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 GFF204 HP15_203 oligopeptide/dipeptide ABC transporter, ATPase subunit
Query= TCDB::Q9X272 (328 letters) >FitnessBrowser__Marino:GFF204 Length = 332 Score = 210 bits (534), Expect = 4e-59 Identities = 119/318 (37%), Positives = 191/318 (60%), Gaps = 10/318 (3%) Query: 13 LLQTVDLKKYFPQGKRILKAVDGISIEIKEGETLGLVGESGCGKSTLGRTILKLLRPDG- 71 LL+ DL F L A+ GIS + +GE LGLVGESG GKS +IL L+ G Sbjct: 3 LLEVKDLDVRFAVRGGDLTALRGISFSLDKGERLGLVGESGAGKSVAAFSILNLIAKPGY 62 Query: 72 ---GKIFFEGKDITNLNDKEMKPYR-KKMQIIFQDPLGSLNPQMTVGRIIEDPLIIHKIG 127 G+I FEG+D+ ++++E++ R ++ +IFQDP+ +LNP +T+G + + ++ H+ Sbjct: 63 IAGGQILFEGRDLAAMSERELRRIRGNRIAMIFQDPMMTLNPVLTIGTQMVEAILAHRKI 122 Query: 128 TKKERRKRVEELLDMVGIG--REFINSFPHEFSGGQQQRIGIARALALNPKFIVCDEPVS 185 +KKE R + L V I + ++ +PHE SGG +QR+ IA AL L+P+ I+ DEP + Sbjct: 123 SKKEARAIALDRLQKVQIPSPEKRLDQYPHELSGGMRQRVIIAIALLLDPEIIIADEPTT 182 Query: 186 ALDVSIQAQIIDLLEEIQQKMGISYLFIAHNLAVVEHISHKVAVMYLGKIVEYGDVDKIF 245 ALDV+IQA+I+DLL + ++ ++ + I H+L VV ++ ++ VMY G+I+E G +I Sbjct: 183 ALDVTIQAEIMDLLLNLCEQENVALMLITHDLGVVSQVTQRMLVMYSGRIIEQGPTREII 242 Query: 246 LNPIHPYTRALLKSVPKIPWDGQKQRFYSLKGELPSPIDLPKGCRFQTRCTEKKAICFEK 305 + HPYT+ L+ ++P++ G +R + + G +PS ++P GC F RC C + Sbjct: 243 NDAQHPYTQGLINALPQMGEPG--ERLFQIPGSMPSLKNVPSGCPFHPRCNFATEQCKQA 300 Query: 306 EPELTEVEKNHFVSCHLV 323 PE N V+C+ V Sbjct: 301 MPEYVR-SGNVNVACYEV 317 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: 274 Number of extensions: 9 Number of successful extensions: 5 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: 332 Length adjustment: 28 Effective length of query: 300 Effective length of database: 304 Effective search space: 91200 Effective search space used: 91200 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