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 3607471 Dshi_0884 oligopeptide/dipeptide ABC transporter, ATPase subunit (RefSeq)
Query= TCDB::Q9X272 (328 letters) >FitnessBrowser__Dino:3607471 Length = 360 Score = 209 bits (532), Expect = 8e-59 Identities = 116/299 (38%), Positives = 175/299 (58%), Gaps = 9/299 (3%) Query: 11 KPLLQTVDLKKYFPQGKRILKAVDGISIEIKEGETLGLVGESGCGKSTLGRTILKLLRP- 69 +P+L +L P +L+ VD +S +I GE LG+VGESG GKS G ++ LL P Sbjct: 3 QPVLSIRNLTVDIPTRYAVLRPVDKVSYDIAPGEILGVVGESGAGKSMAGNAVIGLLTPP 62 Query: 70 ---DGGKIFFEGKDITNLNDKEMKPYR-KKMQIIFQDPLGSLNPQMTVGRIIEDPLIIHK 125 G+++ GK I L ++M+ R K + ++FQDPL SLNP + +G + + ++ H Sbjct: 63 AHISSGEVWLNGKRIDRLTPEQMRRVRGKDIGMVFQDPLTSLNPLLRIGDQLTETMLAHL 122 Query: 126 IGTKKERRKRVEELLDMVGI--GREFINSFPHEFSGGQQQRIGIARALALNPKFIVCDEP 183 ++ E +R L+ VGI R+ +NS+PHEFSGG +QR+ IA AL P ++ DEP Sbjct: 123 PISRAEAEERAVAALEEVGIPAARQRVNSYPHEFSGGMRQRVVIALALCAEPSLVIADEP 182 Query: 184 VSALDVSIQAQIIDLLEEIQQKMGISYLFIAHNLAVVEHISHKVAVMYLGKIVEYGDVDK 243 +ALDVS+QAQII LL+ + ++ G + + I H++ V+ + +VAVMY G++ E G V + Sbjct: 183 TTALDVSVQAQIIALLKRLCRERGTAVMLITHDMGVIAEAADRVAVMYAGRLAELGPVRE 242 Query: 244 IFLNPIHPYTRALLKSVPKIPWDGQKQRFYSLKGELPSPIDLPKGCRFQTRCTEKKAIC 302 + P HPYT L+ S P + G K R + + G +P LP GC F RC + C Sbjct: 243 VLTAPRHPYTFGLMGSTP-LASKGLK-RLHQIPGSMPRLGRLPPGCAFSPRCPRAQDKC 299 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: 337 Number of extensions: 14 Number of successful extensions: 4 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: 360 Length adjustment: 29 Effective length of query: 299 Effective length of database: 331 Effective search space: 98969 Effective search space used: 98969 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: 49 (23.5 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