Align Glucose transport system permease protein aka TT_C0327, component of The glucose/mannose porter TTC0326-8 plus MalK1 (ABC protein, shared with 3.A.1.1.25) (characterized)
to candidate Synpcc7942_0526 Synpcc7942_0526 ABC-type sugar transport systems permease components-like
Query= TCDB::Q72KX3 (369 letters) >FitnessBrowser__SynE:Synpcc7942_0526 Length = 293 Score = 97.1 bits (240), Expect = 5e-25 Identities = 93/353 (26%), Positives = 156/353 (44%), Gaps = 82/353 (23%) Query: 1 MRDRILAFLVLLPSVLAVGVFVYGFIGQNLWVSLTDWGKDPAQALALRPELRFVGLENYR 60 +RDR+ +L L P++ +G+ V+ Q + S T + + L ++VGLEN++ Sbjct: 4 LRDRLSPYLFLAPALTILGLTVFWPALQAFYFSFTRFDYN------LTRSPQWVGLENFQ 57 Query: 61 ELFTGFVDVRFRQSVVNLIFFTLFFMAGSLGLGLLLALAVDKAPRGEGFFRTVFLFPMAL 120 L D F +++ N T ++ G + L VFL P+ L Sbjct: 58 RLLN---DAVFWKTLGN----TFIYLIGVVPL-------------------LVFL-PLGL 90 Query: 121 SFVVTGTIWRWLLQPQGGVNVLPTLFGLPPLSFPWLATREQVLVFDWNRLPFYTALVVGL 180 + +V +P G+ TLF RL +YT ++V + Sbjct: 91 AILVN--------RPLRGI----TLF----------------------RLAYYTPVIVSI 116 Query: 181 VLLYVAYTAYREGERRRALWGLASAGVL-LLWAFAFGQGLRLLPYPEVHGFSLALVGVIL 239 V+ +A+ W A G+L L FG+G + P P + +LAL V+ Sbjct: 117 VVAGIAWR-----------WLYAETGLLNQLGQLVFGEGFQ--PIPWLTSPALALFSVMA 163 Query: 240 AAVWQMSGYTMALYLAGLRGIPVEVLEAARVDGASEWQLFRRVIFPMLAPITLSAMIVLG 299 VW+ GY M +YLAGL+GIP+E+ EAA +DG+ W+ + P++ P + ++ Sbjct: 164 VTVWKGLGYYMVIYLAGLQGIPLELYEAAALDGSDGWRRHLDITLPLMRPYLVLVAVISA 223 Query: 300 HIALKIFDLVFAMA-GLDYAPTDVPAIYMYLLAFRGNQFAKGAAIGILLLLLV 351 A K+F+ VF M G + Y+Y AF+ + + +G+ L L+V Sbjct: 224 ISATKVFEEVFIMTQGGPLNSSKTVVYYVYQQAFQKLEVSYACTVGLALFLVV 276 Lambda K H 0.331 0.146 0.458 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: 291 Number of extensions: 19 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: 369 Length of database: 293 Length adjustment: 28 Effective length of query: 341 Effective length of database: 265 Effective search space: 90365 Effective search space used: 90365 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.2 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.9 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