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 Pf6N2E2_1812 peptide ABC transporter, ATP-binding protein
Query= TCDB::Q9X271 (324 letters) >FitnessBrowser__pseudo6_N2E2:Pf6N2E2_1812 Length = 338 Score = 260 bits (665), Expect = 3e-74 Identities = 139/323 (43%), Positives = 205/323 (63%), Gaps = 11/323 (3%) Query: 2 MELLNVNNLKVEFHR-----VEGIVKAVDGISYKLNKGESLGIVGESGSGKSVSVLSLLR 56 M LL+V NL+V+ + ++ AV G+ +++ +GE L IVGESG GKS++ L+L+ Sbjct: 1 MALLHVENLRVDIPMGNSPTPDDMLHAVRGLDFEVERGEMLCIVGESGCGKSLTSLALMD 60 Query: 57 LINRNGRIVDGEAIFLGKDLLKLNKEELRNIRGKDISIIFQNPMTSLNPIIRVGIQVMEP 116 L+ R R G D+L ++ + ++RG +++IFQ PMTSLNP +G Q+ E Sbjct: 61 LLPRKARRTASRLTLDGIDMLGQSERRMCDLRGNRLAMIFQEPMTSLNPAYSIGDQLSEV 120 Query: 117 IIWHRLMKNEEARERAIELLERVGIPESPKRFLNYPFQFSGGMRQRVMIAMALACHPKLL 176 + HR + ++A RA ++LE+VGI + +R YP Q SGG+RQRV+IAMAL C P L+ Sbjct: 121 LTQHRKVSRKDALARAAQMLEKVGISNAAERLRQYPHQLSGGLRQRVIIAMALMCEPDLI 180 Query: 177 IADEPTTALDVTIQAQIMELLQELKEEYGMSVIFITHDLSVATNFCDRIITMYAGKIVEE 236 IADEPTTALDVTIQAQI+ L++++++E G++VIFITHDL + DR+ MYAG+IVE Sbjct: 181 IADEPTTALDVTIQAQILRLIRDIQKELGLAVIFITHDLGLVARIADRVAVMYAGEIVET 240 Query: 237 APVEEILKTPLHPYTKGLLNSTLEIGSR---GKKLVPIPGNPPNPTKHPSGCKFHPRCSF 293 AP ++ + P HPYT+GLL +++ I R G+ L IPG P+ GC F RC+ Sbjct: 241 APARQLFENPQHPYTRGLL-ASIPIPGRTKPGEALGSIPGLVPSLVGEQQGCAFRNRCAQ 299 Query: 294 AMEICQREEPPLVNISENHRVAC 316 A+ C ++ P + + H C Sbjct: 300 AITACAQDIPEIE--QDGHMARC 320 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: 271 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: 338 Length adjustment: 28 Effective length of query: 296 Effective length of database: 310 Effective search space: 91760 Effective search space used: 91760 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