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 WP_011386731.1 AMB_RS22185 ABC transporter ATP-binding protein
Query= TCDB::Q9X271 (324 letters) >NCBI__GCF_000009985.1:WP_011386731.1 Length = 533 Score = 223 bits (569), Expect = 6e-63 Identities = 126/253 (49%), Positives = 167/253 (66%), Gaps = 5/253 (1%) Query: 4 LLNVNNLKVEFHRVEGIVKAVDGISYKLNKGESLGIVGESGSGKSVSVLSLLRLINRNGR 63 LL V++L V F G V+AV G+S+ L KGE+L +VGESGSGKSV+ LS+L+L+ Sbjct: 7 LLVVDDLAVSF----GPVQAVKGVSFTLAKGETLALVGESGSGKSVTALSILQLLPYPRA 62 Query: 64 IVDGEAIFL-GKDLLKLNKEELRNIRGKDISIIFQNPMTSLNPIIRVGIQVMEPIIWHRL 122 +I L G +L+ + LR +RG I+++FQ PMTSLNP+ + QV E + H Sbjct: 63 THPRGSIRLDGAELVGAPEPALRKVRGGRIAMVFQEPMTSLNPLHSIEAQVGEVLELHLG 122 Query: 123 MKNEEARERAIELLERVGIPESPKRFLNYPFQFSGGMRQRVMIAMALACHPKLLIADEPT 182 ++ R+R +ELL VGIPE KR P + SGG RQRVMIAMALA P +LIADEPT Sbjct: 123 LRGSTLRDRVVELLSLVGIPEPEKRLGALPHELSGGQRQRVMIAMALAGEPDILIADEPT 182 Query: 183 TALDVTIQAQIMELLQELKEEYGMSVIFITHDLSVATNFCDRIITMYAGKIVEEAPVEEI 242 TALDVTIQAQI+ LL+ L+ GM+++FITHDL + DR+ M AG+IVE P+ ++ Sbjct: 183 TALDVTIQAQILALLKGLQARLGMALLFITHDLGIVRKMADRVCVMNAGEIVESGPLPQV 242 Query: 243 LKTPLHPYTKGLL 255 P HPYT+ LL Sbjct: 243 FDAPAHPYTQRLL 255 Score = 174 bits (442), Expect = 3e-48 Identities = 99/249 (39%), Positives = 153/249 (61%), Gaps = 9/249 (3%) Query: 14 FHRVEGIVKAVDGISYKLNKGESLGIVGESGSGKSVSVLSLLRLINRNGRIVDGEAIFLG 73 + + G VKAVDGIS L +G ++G+VGESGSGK+ L+LLRL++ DGE F G Sbjct: 290 WRKTVGHVKAVDGISLDLKRGHTIGVVGESGSGKTTLGLALLRLLDS-----DGEISFGG 344 Query: 74 KDLLKLNKEELRNIRGKDISIIFQNPMTSLNPIIRVGIQVMEPIIWHRLMKNEEARERAI 133 + ++ LR +R + + ++FQ+P SL+P + VG V E + H + R+R I Sbjct: 345 TRIESMSAGTLRPLR-RQMQMVFQDPYGSLSPRMSVGQIVGEGLEVHEPAMHAAERDRLI 403 Query: 134 EL-LERVGIPESPKRFLNYPFQFSGGMRQRVMIAMALACHPKLLIADEPTTALDVTIQAQ 192 LE VG+ + + YP +FSGG RQR+ IA AL PK ++ DEPT+ALDV++QAQ Sbjct: 404 AAALEEVGLDPATRD--RYPHEFSGGQRQRIAIARALVLKPKFIVLDEPTSALDVSVQAQ 461 Query: 193 IMELLQELKEEYGMSVIFITHDLSVATNFCDRIITMYAGKIVEEAPVEEILKTPLHPYTK 252 I++LL++L+ + ++ +FI+HDL V D ++ M GK+VE +E+ K P YT+ Sbjct: 462 IVDLLRDLQARHALAYLFISHDLRVVRALADDLLVMKDGKVVEAGRADELFKAPRTAYTR 521 Query: 253 GLLNSTLEI 261 L+ + ++ Sbjct: 522 ALMAAAFDL 530 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: 464 Number of extensions: 27 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: 533 Length adjustment: 31 Effective length of query: 293 Effective length of database: 502 Effective search space: 147086 Effective search space used: 147086 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: 50 (23.9 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