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 GFF667 PGA1_c06810 putative dipeptide transport ATP-binding protein DppD
Query= TCDB::Q9X271 (324 letters) >FitnessBrowser__Phaeo:GFF667 Length = 326 Score = 273 bits (699), Expect = 3e-78 Identities = 146/320 (45%), Positives = 205/320 (64%), Gaps = 2/320 (0%) Query: 4 LLNVNNLKVEFHRVEGIVKAVDGISYKLNKGESLGIVGESGSGKSVSVLSLLRLINRNGR 63 +L++ +L VE + A D +SY + GE LG+VGESG+GKS++ +++ L+N R Sbjct: 5 VLSIRDLVVEIPTRHARLCATDKVSYDIAPGEILGVVGESGAGKSMAGNAVIGLLNPPAR 64 Query: 64 IVDGEAIFLGKDLLKLNKEELRNIRGKDISIIFQNPMTSLNPIIRVGIQVMEPIIWHRLM 123 I GE G+ + L +E++R +RGK+I +IFQ+P+TSLNP++R+G Q+ E ++ H + Sbjct: 65 ITGGEIRLNGQRIDNLPREKMRRLRGKEIGMIFQDPLTSLNPLLRIGDQLTETMMEHLEL 124 Query: 124 KNEEARERAIELLERVGIPESPKRFLNYPFQFSGGMRQRVMIAMALACHPKLLIADEPTT 183 EAR RAI LE VGIP + +R +YP +FSGGMRQRV+IA+AL P L+IADEPTT Sbjct: 125 TKPEARARAIAALEEVGIPAASERIDSYPHEFSGGMRQRVVIALALCAEPSLIIADEPTT 184 Query: 184 ALDVTIQAQIMELLQELKEEYGMSVIFITHDLSVATNFCDRIITMYAGKIVEEAPVEEIL 243 ALDV++QAQI+ LL+ L E G +V+ ITHD+ V DR+ MYAG++ E V +++ Sbjct: 185 ALDVSVQAQIIALLKRLCRERGTAVMLITHDMGVIAEAADRVAVMYAGRMAEIGDVRDVV 244 Query: 244 KTPLHPYTKGLLNSTLEIGSRGKKLVPIPGNPPNPTKHPSGCKFHPRCSFAMEICQREEP 303 P HPYT GL+ ST + +L IPG P P GC F PRC A E C+ P Sbjct: 245 TRPRHPYTDGLMGSTPSASAGQHRLRQIPGAMPRLHSLPPGCAFSPRCERANERCRNSPP 304 Query: 304 PLVNISENHRVAC-HLIKGE 322 P + ++N R AC H IK E Sbjct: 305 PTLE-ADNGRSACWHAIKLE 323 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: 275 Number of extensions: 15 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: 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