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 PfGW456L13_5058 Dipeptide transport ATP-binding protein DppF (TC 3.A.1.5.2)
Query= TCDB::Q9X271 (324 letters) >FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_5058 Length = 326 Score = 228 bits (581), Expect = 2e-64 Identities = 119/298 (39%), Positives = 185/298 (62%), Gaps = 9/298 (3%) Query: 21 VKAVDGISYKLNKGESLGIVGESGSGKSVSVLSLLRLINRNGRIVDGEAIFLGKDLLKLN 80 V+A++G+S++L G++L +VGESG GKS +L R + G G+++ + Sbjct: 27 VRALNGVSFELEAGKTLAVVGESGCGKS----TLARALTLIEEPSSGSLKIAGQEVAGAD 82 Query: 81 KEELRNIRGKDISIIFQNPMTSLNPIIRVGIQVMEPIIWHRLMKNEEARERAIELLERVG 140 K + + +R KD+ ++FQ+P SLNP +VG Q+ EP++ + + E RE+ ++++VG Sbjct: 83 KAQRKQLR-KDVQMVFQSPYASLNPRQKVGDQLAEPLLINTNLSAAERREKVQAMMKQVG 141 Query: 141 IPESPKRFLNYPFQFSGGMRQRVMIAMALACHPKLLIADEPTTALDVTIQAQIMELLQEL 200 + P+ + YP FSGG RQR+ +A A+ PK+L+ADEPT+ALDV+IQAQ++ L +L Sbjct: 142 L--RPEHYQRYPHMFSGGQRQRIALARAMMLQPKVLVADEPTSALDVSIQAQVLNLFMDL 199 Query: 201 KEEYGMSVIFITHDLSVATNFCDRIITMYAGKIVEEAPVEEILKTPLHPYTKGLLNSTLE 260 ++E+ + +FI+H+L+V + D ++ MY G+ VE E+I PLHPYT+ LL++T Sbjct: 200 QQEFNTAYVFISHNLAVVRHVADHVMVMYLGRPVEMGTKEDIYSRPLHPYTQALLSATPA 259 Query: 261 I-GSRGKKLVPIPGNPPNPTKHPSGCKFHPRCSFAMEICQREEPPLVNISENHRVACH 317 I K + I G PNP PSGC FH RC +A E C EEP L + +VACH Sbjct: 260 IHPDPDKPKIKIVGELPNPLNPPSGCAFHKRCPYATERCSTEEPAL-RLIAGRQVACH 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: 278 Number of extensions: 17 Number of successful extensions: 3 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 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