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_RS07880 HSERO_RS07880 peptide ABC transporter substrate-binding protein
Query= TCDB::Q9X271 (324 letters) >FitnessBrowser__HerbieS:HSERO_RS07880 Length = 330 Score = 277 bits (708), Expect = 3e-79 Identities = 142/313 (45%), Positives = 202/313 (64%), Gaps = 1/313 (0%) Query: 5 LNVNNLKVEFHRVEGIVKAVDGISYKLNKGESLGIVGESGSGKSVSVLSLLRLINRNGRI 64 L V NL+ F EG++ AVD +S + +G LG+VGESGSGKSV+ S+L +++ GRI Sbjct: 6 LEVRNLRTHFFTPEGVLPAVDDVSLSVGRGRILGLVGESGSGKSVTGFSILGMVDAPGRI 65 Query: 65 VDGEAIFLGKDLLKLNKEELRNIRGKDISIIFQNPMTSLNPIIRVGIQVMEPIIWHRLMK 124 V GE +F G+DL++++K LR ++G I++IFQ+PM +LNP+++V Q+++ ++ H + Sbjct: 66 VGGEILFQGRDLVRMDKTSLRELQGNRIAMIFQDPMMTLNPVLKVEAQMVDAVLAHSKVS 125 Query: 125 NEEARERAIELLERVGIPESPKRFLNYPFQFSGGMRQRVMIAMALACHPKLLIADEPTTA 184 ++ARE A + L +GI +R YP Q SGGMRQRV IA+A+ P L+IADEPTTA Sbjct: 126 RQQARELARDTLGMMGIASPEERLQAYPHQLSGGMRQRVAIAIAMLHKPDLIIADEPTTA 185 Query: 185 LDVTIQAQIMELLQELKEEYGMSVIFITHDLSVATNFCDRIITMYAGKIVEEAPVEEILK 244 LDVTIQAQI+ +Q+L ++G ++I+ITHDLSV D + MYAG+IVE+ V+ +L Sbjct: 186 LDVTIQAQILSEVQKLARQHGTALIWITHDLSVVAGLADEVAVMYAGRIVEQGSVDAVLD 245 Query: 245 TPLHPYTKGLLNSTLEIGSRGKKLVPIPGNPPNPTKHPSGCKFHPRCSFAMEICQREEPP 304 PLHPYT+GL+ S RG +L IPG PN P C F RC + C P Sbjct: 246 APLHPYTQGLIGSLPSNNRRGARLRQIPGMTPNLLHLPPTCAFAARCERLSQQC-LVAPA 304 Query: 305 LVNISENHRVACH 317 + HRV C+ Sbjct: 305 ISEPLPAHRVRCY 317 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: 267 Number of extensions: 15 Number of successful extensions: 1 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: 330 Length adjustment: 28 Effective length of query: 296 Effective length of database: 302 Effective search space: 89392 Effective search space used: 89392 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