Align glucose transporter, permease component (characterized)
to candidate 16645 b2546 predicted sugar transporter subunit: membrane component of ABC superfamily (NCBI)
Query= reanno::Phaeo:GFF3640 (433 letters) >FitnessBrowser__Keio:16645 Length = 332 Score = 130 bits (326), Expect = 8e-35 Identities = 93/310 (30%), Positives = 154/310 (49%), Gaps = 31/310 (10%) Query: 140 VGFLTIPA-----FIVTLGGFLVWRNVAWYLTDGQTIGPLDSTFLVFGGTSGTLGTTLSW 194 +G L + A F + GF+ N L D TIG + + + SG + ++ Sbjct: 27 IGLLVVIAILYLVFSLNAPGFISLNNQMNVLRDAATIG-IAAWAMTLIIISGEIDVSVGP 85 Query: 195 VVGIVATLLALAALWNSRRAKQGHGFPVKPAWAEAVIAGSIAASILG----------FVA 244 +V V+ LA + P+ A ++ G++ ++ G FVA Sbjct: 86 MVAFVSVCLAFLLQFE---------VPLAVACLLVLLLGALMGTLAGVLRGVFNVPSFVA 136 Query: 245 ILNAYQIPARRLKRMMEAQGETMPEGLVVGY------GLPISVLILIATAVVMTIIARRT 298 L + M A + E V+ + G+P+S LI+I + I+R+T Sbjct: 137 TLGLWSALRGMGLFMTNALPVPIDENEVLDWLGGQFLGVPVSALIMIVLFALFVFISRKT 196 Query: 299 RLGRYIFATGGNPDAAELSGINTRLLTVKIFALMGFLCALSAVVASARLANHSNDIGTLD 358 GR +FA GGN AA+L GIN R + + IF L G L A++ ++ +ARL + + Sbjct: 197 AFGRSVFAVGGNATAAQLCGINVRRVRILIFTLSGLLAAVTGILLAARLGSGNAGAANGL 256 Query: 359 ELRVIAAAVIGGTALSGGFGTIYGAILGALIMQSLQSGMAMVGVDAPFQNIVVGTVLVAA 418 E VIAA V+GGTALSGG G+++G +LG L++ + +G+ ++G+++ FQ +V G ++V A Sbjct: 257 EFDVIAAVVVGGTALSGGRGSLFGTLLGVLVITLIGNGLVLLGINSFFQQVVRGVIIVVA 316 Query: 419 VWIDILYRKR 428 V +IL +R Sbjct: 317 VLANILLTQR 326 Lambda K H 0.327 0.141 0.419 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: 400 Number of extensions: 22 Number of successful extensions: 3 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 433 Length of database: 332 Length adjustment: 30 Effective length of query: 403 Effective length of database: 302 Effective search space: 121706 Effective search space used: 121706 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.1 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.7 bits) S2: 50 (23.9 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