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 1936449 b1246 oligopeptide transporter ATP-binding component (NCBI)
Query= TCDB::Q9X271 (324 letters) >FitnessBrowser__Keio:1936449 Length = 337 Score = 321 bits (823), Expect = 1e-92 Identities = 162/313 (51%), Positives = 215/313 (68%), Gaps = 2/313 (0%) Query: 4 LLNVNNLKVEFHRVEGIVKAVDGISYKLNKGESLGIVGESGSGKSVSVLSLLRLINRNGR 63 LLNV +L+V F +G V AV+ +++ L GE+LGIVGESGSGKS + +L+ L+ NGR Sbjct: 19 LLNVKDLRVTFSTPDGDVTAVNDLNFSLRAGETLGIVGESGSGKSQTAFALMGLLAANGR 78 Query: 64 IVDGEAIFLGKDLLKLNKEELRNIRGKDISIIFQNPMTSLNPIIRVGIQVMEPIIWHRLM 123 I G A F G+++L L + EL +R + IS+IFQ+PMTSLNP +RVG Q+ME ++ H+ M Sbjct: 79 I-GGSATFNGREILNLPEHELNKLRAEQISMIFQDPMTSLNPYMRVGEQLMEVLMLHKNM 137 Query: 124 KNEEARERAIELLERVGIPESPKRFLNYPFQFSGGMRQRVMIAMALACHPKLLIADEPTT 183 EA E ++ +L+ V +PE+ KR YP +FSGGMRQRVMIAMAL C PKLLIADEPTT Sbjct: 138 SKAEAFEESVRMLDAVKMPEARKRMKMYPHEFSGGMRQRVMIAMALLCRPKLLIADEPTT 197 Query: 184 ALDVTIQAQIMELLQELKEEYGMSVIFITHDLSVATNFCDRIITMYAGKIVEEAPVEEIL 243 ALDVT+QAQIM LL ELK E+ ++I ITHDL V CD+++ MYAG+ +E ++ Sbjct: 198 ALDVTVQAQIMTLLNELKREFNTAIIMITHDLVVVAGICDKVLVMYAGRTMEYGNARDVF 257 Query: 244 KTPLHPYTKGLLNSTLEIGSRGKKLVPIPGNPPNPTKHPSGCKFHPRCSFAMEICQREEP 303 P+HPY+ GLLN+ + + G+ ++ IPGNPPN + P GC F PRC AMEIC P Sbjct: 258 YQPVHPYSIGLLNAVPRLDAEGETMLTIPGNPPNLLRLPKGCPFQPRCPHAMEICS-SAP 316 Query: 304 PLVNISENHRVAC 316 PL + AC Sbjct: 317 PLEEFTPGRLRAC 329 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: 298 Number of extensions: 11 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: 337 Length adjustment: 28 Effective length of query: 296 Effective length of database: 309 Effective search space: 91464 Effective search space used: 91464 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