Align PTS system, IID component, component of The gluconate PTS uptake system. IIAGnt and IIBGnt form a high affinity 2:2 heterotetrameric complex (characterized)
to candidate BWI76_RS17900 BWI76_RS17900 PTS mannose transporter subunit IID
Query= TCDB::Q82ZC6 (290 letters) >FitnessBrowser__Koxy:BWI76_RS17900 Length = 283 Score = 124 bits (311), Expect = 2e-33 Identities = 89/283 (31%), Positives = 141/283 (49%), Gaps = 19/283 (6%) Query: 8 VVPKTTNLAPEEITNKDVTKAYLRWHFANEIPHSFERYLAPSLLYAMMPLLKKLY-KDDE 66 +V T N +++T D+ ++R + +FER A ++M+P +++LY ++++ Sbjct: 1 MVDMTKNTTEKKLTQSDIRGVFIRSNLFQG-SWNFERMQALGFCFSMVPAIRRLYPENND 59 Query: 67 QLKAAYMRQLLFFNTQLSWGGGVITGLMASMEQERAKEEHEGREIMMQDDLMYNTKAGLM 126 K A R L FFNT + + G+ +ME++RA G EI D + K GLM Sbjct: 60 ARKQAIKRHLEFFNTH-PYVAAPVLGVTLAMEEQRAN----GAEI--DDGAINGIKVGLM 112 Query: 127 GALAGIGDAIDSGTVQYIFIAIAVPWAQQGSALGAIFPFVAFALYQVLLGVFFARQSFKM 186 G LAG+GD I GTV+ +F A+ A GS LG + F+ F ++L + ++ Sbjct: 113 GPLAGVGDPIFWGTVRPVFAALGAGIAMSGSLLGPLLFFILFNAVRLLTRYYGVAYGYRK 172 Query: 187 GRNATGLMQSAGIQKAIEMLSVLGLFMMGILAGNYVKVSSTLQFK-LSG-----REFVVQ 240 G + M +QK E S+LGLF+MG L + V+ L ++G R VQ Sbjct: 173 GIDIVKDMGGGFLQKLTEGASILGLFVMGALVNKWTHVNIPLVVSTITGQDGQTRVTTVQ 232 Query: 241 DILDQIVPGLLPLAVVMGVYWFYTKKGLKVTQALLWLTGILIV 283 ILDQ++PGL+PL + W KK AL + G ++ Sbjct: 233 TILDQLMPGLVPLLLTFACMWLLRKK----VNALWIIVGFFVI 271 Lambda K H 0.324 0.138 0.402 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: 232 Number of extensions: 14 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: 290 Length of database: 283 Length adjustment: 26 Effective length of query: 264 Effective length of database: 257 Effective search space: 67848 Effective search space used: 67848 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.0 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (22.0 bits) S2: 47 (22.7 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