Align Myo-Inositol uptake porter, IolT1 (Km=0.2mM) (characterized)
to candidate Pf6N2E2_883 Major myo-inositol transporter IolT
Query= TCDB::Q8NTX0 (491 letters) >FitnessBrowser__pseudo6_N2E2:Pf6N2E2_883 Length = 472 Score = 427 bits (1097), Expect = e-124 Identities = 219/442 (49%), Positives = 301/442 (68%), Gaps = 4/442 (0%) Query: 32 VALVATFGGLLFGYDTGVINGALNPMTRELGLTAFTEGVVTSSLLFGAAAGAMFFGRISD 91 + +ATFGGLLFG+DTGVINGAL M +LGLT FTEG+V S+LL GA GA+F GR+SD Sbjct: 31 ITWIATFGGLLFGFDTGVINGALLYMKDDLGLTPFTEGLVASALLIGAMMGALFSGRLSD 90 Query: 92 NWGRRKTIISLAVAFFVGTMICVFAPSFAVMVVGRVLLGLAVGGASTVVPVYLAELAPFE 151 GRR+ I+ LAV FF+G + C AP+ VMV R LGLAVGGAS VVP YL+E+AP Sbjct: 91 LKGRRRIILFLAVVFFLGALACALAPTLDVMVAARFTLGLAVGGASVVVPAYLSEMAPSS 150 Query: 152 IRGSLAGRNELMIVVGQLAAFVINAIIGNVFGHHDGVWRYMLAIAAIPAIALFFGMLRVP 211 IRG + RNELMIV GQ AF NA +GN+F DGVWR+MLA+A +PA+AL+ GML +P Sbjct: 151 IRGRIITRNELMIVTGQFLAFTTNATLGNLFSDLDGVWRWMLALATLPAVALWLGMLYMP 210 Query: 212 ESPRWLVERGRIDEARAVLETIRPLERAHAEVADVEHLAREEHAVSEKSMGLREILSSKW 271 ESPRWL +GR E VL+ +R A AE+ + E + K G R+ LS K Sbjct: 211 ESPRWLATKGRFREGLEVLKLVREEYYAKAEMEAITQQISNERFI--KKGGWRD-LSQKG 267 Query: 272 LVRILLVGIGLGVAQQLTGINSIMYYGQVVLIEAGFSENAALIANVAPGVIAVVGAFIAL 331 RI L+GIG+ V QLTG+NSIMY+G +L EAG + +ALIANV G+I++ F+ + Sbjct: 268 ARRIFLIGIGIAVTSQLTGVNSIMYFGTQILTEAGLEQRSALIANVVNGIISIGATFVGI 327 Query: 332 WMMDRINRRTTLITGYSLTTISHVLIGIASVAFPVGDPLRPYVILTLVVVFVGSMQTFLN 391 ++DR+ RR ++ G++ TT+S +LIG+ SV F R +IL + +F+ SMQ + Sbjct: 328 ALLDRVGRRPMMLLGFTGTTLSLLLIGLVSV-FVDPSVTRAMLILGAMAMFLASMQGLIG 386 Query: 392 VATWVMLSELFPLAMRGFAIGISVFFLWIANAFLGLFFPTIMEAVGLTGTFFMFAGIGVV 451 A WV+L+E+FP+ +RG +G+++ W+ N +G+FFP+++ +G+ TFF+F G G++ Sbjct: 387 PAFWVLLAEIFPMRIRGGCMGMAIAAFWLTNVMIGMFFPSLVAMIGIGQTFFVFVGAGLL 446 Query: 452 ALIFIYTQVPETRGRTLEEIDE 473 +L F+ VPETRG TLEEI++ Sbjct: 447 SLTFVAVWVPETRGSTLEEIEQ 468 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: 623 Number of extensions: 20 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: 472 Length adjustment: 34 Effective length of query: 457 Effective length of database: 438 Effective search space: 200166 Effective search space used: 200166 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 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