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 Dsui_0414 Dsui_0414 oligopeptide/dipeptide ABC transporter, ATP-binding protein
Query= TCDB::Q9X271 (324 letters) >FitnessBrowser__PS:Dsui_0414 Length = 352 Score = 210 bits (535), Expect = 4e-59 Identities = 127/326 (38%), Positives = 185/326 (56%), Gaps = 21/326 (6%) Query: 4 LLNVNNLKVEF-------HRVEGIVKAVDGISYKLNKGESLGIVGESGSGKSVSVLSLLR 56 LL V +LK F R V AVDG+++ + KG++LGIVGESG GKS + + R Sbjct: 21 LLIVRDLKKHFPVRSSPLDRERKFVHAVDGVNFSVPKGKTLGIVGESGCGKSTTARLVAR 80 Query: 57 LINRNGRIVDGEAIFLGKDLLKLNKEELRNIRGKDISIIFQNPMTSLNPIIRVGIQVMEP 116 L+ + GE IF G+ + + L+ R +++ ++FQ+ SLNP + + + Sbjct: 81 LMPADA----GELIFDGEGVEEFRGLRLKEFR-RNLQMVFQDSFASLNPRLTIAETIAYG 135 Query: 117 IIWHRLMKNEEARERAIELLERVGIPESPKRFLN-YPFQFSGGMRQRVMIAMALACHPKL 175 H + + A +A ELL+RVG+ P F YP + SGG RQRV IA ALA P+L Sbjct: 136 PRVHGIAR---ADHQARELLDRVGL--DPSHFAGRYPHELSGGQRQRVNIARALAFDPRL 190 Query: 176 LIADEPTTALDVTIQAQIMELLQELKEEYGMSVIFITHDLSVATNFCDRIITMYAGKIVE 235 +I DE ALD ++QAQ++ LLQELK E ++ +FI+HDL V D ++ MY G+++E Sbjct: 191 VILDEAVAALDKSVQAQVLNLLQELKAERQLTYLFISHDLHVVHYLSDYVMVMYLGQVIE 250 Query: 236 EAPVEEILKTPLHPYTKGLLNSTLEIGSRGK-KLVPIPGNPPNPTKHPSGCKFHPRCSFA 294 PVE I P HPYT+ LL++ + + + P+ G+PPNP PSGC+F RC A Sbjct: 251 SGPVERIYGQPAHPYTRALLSAVPSMDPEHRTQASPLAGDPPNPINPPSGCRFRDRCPHA 310 Query: 295 MEICQREEPPLVNISEN--HRVACHL 318 +C P L ++ + H ACHL Sbjct: 311 HAVCASATPALRDMGRHSEHLAACHL 336 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: 272 Number of extensions: 14 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: 352 Length adjustment: 28 Effective length of query: 296 Effective length of database: 324 Effective search space: 95904 Effective search space used: 95904 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: 49 (23.5 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