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 H281DRAFT_01031 H281DRAFT_01031 peptide/nickel transport system ATP-binding protein
Query= TCDB::Q9X272 (328 letters) >FitnessBrowser__Burk376:H281DRAFT_01031 Length = 377 Score = 291 bits (745), Expect = 2e-83 Identities = 149/320 (46%), Positives = 217/320 (67%), Gaps = 8/320 (2%) Query: 12 PLLQTVDLKKYFPQGKRI------LKAVDGISIEIKEGETLGLVGESGCGKSTLGRTILK 65 P+++ L K F +++ + AV+ +S + GET +VGESGCGKSTLGR +L+ Sbjct: 16 PIIEASALTKRFGGERQMFTRTPTVHAVNEVSFAVHTGETFAIVGESGCGKSTLGRMLLR 75 Query: 66 LLRPDGGKIFFEGKDITNLNDKEMKPYRKKMQIIFQDPLGSLNPQMTVGRIIEDPLIIHK 125 L+ G++ ++G+DIT+ +++ R+ MQIIFQDP SLNP MTVG+II +P+ H Sbjct: 76 LIDATQGRVLYQGEDITHWQGAKLRRLRRDMQIIFQDPFASLNPGMTVGQIIGEPVAFHG 135 Query: 126 IGTK-KERRKRVEELLDMVGIGREFINSFPHEFSGGQQQRIGIARALALNPKFIVCDEPV 184 + + E R+RV +LL VG+ + +PHEFSGGQ+QRIGIARALA PK IV DEPV Sbjct: 136 LASSGSECRERVAQLLTKVGLQPAYAQRYPHEFSGGQRQRIGIARALAGEPKLIVGDEPV 195 Query: 185 SALDVSIQAQIIDLLEEIQQKMGISYLFIAHNLAVVEHISHKVAVMYLGKIVEYGDVDKI 244 SALDVS+QAQ+I+LLE ++ ++G++ + +AH+LAV+ H+S +VAVMYLG+IVE VD++ Sbjct: 196 SALDVSVQAQVINLLESLKAELGLTLIMVAHDLAVIRHMSDRVAVMYLGEIVELAQVDEL 255 Query: 245 FLNPIHPYTRALLKSVPKIPWDGQKQRFYSLKGELPSPIDLPKGCRFQTRCTEKKAICFE 304 F P+HPYT+ALL+++P +++ +L+G+LPSP P GCRF TRC K C + Sbjct: 256 FDAPLHPYTQALLRAIPASS-PHERRTKPALQGDLPSPTAPPPGCRFHTRCPHAKPRCVQ 314 Query: 305 KEPELTEVEKNHFVSCHLVR 324 + P + V+CH R Sbjct: 315 ERPLSETLPGGRQVACHFWR 334 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: 356 Number of extensions: 13 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: 377 Length adjustment: 29 Effective length of query: 299 Effective length of database: 348 Effective search space: 104052 Effective search space used: 104052 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