Align Inositol transporter 1 (characterized)
to candidate 17022 b2943 D-galactose transporter (NCBI)
Query= SwissProt::Q8VZR6 (509 letters) >FitnessBrowser__Keio:17022 Length = 464 Score = 283 bits (725), Expect = 7e-81 Identities = 165/447 (36%), Positives = 256/447 (57%), Gaps = 26/447 (5%) Query: 38 AGIGGLLFGYDTGVISGALLYIKDDFEVVKQSSFLQETIVSMALVGAMIGAAAGGWINDY 97 A + GLLFG D GVI+GAL +I D+F++ +S QE +VS + GA +GA GW++ Sbjct: 22 AALAGLLFGLDIGVIAGALPFIADEFQI---TSHTQEWVVSSMMFGAAVGAVGSGWLSFK 78 Query: 98 YGRKKATLFADVVFAAGAIVMAAAPDPYVLISGRLLVGLGVGVASVTAPVYIAEASPSEV 157 GRKK+ + ++F AG++ AAAP+ VLI R+L+GL VGVAS TAP+Y++E +P ++ Sbjct: 79 LGRKKSLMIGAILFVAGSLFSAAAPNVEVLILSRVLLGLAVGVASYTAPLYLSEIAPEKI 138 Query: 158 RGGLVSTNVLMITGGQFLSYLVNSAFTQVPGTWRWMLGVSGVPAVIQFILMLFMPESPRW 217 RG ++S LMIT G +YL ++AF+ G WRWMLGV +PA++ I + F+P+SPRW Sbjct: 139 RGSMISMYQLMITIGILGAYLSDTAFSYT-GAWRWMLGVIIIPAILLLIGVFFLPDSPRW 197 Query: 218 LFMKNRKAEAIQVLARTYDIS-RLEDEIDHLSAAEEEEKQRKRTVGYLDVFRSKELRLAF 276 K R +A +VL R D S + E+D E E + + G+ + R A Sbjct: 198 FAAKRRFVDAERVLLRLRDTSAEAKRELD-----EIRESLQVKQSGWALFKENSNFRRAV 252 Query: 277 LAGAGLQAFQQFTGINTVMYYSPTIVQMAGFHSNQLALFLSLIVAAMNAAGTVVGIYFID 336 G LQ QQFTG+N +MYY+P I ++AG+ + ++ ++IV N T + I +D Sbjct: 253 FLGVLLQVMQQFTGMNVIMYYAPKIFELAGYTNTTEQMWGTVIVGLTNVLATFIAIGLVD 312 Query: 337 HCGRKK------LALSSLFGVIISLLILSVSFFKQSETSSDGGLYGWLAVLGLALYIVFF 390 GRK L +++ GV+ +++ + + S ++ + A+ L ++IV F Sbjct: 313 RWGRKPTLTLGFLVMAAGMGVLGTMMHIGI----HSPSAQ------YFAIAMLLMFIVGF 362 Query: 391 APGMGPVPWTVNSEIYPQQYRGICGGMSATVNWISNLIVAQTFLTIAEAAGTGMTFLILA 450 A GP+ W + SEI P + R S NWI+N+IV TFLT+ G TF + A Sbjct: 363 AMSAGPLIWVLCSEIQPLKGRDFGITCSTATNWIANMIVGATFLTMLNTLGNANTFWVYA 422 Query: 451 GIAVLAVIFVIVFVPETQGLTFSEVEQ 477 + VL ++ + VPET+ ++ +E+ Sbjct: 423 ALNVLFILLTLWLVPETKHVSLEHIER 449 Lambda K H 0.323 0.138 0.406 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: 534 Number of extensions: 19 Number of successful extensions: 5 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: 509 Length of database: 464 Length adjustment: 34 Effective length of query: 475 Effective length of database: 430 Effective search space: 204250 Effective search space used: 204250 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.9 bits) S2: 52 (24.6 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