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 AZOBR_RS26735 AZOBR_RS26735 methionine ABC transporter ATP-binding protein
Query= TCDB::Q9X271 (324 letters) >FitnessBrowser__azobra:AZOBR_RS26735 Length = 331 Score = 272 bits (696), Expect = 7e-78 Identities = 142/306 (46%), Positives = 196/306 (64%), Gaps = 5/306 (1%) Query: 2 MELLNVNNLKVEFHRVEGIVKA----VDGISYKLNKGESLGIVGESGSGKSVSVLSLLRL 57 + LL V L+ E +G + +DG+S+ L +G LG+VGESGSGKS + S++ L Sbjct: 5 LPLLEVRGLRTELPARQGALNVPLNVLDGVSFSLGRGRILGLVGESGSGKSATAFSIMGL 64 Query: 58 INRNGRIVDGEAIFLGKDLLKLNKEELRNIRGKDISIIFQNPMTSLNPIIRVGIQVMEPI 117 ++ R+ G F G++L L + ELR +RG I++IFQ+PM +LNP++ +G Q++E + Sbjct: 65 LDPPARVAGGSIRFAGRELAGLPERELRRLRGNRIAMIFQDPMMTLNPVLTIGAQIVETV 124 Query: 118 IWHRLMKNEEARERAIELLERVGIPESPKRFLNYPFQFSGGMRQRVMIAMALACHPKLLI 177 + H + EAR RA + L RVG+P +R +P + SGG+RQRV IA+AL P L+I Sbjct: 125 LAHARVGRAEARRRARDALGRVGVPGPEERLDAHPHELSGGLRQRVAIAIALLHEPDLII 184 Query: 178 ADEPTTALDVTIQAQIMELLQELKEEYGMSVIFITHDLSVATNFCDRIITMYAGKIVEEA 237 ADEPTTALD TIQAQI+ ++ L E +V++ITHDLSVA D I MYAG+IVE+A Sbjct: 185 ADEPTTALDATIQAQILREIRGLVEGGRTAVLWITHDLSVAEQLSDEIAVMYAGRIVEQA 244 Query: 238 PVEEILKTPLHPYTKGLLNSTLEIGSRGKKLVPIPGNPPNPTKHPSGCKFHPRCSFAMEI 297 P E+L P HPYT GLL ++L RG +L PIPG PP + P+GC F PRC+ AM Sbjct: 245 PAAELLSRPAHPYTAGLL-ASLPREPRGSRLTPIPGLPPTLSGRPAGCAFRPRCAAAMPA 303 Query: 298 CQREEP 303 C P Sbjct: 304 CAAAPP 309 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: 282 Number of extensions: 18 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: 331 Length adjustment: 28 Effective length of query: 296 Effective length of database: 303 Effective search space: 89688 Effective search space used: 89688 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