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 AO353_21860 AO353_21860 methionine ABC transporter ATP-binding protein
Query= TCDB::Q9X271 (324 letters) >FitnessBrowser__pseudo3_N2E3:AO353_21860 Length = 328 Score = 278 bits (711), Expect = 1e-79 Identities = 150/314 (47%), Positives = 205/314 (65%), Gaps = 1/314 (0%) Query: 5 LNVNNLKVEFHRVEGIVKAVDGISYKLNKGESLGIVGESGSGKSVSVLSLLRLINRNGRI 64 L+V L V H E V VD +S+ L +GE LG+VGESGSGK+++ +L+RL+ Sbjct: 6 LHVEELSVIAHNGERDVTLVDRLSFDLAEGEILGLVGESGSGKTMACRALMRLLPSPSLR 65 Query: 65 VDGEAIFL-GKDLLKLNKEELRNIRGKDISIIFQNPMTSLNPIIRVGIQVMEPIIWHRLM 123 V G+A+ L GK+LL+L++ +R IRG+ + +IFQNP + L+P++R+G Q+ E I H+ Sbjct: 66 VQGKAVQLAGKNLLQLDEAGMRAIRGRRLGMIFQNPSSHLDPLMRIGEQIGEGIRLHQGA 125 Query: 124 KNEEARERAIELLERVGIPESPKRFLNYPFQFSGGMRQRVMIAMALACHPKLLIADEPTT 183 EAR +AIE+L +VGIP+ P+R +Y +FSGGMRQR MIA+ALAC+P++LIADEPTT Sbjct: 126 SKREARAQAIEVLRQVGIPDPPRRVDSYAHEFSGGMRQRAMIAVALACNPQVLIADEPTT 185 Query: 184 ALDVTIQAQIMELLQELKEEYGMSVIFITHDLSVATNFCDRIITMYAGKIVEEAPVEEIL 243 ALDVT+QAQI+ LL +L+++ G+S+I ITHDL V CD I MYAG++ E E+L Sbjct: 186 ALDVTVQAQILRLLLDLRDQRGLSIILITHDLGVVAQTCDSIAVMYAGRLCEHGSKHELL 245 Query: 244 KTPLHPYTKGLLNSTLEIGSRGKKLVPIPGNPPNPTKHPSGCKFHPRCSFAMEICQREEP 303 P HPYT GL++ L I G PP PSGC F+PRC C P Sbjct: 246 VRPRHPYTAGLIDCQPASSVGHAMLRTIAGQPPLLDALPSGCSFNPRCLQQGSQCTMLLP 305 Query: 304 PLVNISENHRVACH 317 L ++E RVACH Sbjct: 306 DLQIMAEGQRVACH 319 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: 289 Number of extensions: 13 Number of successful extensions: 3 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: 328 Length adjustment: 28 Effective length of query: 296 Effective length of database: 300 Effective search space: 88800 Effective search space used: 88800 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