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 Pf1N1B4_5105 Peptide ABC transporter, ATP-binding protein
Query= TCDB::Q9X271 (324 letters) >FitnessBrowser__pseudo1_N1B4:Pf1N1B4_5105 Length = 323 Score = 224 bits (571), Expect = 2e-63 Identities = 130/312 (41%), Positives = 182/312 (58%), Gaps = 16/312 (5%) Query: 2 MELLNVNNLKVEFHR----VEGI----VKAVDGISYKLNKGESLGIVGESGSGKSVSVLS 53 M LL V +L V F + G+ + AV+G+S L+ GE+LG+VGESGSGKS S Sbjct: 1 MTLLKVKDLHVRFAAPGTGLMGMNRQWLTAVNGVSLTLSAGETLGLVGESGSGKS----S 56 Query: 54 LLRLINRNGRIVDGEAIFLGKDLLKLNKEELRNIRGKDISIIFQNPMTSLNPIIRVGIQV 113 L R I I G+ +F G D+ K ++ +R + +++FQ+P +LNP + +G + Sbjct: 57 LGRAILHLNEIYAGQVLFDGIDMAHAGKVDITRLR-HETAMVFQDPYAALNPRLSIGQTL 115 Query: 114 MEPIIWHRLMKNEEARERAIELLERVGIPESPKRFLNYPFQFSGGMRQRVMIAMALACHP 173 E + R + R ELL VG+ P+ P SGG QRV IA ALA P Sbjct: 116 AEVLRVQRKVPESLIAARVGELLTLVGL--RPELASRKPHALSGGQCQRVGIARALAVEP 173 Query: 174 KLLIADEPTTALDVTIQAQIMELLQELKEEYGMSVIFITHDLSVATNFCDRIITMYAGKI 233 +L++ADE ALDV+IQ QI+ LL EL++ ++++FI HDL++ CDR+ MY GKI Sbjct: 174 RLIVADECVAALDVSIQGQIINLLLELRQRMNLAIVFIAHDLAIVRRLCDRVAVMYLGKI 233 Query: 234 VEEAPVEEILKTPLHPYTKGLLNSTLEIG-SRGKKLVPIPGNPPNPTKHPSGCKFHPRCS 292 VEE PVEE+ ++P HPYT L+ S EI +R P+PG PP+P + PSGC FHPRC Sbjct: 234 VEEGPVEEVFRSPRHPYTAALIQSIPEIDPARALPTDPLPGEPPSPLQLPSGCAFHPRCR 293 Query: 293 FAMEICQREEPP 304 + C + PP Sbjct: 294 YVRATCSQVVPP 305 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: 265 Number of extensions: 13 Number of successful extensions: 4 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: 323 Length adjustment: 28 Effective length of query: 296 Effective length of database: 295 Effective search space: 87320 Effective search space used: 87320 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