Align Myo-Inositol uptake porter, IolT1 (Km=0.2mM) (characterized)
to candidate WP_084931685.1 HA51_RS02405 sugar porter family MFS transporter
Query= TCDB::Q8NTX0 (491 letters) >NCBI__GCF_002095475.1:WP_084931685.1 Length = 469 Score = 331 bits (849), Expect = 3e-95 Identities = 187/464 (40%), Positives = 278/464 (59%), Gaps = 18/464 (3%) Query: 22 EGPYRKRLFYVALVATFGGLLFGYDTGVINGALNPMTRELGLTAFTEGVVTSSLLFGAAA 81 + P R RL + +V+T GGL FGYDTGVI+GAL M +L LT EG +TS LLFGAA Sbjct: 8 QNPQRMRL--ITIVSTIGGLCFGYDTGVISGALIFMKYDLNLTPTQEGFITSFLLFGAAL 65 Query: 82 GAMFFGRISDNWGRRKTIISLAVAFFVGTMICVFAPSFAVMVVGRVLLGLAVGGASTVVP 141 G++F G +SD GRRK ++ +A F G + FA M+V R +LGLAVG AS VP Sbjct: 66 GSLFGGYLSDKQGRRKNLLWVAAIFMFGALGTAFAWDVPSMIVARFILGLAVGCASVTVP 125 Query: 142 VYLAELAPFEIRGSLAGRNELMIVVGQLAAFVINAIIGNVFGHHDGVWRYMLAIAAIPAI 201 +Y++ELA + R L NELMIV GQ A+ +NA I N++ WR MLAI A+P Sbjct: 126 IYISELARADQRERLVTVNELMIVTGQFLAYSVNAAIVNLYPEMQHNWRIMLAIPALPGA 185 Query: 202 ALFFGMLRVPESPRWLVERGRIDEARAVLETIRPLERAHAEVADVEHLAREEHAVSEKSM 261 L+FGML +PESPR+ + RG ++A VL+T+R E EV +++ + + + E Sbjct: 186 LLWFGMLMMPESPRFFIRRGETEKAVKVLKTLRLPEEVDREVKEIQQIVKAD----EVKF 241 Query: 262 GLREILSSKWLVRILLVGIGLGVAQQLTGINSIMYYGQVVLIEAGFSENAALIANVAPGV 321 L L ++W+++++L+G+ + +A ++TG+N+IMYY VL G + AA+ VA G+ Sbjct: 242 NLFAELKNRWVIQLVLIGLMIVLATRVTGVNTIMYYAPTVLKATGLGDAAAVTGAVANGI 301 Query: 322 IAVVGAFIALWMMDRINRRTTLITGYSLTTISHVLIGIASVAFPVGDPLR---------- 371 I+V+ + + ++ + +RR TG + T+S VLIG+A F + + Sbjct: 302 ISVLATLLGMALIGKHSRRKMFFTGQAGVTVSLVLIGLAFKLFFHTETINGVDTLHANFA 361 Query: 372 --PYVILTLVVVFVGSMQTFLNVATWVMLSELFPLAMRGFAIGISVFFLWIANAFLGLFF 429 PYVIL L++VF+ MQ ++ W+ML+E++PL MRG +G +VF LWI + + F Sbjct: 362 NAPYVILGLMLVFLVFMQGWIAPVFWLMLAEIYPLRMRGVGMGFAVFGLWIFDFMIQSIF 421 Query: 430 PTIMEAVGLTGTFFMFAGIGVVALIFIYTQVPETRGRTLEEIDE 473 P ++ G TF F V+ LI + +PETRG TLE+I++ Sbjct: 422 PYLLGHYGGGMTFGFFGATNVIMLILLVKYLPETRGLTLEQIEK 465 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: 572 Number of extensions: 26 Number of successful extensions: 3 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: 469 Length adjustment: 34 Effective length of query: 457 Effective length of database: 435 Effective search space: 198795 Effective search space used: 198795 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: 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