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_2799 Dsui_2799 oligopeptide/dipeptide ABC transporter, ATP-binding protein
Query= TCDB::Q9X271 (324 letters) >FitnessBrowser__PS:Dsui_2799 Length = 670 Score = 296 bits (757), Expect = 1e-84 Identities = 152/319 (47%), Positives = 205/319 (64%) Query: 1 MMELLNVNNLKVEFHRVEGIVKAVDGISYKLNKGESLGIVGESGSGKSVSVLSLLRLINR 60 M +LL+V NLK F ++ AVDG+S+ + GE+ ++GESG GKS + L+LLRL+ Sbjct: 1 MSDLLSVRNLKAGFLAGGRVLTAVDGVSFAVAPGETFALLGESGCGKSATALALLRLLPN 60 Query: 61 NGRIVDGEAIFLGKDLLKLNKEELRNIRGKDISIIFQNPMTSLNPIIRVGIQVMEPIIWH 120 GRI GE G+++L L + +R+ RG ++IFQ P TSLNP++ +G Q+ E + H Sbjct: 61 AGRIQGGEVWLEGEEILALPEAAMRDRRGSAAAMIFQEPATSLNPVLTIGRQIGESLERH 120 Query: 121 RLMKNEEARERAIELLERVGIPESPKRFLNYPFQFSGGMRQRVMIAMALACHPKLLIADE 180 R MK E AR A+ LL VGI + +R YPFQ SGGM+QR MIA+ALA P+LLIADE Sbjct: 121 RGMKGEAARREALALLTAVGIADPERRLEEYPFQLSGGMKQRAMIAIALAGEPRLLIADE 180 Query: 181 PTTALDVTIQAQIMELLQELKEEYGMSVIFITHDLSVATNFCDRIITMYAGKIVEEAPVE 240 PTTALDVTIQAQI++LL L+ E M ++ ITHDL V R+ MYAG+IVE AP + Sbjct: 181 PTTALDVTIQAQILDLLARLQAERAMGMLLITHDLGVVARSAHRVGVMYAGEIVETAPRQ 240 Query: 241 EILKTPLHPYTKGLLNSTLEIGSRGKKLVPIPGNPPNPTKHPSGCKFHPRCSFAMEICQR 300 E +P HPYT+ L + ++G RG +L IPG P P+GC+F PRC AM+ C+ Sbjct: 241 EFFASPRHPYTQKLFAALPDLGQRGAQLATIPGQVPGLAAMPAGCRFAPRCPVAMDRCRL 300 Query: 301 EEPPLVNISENHRVACHLI 319 E P + H+V CH + Sbjct: 301 ESPGWTELEAGHQVRCHWV 319 Score = 241 bits (614), Expect = 5e-68 Identities = 137/325 (42%), Positives = 202/325 (62%), Gaps = 19/325 (5%) Query: 4 LLNVNNLKVEF-------HRVEGIVKAVDGISYKLNKGESLGIVGESGSGKSVSVLSLLR 56 LL V LKV F R G VKAVDG+S +L +G +L +VGESG GK+ + ++LR Sbjct: 351 LLAVGELKVHFPIRKGLFKRTVGHVKAVDGVSLELQRGRTLALVGESGCGKTTAGKAVLR 410 Query: 57 LINRNGRI-VDGEAIFLGKDLLKLNKEELRNIRGKDISIIFQNPMTSLNPIIRVGIQVME 115 L+ G + +DG ++LL L + EL+ +R + + ++FQ+P SLNP + VG + E Sbjct: 411 LLPATGSVRLDG------RELLGLPERELKPLRRR-MQMVFQDPFASLNPRLTVGEIIEE 463 Query: 116 PIIWHRLMKNEEARERAIE-LLERVGIPESPKRFLNYPFQFSGGMRQRVMIAMALACHPK 174 + R+ + + R A+ LLE VG+P + YP +FSGG RQR+ IA ALA P+ Sbjct: 464 GMTALRVAASRDERRAALAALLESVGLPA--EALGRYPHEFSGGQRQRIAIARALAVQPE 521 Query: 175 LLIADEPTTALDVTIQAQIMELLQELKEEYGMSVIFITHDLSVATNFCDRIITMYAGKIV 234 LL+ DEPT+ALDV++QAQI+ LL+ L+EE G++ +FITH+ +V + MY G+IV Sbjct: 522 LLVCDEPTSALDVSVQAQILNLLRRLQEELGLAYLFITHNFAVVEYLAHDVAVMYLGRIV 581 Query: 235 EEAPVEEILKTPLHPYTKGLLNSTLEIGSRG-KKLVPIPGNPPNPTKHPSGCKFHPRCSF 293 E+ PV+++L P HPYT+ LL++ E G +++V +PG P+P + P GC FHPRC+ Sbjct: 582 EQGPVQQVLAAPCHPYTRALLSAVPEPRLAGQREMVRLPGETPSPARPPQGCHFHPRCAQ 641 Query: 294 AMEICQREEPPLVNISENHRVACHL 318 A E C++E P + V CHL Sbjct: 642 ASERCRQEYPAPSTQAGGVVVRCHL 666 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: 549 Number of extensions: 19 Number of successful extensions: 5 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 324 Length of database: 670 Length adjustment: 33 Effective length of query: 291 Effective length of database: 637 Effective search space: 185367 Effective search space used: 185367 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: 51 (24.3 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