Align TM1750, component of Probable mannose/mannoside porter. Induced by beta-mannan (Conners et al., 2005). Regulated by mannose-responsive regulator manR (characterized)
to candidate GFF16 Psest_0016 ectoine/hydroxyectoine ABC transporter, ATP-binding protein
Query= TCDB::Q9X272 (328 letters) >FitnessBrowser__psRCH2:GFF16 Length = 278 Score = 138 bits (348), Expect = 1e-37 Identities = 86/270 (31%), Positives = 150/270 (55%), Gaps = 19/270 (7%) Query: 2 PFDQGGIKMKPLLQTVDLKKYFPQGKRILKAVDGISIEIKEGETLGLVGESGCGKSTLGR 61 P Q + +PL++ + K + + L +DG+ ++I+EGE + ++G SG GKSTL R Sbjct: 13 PTPQQPEQAQPLVRFAGVTKRYGE----LTVLDGLDLQIEEGEKVAIIGPSGSGKSTLLR 68 Query: 62 TILKLLRPDGGKIFFEGKDITNLND----------KEMKPYRKKMQIIFQDPLGSLNPQM 111 ++ L D G I +G+ +T++ D + ++ R K+ ++FQ +L P M Sbjct: 69 VLMTLEGIDEGVIEVDGEPLTHMPDASGQLVPANARHLRRVRGKVGMVFQS--FNLFPHM 126 Query: 112 T-VGRIIEDPLIIHKIGTKKERRKRVEELLDMVGIGREFINSFPHEFSGGQQQRIGIARA 170 + ++E P+ + + +K E R R EELL MVG+ + + FP + SGGQQQR+ IARA Sbjct: 127 NALQNVMEAPVQVLGL-SKAEARGRAEELLAMVGL-EDKLEHFPAQLSGGQQQRVAIARA 184 Query: 171 LALNPKFIVCDEPVSALDVSIQAQIIDLLEEIQQKMGISYLFIAHNLAVVEHISHKVAVM 230 LA+ PK ++ DE SALD + ++++++ + + ++ L + H + + +V Sbjct: 185 LAMRPKVMLFDEVTSALDPELCGEVLNVIRRLGEAHNLTMLMVTHQMGFAREFADRVCFF 244 Query: 231 YLGKIVEYGDVDKIFLNPIHPYTRALLKSV 260 + G+I E G D++F NP TR L +V Sbjct: 245 HQGRIHEQGSPDELFNNPQEERTREFLSAV 274 Lambda K H 0.321 0.142 0.417 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: 243 Number of extensions: 15 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: 328 Length of database: 278 Length adjustment: 27 Effective length of query: 301 Effective length of database: 251 Effective search space: 75551 Effective search space used: 75551 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