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 GFF3697 PGA1_262p01010 dipeptide transport ATP-binding protein DppD
Query= TCDB::Q9X271 (324 letters) >FitnessBrowser__Phaeo:GFF3697 Length = 330 Score = 288 bits (736), Expect = 2e-82 Identities = 149/316 (47%), Positives = 210/316 (66%), Gaps = 1/316 (0%) Query: 2 MELLNVNNLKVEFHRVEGIVKAVDGISYKLNKGESLGIVGESGSGKSVSVLSLLRLINRN 61 M LL+V +L V+F + V A++ IS+ L KGE LGIVGESG+GKS++ SL+ L++R Sbjct: 1 MSLLSVRDLTVKFAMRDHTVTALNQISFDLGKGERLGIVGESGAGKSITGFSLMNLLSRP 60 Query: 62 GRIVDGEAIFLGKDLLKLNKEELRNIRGKDISIIFQNPMTSLNPIIRVGIQVMEPIIWHR 121 G I G+ +F KD++KL+ E+R IRG +++IFQ+PM +LNP++ +G Q++E + HR Sbjct: 61 GFIDSGQILFGDKDIVKLSDAEMRKIRGNRMAMIFQDPMVTLNPVLTIGQQMVETLKAHR 120 Query: 122 LMKNEEARERAIELLERVGIPESPKRFLNYPFQFSGGMRQRVMIAMALACHPKLLIADEP 181 + EA + AI L V IP +R YP + SGGMRQR++IAMAL P+L+IADEP Sbjct: 121 SLSKAEAEQIAILKLREVYIPSPEERLNQYPHELSGGMRQRIIIAMALLLDPELIIADEP 180 Query: 182 TTALDVTIQAQIMELLQELKEEYGMSVIFITHDLSVATNFCDRIITMYAGKIVEEAPVEE 241 TTALDVTIQA IMELL EL + + +I ITHDL V + +R + MYAG+++E P E Sbjct: 181 TTALDVTIQADIMELLLELCQSNKVGLILITHDLGVVSQMTERTLVMYAGRLIEAGPTRE 240 Query: 242 ILKTPLHPYTKGLLNSTLEIGSRGKKLVPIPGNPPNPTKHPSGCKFHPRCSFAMEICQRE 301 I+ P HPYT+GL+N+ + G++L IPGN P P GC F PRC +A++ C++ Sbjct: 241 IINDPQHPYTQGLINALPQQTLPGQRLKQIPGNMPGLASIPPGCPFSPRCEYAVDHCRKV 300 Query: 302 EPPLVNISENHRVACH 317 P V+ + VACH Sbjct: 301 LPETVSYRQ-VEVACH 315 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: 263 Number of extensions: 10 Number of successful extensions: 1 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: 330 Length adjustment: 28 Effective length of query: 296 Effective length of database: 302 Effective search space: 89392 Effective search space used: 89392 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