Align Myo-Inositol uptake porter, IolT1 (Km=0.2mM) (characterized)
to candidate WP_084931443.1 HA51_RS01415 sugar porter family MFS transporter
Query= TCDB::Q8NTX0 (491 letters) >NCBI__GCF_002095475.1:WP_084931443.1 Length = 477 Score = 334 bits (856), Expect = 5e-96 Identities = 189/465 (40%), Positives = 283/465 (60%), Gaps = 19/465 (4%) Query: 20 LTEGPYRKRLFYVALVATFGGLLFGYDTGVINGALNPMTRELGLTAFTEGVVTSSLLFGA 79 + P KR + LV+T GGL FGYDTGVI+GAL MT++LGL+ +EG++TSSLLFGA Sbjct: 15 IAASPNMKR---ITLVSTIGGLCFGYDTGVISGALLFMTKDLGLSPTSEGIITSSLLFGA 71 Query: 80 AAGAMFFGRISDNWGRRKTIISLAVAFFVGTMICVFAPSFAVMVVGRVLLGLAVGGASTV 139 A G++F G +SD GRRK ++ +A+ F G + A M+ R +LGLAVG AS Sbjct: 72 AFGSLFGGLLSDRQGRRKNLLWVAIIFIFGALATAVAWDITSMLAARFILGLAVGCASVT 131 Query: 140 VPVYLAELAPFEIRGSLAGRNELMIVVGQLAAFVINAIIGNVFGHHDGVWRYMLAIAAIP 199 VPVY+AELAP R L NELMIV GQ A+ +NA I N + WR MLAI AIP Sbjct: 132 VPVYIAELAPANQRERLVTVNELMIVTGQFLAYSVNAGIVNAYPELSHNWRIMLAIPAIP 191 Query: 200 AIALFFGMLRVPESPRWLVERGRIDEARAVLETIRPLERAHAEVADVEHLAREEHAVSEK 259 + L+FGM+ +PESPR+ ++RG+ EAR VL +R E+ D+ ++ A+ Sbjct: 192 GVLLWFGMMMMPESPRFFLQRGKEKEARHVLSGVREPGEIDKEIEDIRNII----ALDAS 247 Query: 260 SMGLREILSSKWLVRILLVGIGLGVAQQLTGINSIMYYGQVVLIEAGFSENAALIANVAP 319 LR+ LS KW+++++L+G+ + +A ++TG+N+IMYY VL G + AA+ A VA Sbjct: 248 QPSLRQELSKKWVIQLILIGLMIVLATRVTGVNTIMYYAPTVLKSTGLGDAAAVTAAVAN 307 Query: 320 GVIAVVGAFIALWMMDRINRRTTLITGYSLTTISHVLIGIASVAF---PVGDPL------ 370 G+I+++ + + ++ + RR ++G T+ V+IG+A F + D + Sbjct: 308 GLISILATILGMALIGKFPRRKMFLSGQIGVTVVLVMIGLAFKMFFHTEIRDGVSVLQGN 367 Query: 371 ---RPYVILTLVVVFVGSMQTFLNVATWVMLSELFPLAMRGFAIGISVFFLWIANAFLGL 427 Y+IL L+ +F+ MQ ++ W+MLSE++PL +RG +GI+VF L+ + + Sbjct: 368 FEGASYIILGLMSLFLVFMQGWIAPVFWLMLSEIYPLRIRGLGMGIAVFGLFAFDFVIQS 427 Query: 428 FFPTIMEAVGLTGTFFMFAGIGVVALIFIYTQVPETRGRTLEEID 472 FP ++ A G TF +FAG +V L ++ +PETRG +LEEI+ Sbjct: 428 LFPIMLNAWGGGATFGIFAGCNLVMLALLFKFLPETRGLSLEEIE 472 Lambda K H 0.327 0.142 0.420 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: 556 Number of extensions: 21 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: 491 Length of database: 477 Length adjustment: 34 Effective length of query: 457 Effective length of database: 443 Effective search space: 202451 Effective search space used: 202451 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: 52 (24.6 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