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 8500263 DvMF_1020 oligopeptide/dipeptide ABC transporter, ATPase subunit (RefSeq)
Query= TCDB::Q9X272 (328 letters) >FitnessBrowser__Miya:8500263 Length = 358 Score = 209 bits (533), Expect = 6e-59 Identities = 116/287 (40%), Positives = 170/287 (59%), Gaps = 7/287 (2%) Query: 30 LKAVDGISIEIKEGETLGLVGESGCGKSTLGRTILKLLRPDG----GKIFFEGKDITNLN 85 L+AV GIS I G TL LVGESGCGKS +L+L+ G G + EG+++ L Sbjct: 41 LRAVAGISFSIAPGGTLCLVGESGCGKSMTALALLRLVPEPGRVASGSVRLEGRELLTLP 100 Query: 86 DKEMKPYR-KKMQIIFQDPLGSLNPQMTVGRIIEDPLIIHKIGTKKERRKRVEELLDMVG 144 + EM+ R + + +IFQ+P+ SLNP VG I + + +H ++ + R +LL VG Sbjct: 101 EPEMRGVRGRSISMIFQEPMTSLNPVFRVGEQIAEGVRLHLGLSRSDAAARAVDLLRQVG 160 Query: 145 IGREFINS--FPHEFSGGQQQRIGIARALALNPKFIVCDEPVSALDVSIQAQIIDLLEEI 202 I + + FPH+ SGG +QR+ IA ALA +P+ ++ DEP +ALDV+IQ QI+ L+ ++ Sbjct: 161 IPSPELRARDFPHQMSGGMRQRVMIAMALACDPRLLIADEPTTALDVTIQRQILRLMRDL 220 Query: 203 QQKMGISYLFIAHNLAVVEHISHKVAVMYLGKIVEYGDVDKIFLNPIHPYTRALLKSVPK 262 G S L I H+L VV + VAVMY G+I+E+ V F P+HPY + L++SVP+ Sbjct: 221 AAHRGASVLLITHDLGVVAETADHVAVMYAGRIMEHASVGDFFARPLHPYAQGLMRSVPQ 280 Query: 263 IPWDGQKQRFYSLKGELPSPIDLPKGCRFQTRCTEKKAICFEKEPEL 309 + +R ++ G +P LP GC F+ RC A C E+EP L Sbjct: 281 AVSGPRAERLSAIPGTVPPLWALPSGCTFRDRCPHAFARCAEQEPPL 327 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: 297 Number of extensions: 9 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: 358 Length adjustment: 29 Effective length of query: 299 Effective length of database: 329 Effective search space: 98371 Effective search space used: 98371 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