Align Inositol transporter 1 (characterized)
to candidate BWI76_RS24055 BWI76_RS24055 MFS transporter
Query= SwissProt::Q8VZR6 (509 letters) >FitnessBrowser__Koxy:BWI76_RS24055 Length = 464 Score = 285 bits (730), Expect = 2e-81 Identities = 162/441 (36%), Positives = 250/441 (56%), Gaps = 14/441 (3%) Query: 38 AGIGGLLFGYDTGVISGALLYIKDDFEVVKQSSFLQETIVSMALVGAMIGAAAGGWINDY 97 A + GLLFG D GVI+GAL +I ++F++ S+ QE +VS + GA +GA GW++ Sbjct: 22 AALAGLLFGLDIGVIAGALPFIANEFQI---SAHTQEWVVSSMMFGAAVGAVGSGWLSFK 78 Query: 98 YGRKKATLFADVVFAAGAIVMAAAPDPYVLISGRLLVGLGVGVASVTAPVYIAEASPSEV 157 GRKK+ + ++F AG++ AAAP+ VL+ R+L+GL VGVAS TAP+Y++E +P ++ Sbjct: 79 LGRKKSLMIGAILFVAGSLFSAAAPNVEVLLISRVLLGLAVGVASYTAPLYLSEIAPEKI 138 Query: 158 RGGLVSTNVLMITGGQFLSYLVNSAFTQVPGTWRWMLGVSGVPAVIQFILMLFMPESPRW 217 RG ++S LMIT G +YL ++AF+ G WRWMLGV +PAV+ I ++F+P+SPRW Sbjct: 139 RGSMISMYQLMITIGILGAYLSDTAFS-YSGAWRWMLGVIIIPAVLLLIGVVFLPDSPRW 197 Query: 218 LFMKNRKAEAIQVLARTYDIS-RLEDEIDHLSAAEEEEKQRKRTVGYLDVFRSKELRLAF 276 K R +A +VL R D S + E+D E E + + G+ + R A Sbjct: 198 FAAKRRFVDAERVLLRLRDTSAEAKRELD-----EIRESLKVKQSGWSLFKENSNFRRAV 252 Query: 277 LAGAGLQAFQQFTGINTVMYYSPTIVQMAGFHSNQLALFLSLIVAAMNAAGTVVGIYFID 336 G LQ QQFTG+N +MYY+P I ++AG+ + ++ ++IV N T + I +D Sbjct: 253 FLGVLLQVMQQFTGMNVIMYYAPKIFELAGYANTTEQMWGTVIVGLTNVLATFIAIGLVD 312 Query: 337 HCGRKKLALSSLFGVIISLLILSVSFFKQSETSSDGGLYGWLAVLGLALYIVFFAPGMGP 396 GRK + + + + IL + AVL L ++IV FA GP Sbjct: 313 RWGRKPTLILGFIVMALGMGILG----SMMHIGIHSATAQYFAVLMLLMFIVGFAMSAGP 368 Query: 397 VPWTVNSEIYPQQYRGICGGMSATVNWISNLIVAQTFLTIAEAAGTGMTFLILAGIAVLA 456 + W + SEI P + R S NWI+N+IV TFLT+ + G+ TF + G+ +L Sbjct: 369 LIWVLCSEIQPLKGRDFGITCSTATNWIANMIVGATFLTMLNSLGSANTFWVYGGLNILF 428 Query: 457 VIFVIVFVPETQGLTFSEVEQ 477 + + +PET+ ++ +E+ Sbjct: 429 IFLTLWLIPETKNVSLEHIER 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: 538 Number of extensions: 25 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 Apr 09 2024. 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