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 Ga0059261_1870 Ga0059261_1870 ABC-type transport system involved in resistance to organic solvents, ATPase component
Query= TCDB::Q9X272 (328 letters) >FitnessBrowser__Korea:Ga0059261_1870 Length = 273 Score = 118 bits (295), Expect = 2e-31 Identities = 76/228 (33%), Positives = 126/228 (55%), Gaps = 20/228 (8%) Query: 34 DGISIEIKEGETLGLVGESGCGKSTLGRTILKLLRPDGGKIFFEGKDITNLNDKEMKPYR 93 +G+ +++++GE LG+VG SG GKS L R+I+ L PD G I G+D+ +LN +E R Sbjct: 32 EGLDLDVRQGEILGVVGGSGTGKSVLMRSIIGLQEPDAGSIEVFGEDVQHLNTEEAIELR 91 Query: 94 KKMQIIFQDPLGSLNPQMTVGRIIEDPLIIHKIGTKKERRKRVEE-LLD--------MVG 144 K+ ++FQ G+L +TV ++ PL KE ++ LLD M G Sbjct: 92 KRWGVLFQG--GALFSTLTVAENVQVPL--------KEFYPAFDQALLDEIAAYKVVMTG 141 Query: 145 IGREFINSFPHEFSGGQQQRIGIARALALNPKFIVCDEPVSALDVSIQAQIIDLLEEIQQ 204 + + +P E SGG ++R G+AR+LAL+P+ + DEP + LD A +L +Q+ Sbjct: 142 LPSDAGPKYPAELSGGMKKRAGLARSLALDPELLFLDEPTAGLDPIGAAAFDELTLALQR 201 Query: 205 KMGISYLFIAHNLAVVEHISHKVAVMYLGKIVEYGDVDKIFLNPIHPY 252 +G++ I H+L + I +VAV+ ++ G +D++ L HP+ Sbjct: 202 TLGLTVFLITHDLDTLYAICDRVAVLADKHVIAVGTIDEL-LALDHPW 248 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: 238 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: 273 Length adjustment: 27 Effective length of query: 301 Effective length of database: 246 Effective search space: 74046 Effective search space used: 74046 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