Align The Na+-dependent sugar transporter, HP1174 (transports glucose, galactose, mannose and 2-deoxyglucose (Psakis et al. 2009)). (most similar to 2.A.1.7.2; 49% identity) (characterized)
to candidate Echvi_3909 Echvi_3909 Fucose permease
Query= TCDB::O25788 (407 letters) >FitnessBrowser__Cola:Echvi_3909 Length = 469 Score = 321 bits (823), Expect = 2e-92 Identities = 192/452 (42%), Positives = 263/452 (58%), Gaps = 72/452 (15%) Query: 13 LTALFFLMGFITVLNDILIPHLKPIFDLTYFEASLIQFCFFGAYFIMG-GVF------GN 65 +T LFF+ GFIT +NDILIPHL+ +F L ++A LIQ FFGAYF + G + G+ Sbjct: 30 VTMLFFMWGFITCMNDILIPHLQQVFTLQNWQAMLIQTAFFGAYFFISLGYYLISITKGD 89 Query: 66 VISKIGYPFGVVLGFVITATGCALFYPAAHFGSYGFFLGALFILASGIVCLQTAGNPFVT 125 I +IGY G++LG VI+A GC FYPAA S+GFFL ALF+LASGI LQ A NP+VT Sbjct: 90 PIGRIGYKNGIILGLVISAVGCLFFYPAASLVSFGFFLFALFVLASGITILQIAANPYVT 149 Query: 126 LLSKGKEARN-LVLVQAFNSLGTTLGPIFGSLLIFSTTKMGDNASLIDKLADAKSVQMPY 184 +L K A + L + QAFNSLGTT+ P+ G LIF +GD +D AD SV+MPY Sbjct: 150 ILGKPSGASSRLNMTQAFNSLGTTIAPLIGGYLIFGA--IGD----VDISAD--SVKMPY 201 Query: 185 LGLAVFSLLLALIMYLLKLPDVEKEMPKETTQKSLFSHKHFVFGALGIFFYVGGEVAIGS 244 + LA+ LL+ALI L KLP++ + + H+H + G IF YVGGEV +GS Sbjct: 202 VALALTLLLIALIFKLFKLPEIGSQ-GVIISDSGALKHRHLMLGIGAIFAYVGGEVTVGS 260 Query: 245 FLV--LSFEKLLNLDSQSSAHYLVYYWGGAMVGRFLGSVLMN--KIAPNKYLAFNALSSI 300 L+ ++ LD ++HYL +WGGAMVGRF G+V + K N++L A+++I Sbjct: 261 NLINFARLPEIAGLDEAEASHYLALFWGGAMVGRFFGAVALADFKHNLNRFLIIGAITAI 320 Query: 301 VLIALAIIIGGKIALFALTFV--------------------------------------- 321 + + + GG++AL+AL F+ Sbjct: 321 SYVTIYYVYGGEMALYALAFIGLNIVVIIIGQFIPNRTLWLFGITGIGLLVIGLLTSGQL 380 Query: 322 --------GFFNSIMFPTIFSLATLNLGHLTSKASGVISMAIVGGALIPPIQGAVTDMLT 373 G FNSIMFPTIFSLA LG T++AS ++ MAIVGGA++P +QG + D+ Sbjct: 381 ALWSIVALGLFNSIMFPTIFSLAIKGLGKYTAQASSLLVMAIVGGAIVPLLQGLLADISG 440 Query: 374 ATESNLLYAYGVPLLCYFYILFFALKGYKQEE 405 + + + L VPL CY YI+F+ +KGY+ EE Sbjct: 441 SVQLSFL----VPLACYLYIVFYGMKGYRVEE 468 Lambda K H 0.328 0.144 0.423 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: 666 Number of extensions: 41 Number of successful extensions: 9 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: 407 Length of database: 469 Length adjustment: 32 Effective length of query: 375 Effective length of database: 437 Effective search space: 163875 Effective search space used: 163875 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: 51 (24.3 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