), Expect = 1e-65 Identities = 124/324 (38%), Positives = 196/324 (60%), Gaps = 15/324 (4%) Query: 1 MMELLNVNNLKVEFHRVEGI------VKAVDGISYKLNKGESLGIVGESGSGKSVSVLSL 54 M +L NL + G+ V+A++G+S++L G++L +VGESG GKS +L Sbjct: 1 MAVVLTARNLTRHYEVSRGLFKGHATVRALNGVSFELEAGKTLAVVGESGCGKS----TL 56 Query: 55 LRLINRNGRIVDGEAIFLGKDLLKLNKEELRNIRGKDISIIFQNPMTSLNPIIRVGIQVM 114 R + G G+++ +K + + +R KD+ ++FQ+P SLNP +VG Q+ Sbjct: 57 ARALTLIEEPSSGSLKIAGQEVAGADKAQRKQLR-KDVQMVFQSPYASLNPRQKVGDQLA 115 Query: 115 EPIIWHRLMKNEEARERAIELLERVGIPESPKRFLNYPFQFSGGMRQRVMIAMALACHPK 174 EP++ + + E RE+ ++++VG+ P+ + YP FSGG RQR+ +A A+ PK Sbjct: 116 EPLLINTNLSASERREKVQAMMKQVGL--RPEHYQRYPHMFSGGQRQRIALARAMMLQPK 173 Query: 175 LLIADEPTTALDVTIQAQIMELLQELKEEYGMSVIFITHDLSVATNFCDRIITMYAGKIV 234 +L+ADEPT+ALDV+IQAQ++ L +L++E+ + +FI+H+L+V + D ++ MY G+ V Sbjct: 174 VLVADEPTSALDVSIQAQVLNLFMDLQQEFNTAYVFISHNLAVVRHVADHVMVMYLGRPV 233 Query: 235 EEAPVEEILKTPLHPYTKGLLNSTLEI-GSRGKKLVPIPGNPPNPTKHPSGCKFHPRCSF 293 E P E+I PLHPYT+ LL++T I K + I G PNP PSGC FH RC + Sbjct: 234 EMGPKEDIYTRPLHPYTQALLSATPTIHPDPTKPKIKIVGELPNPLNPPSGCAFHKRCPY 293 Query: 294 AMEICQREEPPLVNISENHRVACH 317 A + C EE PL+ + + +VACH Sbjct: 294 ATDRCTTEE-PLLRLVDTRQVACH 316 Lambda K H 0.320 0.139 0.401 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: 281 Number of extensions: 20 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: 324 Length of database: 326 Length adjustment: 28 Effective length of query: 296 Effective length of database: 298 Effective search space: 88208 Effective search space used: 88208 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