Align Inositol transporter 1 (characterized)
to candidate N515DRAFT_1228 N515DRAFT_1228 MFS transporter, SP family, galactose:H+ symporter
Query= SwissProt::Q8VZR6 (509 letters) >FitnessBrowser__Dyella79:N515DRAFT_1228 Length = 463 Score = 277 bits (709), Expect = 5e-79 Identities = 157/446 (35%), Positives = 248/446 (55%), Gaps = 21/446 (4%) Query: 36 VTAGIGGLLFGYDTGVISGALLYIKDDFEVVKQSSFLQETIVSMALVGAMIGAAAGGWIN 95 V A + GL+FG D GVISGA +IK +F + S E IVS + GA +GA GW++ Sbjct: 22 VLAALAGLMFGLDIGVISGASQFIKAEFAI---SDHTIEWIVSSMMFGAAVGALGAGWLS 78 Query: 96 DYYGRKKATLFADVVFAAGAIVMAAAPDPYVLISGRLLVGLGVGVASVTAPVYIAEASPS 155 + GRK++ + ++F G+++ A P LI+ R+++GL +G+A+ TAP+Y+AE +P Sbjct: 79 SHLGRKRSLILGAILFVIGSLLCGLAWSPETLIAARVILGLAIGIATFTAPLYLAEVAPE 138 Query: 156 EVRGGLVSTNVLMITGGQFLSYLVNSAFTQVPGTWRWMLGVSGVPAVIQFILMLFMPESP 215 +RG ++ST LMIT G +++L ++A + G WRWMLGV +P + + +L +P+SP Sbjct: 139 HIRGAMISTYQLMITIGILVAFLSDTALS-YHGAWRWMLGVIAIPGALFLLGVLGLPDSP 197 Query: 216 RWLFMKNRKAEAIQVLARTYDISRLEDEIDHLSAAEEEEKQRKRTVGYLDVFRSKELRLA 275 RWL M+ R+ EAI VL R R ++ + AA+ EE+ + G+ + R + Sbjct: 198 RWLMMRGRRDEAIDVLRRL----RGDEVVVAREAADIEEQLKTPQRGWDLFAENPNFRRS 253 Query: 276 FLAGAGLQAFQQFTGINTVMYYSPTIVQMAGFHSNQLALFLSLIVAAMNAAGTVVGIYFI 335 GA LQ QQFTG+N VMYY+P I Q G+ ++ + +V N T + I I Sbjct: 254 VFLGALLQIMQQFTGMNVVMYYAPRIFQEMGY-DTAAQMWFTALVGLTNVLATFIAIALI 312 Query: 336 DHCGRKKLALSSLFGVIISLLILSVSFFKQSETSSDGGLYG----WLAVLGLALYIVFFA 391 D GRK + + + + L ++ +GG+ G + V L +IV FA Sbjct: 313 DRWGRKPILYTGFAVMAVGLGVVGALM--------NGGINGQTEQYTCVAMLLFFIVGFA 364 Query: 392 PGMGPVPWTVNSEIYPQQYRGICGGMSATVNWISNLIVAQTFLTIAEAAGTGMTFLILAG 451 GP+ WT+ SEI P + R G+S NWI+N++V TFL++ G TF + A Sbjct: 365 MSAGPLVWTLCSEIQPLKGRDFGIGVSTFTNWITNMVVGFTFLSLLNTIGNASTFWLYAA 424 Query: 452 IAVLAVIFVIVFVPETQGLTFSEVEQ 477 + + ++ VPET+G+T ++E+ Sbjct: 425 LNAVFIVLTFWLVPETKGVTLEQIER 450 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: 552 Number of extensions: 36 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: 463 Length adjustment: 34 Effective length of query: 475 Effective length of database: 429 Effective search space: 203775 Effective search space used: 203775 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