Align MFS transporter (characterized, see rationale)
to candidate Ga0059261_2977 Ga0059261_2977 Sugar phosphate permease
Query= uniprot:A0A166QG26 (467 letters) >FitnessBrowser__Korea:Ga0059261_2977 Length = 432 Score = 347 bits (891), Expect = e-100 Identities = 178/444 (40%), Positives = 248/444 (55%), Gaps = 39/444 (8%) Query: 17 GNYRWTICALLFFATTVNYLDRQVLSLLAPDLSTQFGWSNSDYANIASVFQFVYAISMLF 76 G YRW I ALLF AT +NY+DRQ++ +L P L WS D+A + FQ YAI + Sbjct: 18 GRYRWMIVALLFAATVINYIDRQMIGVLKPTLMQDLHWSERDFAGVIIWFQIAYAIGYIG 77 Query: 77 AGRVVDKIGTKTAYVVAICIWSTGAVMHAFAVPMGEGIGAVSSALGIAMIPVSIAGFMVS 136 G+ VD +G + Y VA IW + H A M + F ++ Sbjct: 78 FGKFVDMVGARVGYAVAFVIWQLAHIAHGGAYSMTQ--------------------FAMA 117 Query: 137 RAVLAIGEAGNFPIAIKATAEYFPKKERSFATGIFNSGANVGAILAPICVPLIASLWGWE 196 R L IGE+GNFP IKA E+FP KER+FA G+FN+GAN+GA++ P+ VPL+ WGW Sbjct: 118 RFGLGIGESGNFPAGIKAVTEWFPAKERAFAIGVFNAGANIGAVITPLVVPLMVIAWGWR 177 Query: 197 AAFIVIGMLGFVWVGVWIALYEKPEQQKRLSAQELAYIRSDQVVPVVTRPVPGVADKKVS 256 AF+V G++ FVW+ W A+Y P Q ++S ELA+I D PV K + Sbjct: 178 MAFVVTGVISFVWLIAWWAMYRSPRQHPKVSEGELAWIEQDPADPV----------KPIG 227 Query: 257 WFKLLTYRQTWAFAFGKFMTDGVWWFFLFWLPTYLSAQYGMKGQAIVMPLAVLYSMTMIG 316 + +LT ++TWA++ GKF D +WWFFLFWLP YL QY + +PLA +Y ++ +G Sbjct: 228 YATVLTRKETWAYSLGKFFIDPIWWFFLFWLPGYLFKQYDLNLLTFGIPLAAIYLISDVG 287 Query: 317 SIGGGWFPSYFMSRGDAPYDGRMKAMLVIAFFPLLVLLAQPLGYISFWVPVLLIGVGASA 376 S+ GGW S M G + R M V A L V+ A+ + S WV VL+IGV + Sbjct: 288 SVFGGWMSSKLMKAGKSANYARKLTMFVCACLVLPVVFAESI--TSVWVAVLVIGVATAG 345 Query: 377 HQAWSCNIFTTVSDMFPQKSIASVVGIGGLAGGLGGVVMTKIGGWVIDHYKLIGDIHTGY 436 HQA+S N++ SD+FP+ ++ SVVGIGG G +GG++M G ++D + Y Sbjct: 346 HQAFSANLYALPSDLFPRGAVGSVVGIGGTVGAVGGILMAFYAGEILDRLGV-------Y 398 Query: 437 MIMFAICALAYLVAWSVMKALVPR 460 +F + AY VA V+ L PR Sbjct: 399 WPLFWVAGSAYFVALLVVHLLSPR 422 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: 762 Number of extensions: 39 Number of successful extensions: 4 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: 432 Length adjustment: 33 Effective length of query: 434 Effective length of database: 399 Effective search space: 173166 Effective search space used: 173166 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