Align Myo-Inositol uptake porter, IolT1 (Km=0.2mM) (characterized)
to candidate AO356_27270 AO356_27270 MFS transporter
Query= TCDB::Q8NTX0 (491 letters) >FitnessBrowser__pseudo5_N2C3_1:AO356_27270 Length = 472 Score = 429 bits (1104), Expect = e-125 Identities = 228/472 (48%), Positives = 314/472 (66%), Gaps = 16/472 (3%) Query: 2 ASTFIQADSPEKSKKLPPLTEGPYRKRLFYVALVATFGGLLFGYDTGVINGALNPMTREL 61 ++TF+ SPEK + ++ L + +ATFGGLLFG+DTGVINGAL M +L Sbjct: 13 SATFV---SPEKHQA---------QRYLQKITWIATFGGLLFGFDTGVINGALLYMKDDL 60 Query: 62 GLTAFTEGVVTSSLLFGAAAGAMFFGRISDNWGRRKTIISLAVAFFVGTMICVFAPSFAV 121 GLT FTEG+V S+LL GA GA+F GR+SD GRR+ I+ LAV FF+G + C AP+ V Sbjct: 61 GLTPFTEGLVASALLIGAMMGALFSGRLSDLKGRRRIILFLAVVFFLGALACALAPTLNV 120 Query: 122 MVVGRVLLGLAVGGASTVVPVYLAELAPFEIRGSLAGRNELMIVVGQLAAFVINAIIGNV 181 MV R LGLAVGGAS VVP YLAE+AP IRG + RNELMIV GQ AF NA +GN+ Sbjct: 121 MVAARFTLGLAVGGASVVVPAYLAEMAPSSIRGRIITRNELMIVTGQFLAFTTNATLGNL 180 Query: 182 FGHHDGVWRYMLAIAAIPAIALFFGMLRVPESPRWLVERGRIDEARAVLETIRPLERAHA 241 F DGVWR+MLA+A +PA+AL+ GML +PESPRWL +GR E VL+ +R A A Sbjct: 181 FSDLDGVWRWMLALATLPAVALWLGMLYMPESPRWLATKGRFREGLEVLKLVREEYYAKA 240 Query: 242 EVADVEHLAREEHAVSEKSMGLREILSSKWLVRILLVGIGLGVAQQLTGINSIMYYGQVV 301 E+ + E + K G R+ LS K RI L+GIG+ V QLTG+NSIMY+G + Sbjct: 241 EMEAITQQISNERFI--KKGGWRD-LSQKGARRIFLIGIGIAVTSQLTGVNSIMYFGTQI 297 Query: 302 LIEAGFSENAALIANVAPGVIAVVGAFIALWMMDRINRRTTLITGYSLTTISHVLIGIAS 361 L EAG + +ALIANV GVI++ F+ + ++DR+ RR ++ G++ TT+S +LIG+ S Sbjct: 298 LTEAGLEQRSALIANVVNGVISIGATFVGIALLDRVGRRPMMLLGFTGTTLSLLLIGLVS 357 Query: 362 VAFPVGDPLRPYVILTLVVVFVGSMQTFLNVATWVMLSELFPLAMRGFAIGISVFFLWIA 421 V F R +IL + +F+ SMQ + A WV+L+E+FP+ +RG +G+++ W+ Sbjct: 358 V-FVDPSVTRAMLILGAMAMFLASMQGLIGPAFWVLLAEIFPMRIRGGCMGMAIAAFWLT 416 Query: 422 NAFLGLFFPTIMEAVGLTGTFFMFAGIGVVALIFIYTQVPETRGRTLEEIDE 473 N +G+FFP+++ +G+ TFF+F G G+++L F+ VPETRG TLEEI++ Sbjct: 417 NVMIGMFFPSLVATIGIGQTFFVFVGAGLLSLTFVAVWVPETRGSTLEEIEQ 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: 629 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