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 HSERO_RS17130 HSERO_RS17130 ABC transporter
Query= TCDB::Q9X271 (324 letters) >FitnessBrowser__HerbieS:HSERO_RS17130 Length = 529 Score = 239 bits (610), Expect = 1e-67 Identities = 124/254 (48%), Positives = 174/254 (68%), Gaps = 6/254 (2%) Query: 4 LLNVNNLKVEFHRVEGIVKAVDGISYKLNKGESLGIVGESGSGKSVSVLSLLRLINRNGR 63 LL VNNL V F G VD +S+ + GE +VGESGSGK+VS L++++L N++ R Sbjct: 5 LLEVNNLTVRF----GDTVVVDRVSFAIAPGEKFALVGESGSGKTVSSLAVMQL-NQDAR 59 Query: 64 IVDGEAIFLGKDLLKLNKEELRNIRGKDISIIFQNPMTSLNPIIRVGIQVMEPIIWHRLM 123 +G + G+D+L ++ +++ +RG D+++IFQ PMT+LNP+ +G Q+ E ++ H + Sbjct: 60 Y-EGSILLDGQDVLAKSERQMQQVRGNDVAMIFQEPMTALNPLFTIGNQIAEVLMHHEGL 118 Query: 124 KNEEARERAIELLERVGIPESPKRFLNYPFQFSGGMRQRVMIAMALACHPKLLIADEPTT 183 +A RA+ LLE+ GIPE +R L+YP + SGG RQR MIAMALAC PKLLIADEPTT Sbjct: 119 NARDAARRAVALLEKTGIPEPARRALSYPHELSGGQRQRAMIAMALACKPKLLIADEPTT 178 Query: 184 ALDVTIQAQIMELLQELKEEYGMSVIFITHDLSVATNFCDRIITMYAGKIVEEAPVEEIL 243 ALDVTIQ QI+ LL +L+ E M+V+ I+HDL++ +F DR+ M GK+VE A V E+ Sbjct: 179 ALDVTIQVQILALLNQLQREENMAVLIISHDLNLVRHFADRVGVMEKGKLVESASVAELF 238 Query: 244 KTPLHPYTKGLLNS 257 P PYT+ LL S Sbjct: 239 ANPQQPYTRKLLQS 252 Score = 171 bits (433), Expect = 4e-47 Identities = 102/258 (39%), Positives = 153/258 (59%), Gaps = 12/258 (4%) Query: 4 LLNVNNLKVEFHRVEG-----IVKAVDGISYKLNKGESLGIVGESGSGKSVSVLSLLRLI 58 +L L+ +H +G AVDG+ +L +GE+LGIVGESGSGKS ++LLRL Sbjct: 268 VLQAERLRCTYHIKQGWFAKRAFHAVDGVDLQLRRGETLGIVGESGSGKSTLGMALLRL- 326 Query: 59 NRNGRIVDGEAIFLGKDLLKLNKEELRNIRGKDISIIFQNPMTSLNPIIRVGIQVMEPII 118 + V G F G + + + ELR +R + + ++FQ+P SL+P V V E + Sbjct: 327 --SAASVAGSIRFDGVPISERPQRELRPLRSR-MQVVFQDPFASLSPRRTVEQIVGEGLE 383 Query: 119 WHRLMKN-EEARERAIELLERVGIPESPKRFLNYPFQFSGGMRQRVMIAMALACHPKLLI 177 H ++ E+ R+ + LE VG+ S YP +FSGG RQR+ IA AL P+LL+ Sbjct: 384 LHHPDRSAEQQRQAIVAALEEVGL--SAAVLERYPHEFSGGQRQRIAIARALVLQPELLL 441 Query: 178 ADEPTTALDVTIQAQIMELLQELKEEYGMSVIFITHDLSVATNFCDRIITMYAGKIVEEA 237 DEPT+ALDVT+Q Q+++LL EL+ +G++ +FITHDL+V ++I M GK+VE Sbjct: 442 LDEPTSALDVTVQQQVLQLLAELQRRHGLAYLFITHDLAVVQAMAHQVIVMKDGKVVESG 501 Query: 238 PVEEILKTPLHPYTKGLL 255 ++L+ P YT+ L+ Sbjct: 502 ATAQVLQQPQQEYTRRLV 519 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: 380 Number of extensions: 14 Number of successful extensions: 4 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: 529 Length adjustment: 31 Effective length of query: 293 Effective length of database: 498 Effective search space: 145914 Effective search space used: 145914 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