Align Phosphotransferase system, mannose/fructose-specific component IIA, component of The hexose (glucose and fructose demonstrated) PTS uptake system (characterized)
to candidate WP_010630732.1 RH97_RS02405 PTS mannose transporter subunit IIAB
Query= TCDB::Q04GK1 (331 letters) >NCBI__GCF_000246965.1:WP_010630732.1 Length = 325 Score = 397 bits (1019), Expect = e-115 Identities = 192/331 (58%), Positives = 258/331 (77%), Gaps = 9/331 (2%) Query: 1 MVGIVLASHGNFAEGIYQSAEMIFGKQQNVQTVTLSPNEGPEDFLNKLKQAIDSFDDQKQ 60 MVGI+LASHG FAEGI+QS MIFG+Q+NV+TVTL PNEGP D K+K+AI SFDDQ++ Sbjct: 1 MVGIILASHGGFAEGIFQSGSMIFGEQKNVKTVTLMPNEGPNDIKEKMKKAIASFDDQEE 60 Query: 61 VLLLIDLWGGTPFNQSSGLLSGHEDSWAVVTGMNLPMVIEAYGSRSSMDSAQEIATHIIE 120 VL L+DLWGGTPFNQ++ L H+D WA+V G+NLPM+IEAY SR+S+++A++IA HI+ Sbjct: 61 VLFLVDLWGGTPFNQANSLFEAHKDKWAIVAGLNLPMLIEAYASRASLNTARDIAAHILG 120 Query: 121 TGKDGIRIKPESLEPKKATATVKSSGQPHGTIAPGTVLGDGKIKYVLARVDSRLLHGQVA 180 K+G++I+PE+L P K A S G G AP G+ KYVLARVDSRLLHGQVA Sbjct: 121 AAKEGVKIRPEALAPAKEAAAASSQGSNAG--AP------GQFKYVLARVDSRLLHGQVA 172 Query: 181 MSWTKSTNPNRILVVSDSVAKDRLRKSMIVEAAPPGVNTNVIPIKKMIEVAKDPR-FGNT 239 +W K+T P RI+VVSD+VA+D LRK +I +AAPPGV +V+P+ +MI++AKD + FG Sbjct: 173 TAWAKTTQPTRIIVVSDAVAEDDLRKKLIQQAAPPGVKAHVVPVDQMIKLAKDDKHFGGQ 232 Query: 240 KALVLFENPEDALKTIEGGVDIKELNIGSMSHAVGKVAVNKVLSLGKEDVEAFDGLKKLG 299 +AL+LFENP+DAL+ +EGGV +K +N+GSM+H+ GKV NKVL+ G+ED++AF LK+ G Sbjct: 233 RALLLFENPQDALRAVEGGVPLKTINVGSMAHSPGKVQPNKVLAFGQEDIDAFVKLKEYG 292 Query: 300 VKFDVRKVPGDSSENMDNIVNKARKDLSSVK 330 + FDVRKVP DS +M+ I+ KA+ +L+ +K Sbjct: 293 LDFDVRKVPNDSKGDMNEILKKAQDELNRLK 323 Lambda K H 0.313 0.132 0.366 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: 370 Number of extensions: 17 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: 331 Length of database: 325 Length adjustment: 28 Effective length of query: 303 Effective length of database: 297 Effective search space: 89991 Effective search space used: 89991 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.2 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 42 (21.9 bits) S2: 49 (23.5 bits)
This GapMind analysis is from Sep 24 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