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 353365 BT3839 ABC transporter ATP-binding protein (NCBI ptt file)
Query= TCDB::Q9X272 (328 letters) >FitnessBrowser__Btheta:353365 Length = 256 Score = 125 bits (314), Expect = 1e-33 Identities = 75/213 (35%), Positives = 120/213 (56%), Gaps = 3/213 (1%) Query: 33 VDGISIEIKEGETLGLVGESGCGKSTLGRTILKLLRPDGGKIFFEGKDITNLNDKEMKPY 92 + I+ + G+T ++G+SG GK+ L + I+ LL P+ G++ ++G+++ + KE K Sbjct: 17 LSNINASFENGKTNLIIGQSGSGKTVLMKCIVGLLTPEKGEVLYDGRNLVLMGKKEKKML 76 Query: 93 RKKMQIIFQDPLGSLNPQMTVGRIIEDPLIIHKIGTKKERRKRVEELLDMVGIGREFINS 152 RK+M +IFQ +L M+V + PL + T ++R KR L+ V + E + Sbjct: 77 RKEMGMIFQS--AALFDSMSVLDNVMFPLNMFSNDTLRDRTKRAMFCLERVNL-TEAKDK 133 Query: 153 FPHEFSGGQQQRIGIARALALNPKFIVCDEPVSALDVSIQAQIIDLLEEIQQKMGISYLF 212 FP E SGG Q+R+ IARA+ALNP+++ CDEP S LD I DL+ +I Q+ ++ + Sbjct: 134 FPGEISGGMQKRVAIARAIALNPQYLFCDEPNSGLDPKTSLVIDDLIHDITQEYNMTTII 193 Query: 213 IAHNLAVVEHISHKVAVMYLGKIVEYGDVDKIF 245 H++ V I KV +Y G G D IF Sbjct: 194 NTHDMNSVLGIGEKVIYIYEGHKEWEGTKDDIF 226 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: 221 Number of extensions: 13 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: 328 Length of database: 256 Length adjustment: 26 Effective length of query: 302 Effective length of database: 230 Effective search space: 69460 Effective search space used: 69460 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