Align MFS transporter (characterized, see rationale)
to candidate Echvi_3106 Echvi_3106 Sugar phosphate permease
Query= uniprot:A0A166QG26 (467 letters) >FitnessBrowser__Cola:Echvi_3106 Length = 441 Score = 277 bits (709), Expect = 4e-79 Identities = 154/470 (32%), Positives = 245/470 (52%), Gaps = 58/470 (12%) Query: 11 RIGQAVGNYRWTICALLFFATTVNYLDRQVLSLLAPD---------------LSTQF-GW 54 ++ + YRW I ALLF AT + Y+DR VLS D LS++ G Sbjct: 5 KLNSIIKGYRWRIVALLFLATAIKYIDRNVLSFTMIDEGFRREMLGVSDTTALSSELIGK 64 Query: 55 SNSDYANIASVFQFVYAISMLFAGRVVDKIGTKTAYVVAICIWSTGAVMHAFAVPMGEGI 114 + + F+F YAI + G +D++ + Y +AI IWS ++ AF Sbjct: 65 FKILMGYVDASFKFAYAIGFVLMGYFIDRVLVRKGYSIAIAIWSLAGIVTAF-------- 116 Query: 115 GAVSSALGIAMIPVSIAGFMVSRAVLAIGEAGNFPIAIKATAEYFPKKERSFATGIFNSG 174 VSS G++ +R V GE+ NFP AIK AE+FPKKERSFATGI+N+G Sbjct: 117 --VSSFRGLSF----------TRFVFGFGESANFPAAIKTIAEWFPKKERSFATGIYNAG 164 Query: 175 ANVGAILAPICVPLIASLWGWEAAFIVIGMLGFVWVGVWIALYEKPEQQKRLSAQELAYI 234 ANVG + + VP + GW +F+ G+LG V + W+ +Y+ P+ ++S E +I Sbjct: 165 ANVGIMATVLIVPALILNLGWRWSFLCTGLLGLVLLACWLLIYKPPKAHPKVSQDEQEHI 224 Query: 235 RSDQVVPVVTRPVPGVADKKVSWFKLLTYRQTWAFAFGKFMTDGVWWFFLFWLPTYLSAQ 294 +D+ VP W LL + WA A GKF+TD +WWF+L WLP + ++ Sbjct: 225 HADEESEHEAEKVP--------WKDLLKTKGAWAIALGKFLTDPIWWFYLTWLPDFFNSN 276 Query: 295 YGMKGQ----AIVMPLAVLYSMTMIGSIGGGWFPSYFMSRGDAPYDGRMKAMLVIAFFPL 350 ++ + + +P +Y + +GS+ GW F++ G + R +L+ A + Sbjct: 277 EALETKLDLTGLALPFIFIYFTSDLGSVFFGWLSGKFINMGWSLNKSRKVTLLLCALLVV 336 Query: 351 LVLLAQPLGYISFWVPVLLIGVGASAHQAWSCNIFTTVSDMFPQKSIASVVGIGGLAGGL 410 ++ A + + +V ++L+ + A+AHQ WS N+FT SD+FP++ + SVVG+ G+ GG+ Sbjct: 337 PLIFAAKVANV--YVAMVLVALAAAAHQGWSANLFTLSSDIFPKRVVGSVVGLAGMVGGI 394 Query: 411 GGVVMTKIGGWVIDHYKLIGDIHTGYMIMFAICALAYLVAWSVMKALVPR 460 GG + G ++ + GY +F I + AYL+AW ++ LVP+ Sbjct: 395 GGTIFAAFAGIIL--------VKWGYFPIFIIASSAYLLAWLIIHLLVPK 436 Lambda K H 0.327 0.140 0.449 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: 659 Number of extensions: 39 Number of successful extensions: 8 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: 467 Length of database: 441 Length adjustment: 33 Effective length of query: 434 Effective length of database: 408 Effective search space: 177072 Effective search space used: 177072 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