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 RR42_RS11230 RR42_RS11230 peptide ABC transporter ATP-binding protein
Query= TCDB::Q9X271 (324 letters) >FitnessBrowser__Cup4G11:RR42_RS11230 Length = 347 Score = 302 bits (773), Expect = 9e-87 Identities = 153/317 (48%), Positives = 211/317 (66%) Query: 4 LLNVNNLKVEFHRVEGIVKAVDGISYKLNKGESLGIVGESGSGKSVSVLSLLRLINRNGR 63 LL V++L F + G ++V+G+SY + G++LG+VGESG GKSV+ LS++RL+ Sbjct: 16 LLEVDDLHTHFDTLTGPARSVNGVSYTVRAGQTLGVVGESGCGKSVTALSIMRLLPTPPA 75 Query: 64 IVDGEAIFLGKDLLKLNKEELRNIRGKDISIIFQNPMTSLNPIIRVGIQVMEPIIWHRLM 123 + G G DLL+L++ E+R IRG +S+IFQ PMTSLNP++ +G Q+ E + H+ Sbjct: 76 RMRGAVRLRGIDLLQLSEREMRRIRGNRVSMIFQEPMTSLNPVLTIGRQIAETVQLHQGA 135 Query: 124 KNEEARERAIELLERVGIPESPKRFLNYPFQFSGGMRQRVMIAMALACHPKLLIADEPTT 183 +A +RA E+L V IPE +R YP Q SGGMRQRVMIA+ALAC+P++LIADEPTT Sbjct: 136 SRADALKRAAEMLRLVQIPEPERRVNEYPHQLSGGMRQRVMIALALACNPEVLIADEPTT 195 Query: 184 ALDVTIQAQIMELLQELKEEYGMSVIFITHDLSVATNFCDRIITMYAGKIVEEAPVEEIL 243 ALDVTIQAQI++L++ L++E GM V+ ITHDL V CDR+I MYAG+ VEEA V ++ Sbjct: 196 ALDVTIQAQILDLIRRLQKELGMGVVMITHDLGVVAECCDRVIVMYAGRKVEEASVIDLF 255 Query: 244 KTPLHPYTKGLLNSTLEIGSRGKKLVPIPGNPPNPTKHPSGCKFHPRCSFAMEICQREEP 303 PLHPYT+ L+ S + + ++L IPG P+P + GC F RC A C RE P Sbjct: 256 DRPLHPYTRALMASMPSMNTSSQRLAEIPGLVPSPQQARRGCAFAARCPHADTRCAREIP 315 Query: 304 PLVNISENHRVACHLIK 320 L +H VAC ++ Sbjct: 316 QLTRHGADHAVACFAVE 332 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: 264 Number of extensions: 7 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: 347 Length adjustment: 28 Effective length of query: 296 Effective length of database: 319 Effective search space: 94424 Effective search space used: 94424 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