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_0415 Dsui_0415 oligopeptide/dipeptide ABC transporter, ATP-binding protein
Query= TCDB::Q9X271 (324 letters) >FitnessBrowser__PS:Dsui_0415 Length = 326 Score = 280 bits (717), Expect = 3e-80 Identities = 145/302 (48%), Positives = 200/302 (66%), Gaps = 1/302 (0%) Query: 4 LLNVNNLKVEFHRVEGIVKAVDGISYKLNKGESLGIVGESGSGKSVSVLSLLRLINRNGR 63 L+++ +L V+F+ A++ +S +L +GE LG++GESGSGKSV++ +LLRL Sbjct: 5 LVSIQDLTVQFNGARR-ASALNQVSLELGQGEVLGLLGESGSGKSVTLRTLLRLHPERHT 63 Query: 64 IVDGEAIFLGKDLLKLNKEELRNIRGKDISIIFQNPMTSLNPIIRVGIQVMEPIIWHRLM 123 G G+D+L L EL RG +S++FQ P + +P+ +G Q+ E + H + Sbjct: 64 RTAGRIRVDGQDVLALRGRELDRYRGGTVSMVFQEPGLAFDPVYTIGQQISEAVRVHEGV 123 Query: 124 KNEEARERAIELLERVGIPESPKRFLNYPFQFSGGMRQRVMIAMALACHPKLLIADEPTT 183 A RA+ +LERV IP++ +RF YP + SGGMRQR MIA+ALAC PKLL+ADEPTT Sbjct: 124 DQATAAARALAMLERVQIPQARRRFDAYPHELSGGMRQRAMIALALACKPKLLLADEPTT 183 Query: 184 ALDVTIQAQIMELLQELKEEYGMSVIFITHDLSVATNFCDRIITMYAGKIVEEAPVEEIL 243 ALD T+Q QI+ LL+EL+ E GMSVIF+THD+ A DRI MYAG+IVE+ PV +++ Sbjct: 184 ALDATVQIQILLLLRELQRETGMSVIFVTHDIGAAVEVADRIAVMYAGRIVEQGPVGQLV 243 Query: 244 KTPLHPYTKGLLNSTLEIGSRGKKLVPIPGNPPNPTKHPSGCKFHPRCSFAMEICQREEP 303 + P HPYT+GLL +T+ RG+ L IPG+PP+ P GC F PRCS A E C R+ P Sbjct: 244 RQPCHPYTRGLLAATVGHEHRGRPLEAIPGSPPDLAALPPGCSFAPRCSHASERCHRDIP 303 Query: 304 PL 305 PL Sbjct: 304 PL 305 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: 273 Number of extensions: 9 Number of successful extensions: 2 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