Align Inositol transporter 1 (characterized)
to candidate WP_008629477.1 C943_RS15175 sugar porter family MFS transporter
Query= SwissProt::Q8VZR6 (509 letters) >NCBI__GCF_000330725.2:WP_008629477.1 Length = 447 Score = 244 bits (622), Expect = 6e-69 Identities = 158/452 (34%), Positives = 243/452 (53%), Gaps = 19/452 (4%) Query: 29 SYILGLTVTAGIGGLLFGYDTGVISGALLYIKDDFEVVKQSSFLQETIVSMALVGAMIGA 88 +Y L L++TA +GG LFG+DT VISGA I++ +E+ S L V+MAL G ++GA Sbjct: 5 NYALFLSITAALGGFLFGFDTAVISGAERDIQNLWELDDWSHGLA---VAMALYGTVLGA 61 Query: 89 AAGGWINDYYGRKKATLFADVVFAAGAIVMAAAPDPYVLISGRLLVGLGVGVASVTAPVY 148 GG D YGRK ++ + + A+ A D Y + R + GLGVG +SV AP+Y Sbjct: 62 LLGGIPADKYGRKVTLIWIGIFYFVSALGSALVDDVYSFMFYRFIGGLGVGASSVVAPMY 121 Query: 149 IAEASPSEVRGGLVSTNVLMITGGQFLSYLVNSAF--TQVPGTWRWMLGVSGVPAVIQFI 206 I+E +P++ RG LV+ I G ++Y N + WRWMLGV +PA+I I Sbjct: 122 ISEIAPAKSRGQLVALYQFNIVFGILMAYFSNYLIGTANLDEAWRWMLGVEAIPALIYSI 181 Query: 207 LMLFMPESPRWLFMKNRKAE-AIQVLARTYDISRLEDEIDHLSAAEEEEKQRKRTVGYLD 265 L+L +P+SPRWL K + + A ++L RT D +++ I A EE K K Sbjct: 182 LILKVPKSPRWLIAKKQDYQTAREILTRT-DPEGVDEAI---KLAIEESKSIKGKTSVAA 237 Query: 266 VFRSKELRLAFLAGAGLQAFQQFTGINTVMYYSPTIVQMAGFHSNQLALFLSLIVAAMNA 325 +F S+ +++F A + F Q +GIN ++Y++P I + AG S + ALF ++ + +N Sbjct: 238 LFDSRFRKISFFAFL-MAFFNQMSGINAIIYFAPRIFESAGI-STEDALFSTIGIGVINL 295 Query: 326 AGTVVGIYFIDHCGRKKLALSSLFGVIISLLILSVSFFKQSETSSDGGLYGWLAVLGLAL 385 T+ G+Y ID GRKKL G IISL +++ S+F G + L + + Sbjct: 296 IATMAGLYLIDKLGRKKLMYIGSVGYIISLSLMAYSYF-------GGMISSNLLPYFVFV 348 Query: 386 YIVFFAPGMGPVPWTVNSEIYPQQYRGICGGMSATVNWISNLIVAQTFLTIAEAAGTGMT 445 +I A G G V W +EI+P + R + + +WI ++A F A G G Sbjct: 349 FIASHAIGQGSVIWVFIAEIFPNELRAFGQSLGSFTHWILAALIANVFPFFANTFGAGSI 408 Query: 446 FLILAGIAVLAVIFVIVFVPETQGLTFSEVEQ 477 F A + VL +++V +PET+G + E++Q Sbjct: 409 FAFFALMMVLQLLWVAFRMPETKGKSLEEIQQ 440 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: 509 Number of extensions: 25 Number of successful extensions: 6 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: 447 Length adjustment: 33 Effective length of query: 476 Effective length of database: 414 Effective search space: 197064 Effective search space used: 197064 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: 51 (24.3 bits)
This GapMind analysis is from Sep 24 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