Align Major myo-inositol transporter IolT (characterized)
to candidate 353923 BT4397 xylose/H+ symporter (NCBI ptt file)
Query= SwissProt::O34718 (473 letters) >FitnessBrowser__Btheta:353923 Length = 460 Score = 248 bits (633), Expect = 3e-70 Identities = 162/464 (34%), Positives = 248/464 (53%), Gaps = 33/464 (7%) Query: 10 FLRTIILVSTFGGLLFGYDTGVLNGALP----YMGEPDQLNLNAFTEGLVTSSLLFGAAL 65 F+ +I LVS GGLLFGYD V+ GA P Y G D + +GL S L G + Sbjct: 8 FVYSICLVSAMGGLLFGYDWVVIGGAKPFYELYFGIADSPTM----QGLAMSVALLGCLI 63 Query: 66 GAVFGGRMSDFNGRRKNILFLAVIFFISTIGCTFAPNVTVMIISRFVLGIAVGGASVTVP 125 GA+ G M+D GR+ +L A IF S + + +RF+ GI +G AS P Sbjct: 64 GAMVAGMMADRYGRKPLLLISAFIFLSSAYATGAFSVFSWFLAARFLGGIGIGIASGLSP 123 Query: 126 AYLAEMSPVESRGRMVTQNELMIVSGQLLAFVFNAILGTTMG------------DNSHVW 173 Y+AE++P RG++V+ N+L IV G L A + N ++ + + W Sbjct: 124 MYIAEVAPTSIRGKLVSLNQLTIVLGILGAQIANWLIAEPIPADFTPADICASWNGQMGW 183 Query: 174 RFMLVIASLPALFLFFGMIRMPESPRWLVSKGRKEDALRVLKKIRDEKRAAAELQEIE-- 231 R+M A+ PA +PESPRWL KG++E A VL +I + A ELQ +E Sbjct: 184 RWMFWGAAFPAAVFLLLACFIPESPRWLAMKGKREKAWSVLSRIGGNRYAEQELQMVEQT 243 Query: 232 FAFKKEDQLEKATFKDLSVPWVRRIVFIGLGIAIVQQITGVNSIMYYGTEILRNSGFQTE 291 A K E L+ S P+ R+++ +G+ +A+ QQ G N I Y EI +++G+ Sbjct: 244 SASKSEGGLKLL----FSRPF-RKVLVLGVIVAVFQQWCGTNVIFNYAQEIFQSAGYSLG 298 Query: 292 AALIGNIANGVISVLATFVGIWLLGRVGRRPMLMTGLIGTTTALLLIGI-FSLVLEGSPA 350 L + GV +V+ TFV I+ + R+GRR +++ G G L++G + + G Sbjct: 299 DVLFNIVVTGVANVIFTFVAIYTVERLGRRALMLLGAGGLAGIYLVLGTCYFFQVSG--- 355 Query: 351 LPYVVLSLTVTFLAFQQGAISPVTWLMLSEIFPLRLRGLGMGVTVFCLWMVNFAVSFTFP 410 + ++ L V +A ++ P+TW++L+EIFP R+RG+ M F LW+ +F +++TFP Sbjct: 356 --FFMVVLVVLAIACYAMSLGPITWVLLAEIFPNRVRGVAMATCTFALWVGSFTLTYTFP 413 Query: 411 ILLAAIGLSTTFFIFVGLGICSVLFVKRFLPETKGLSLEQLEEN 454 +L A+G TF+I+ + + LF R LPETKG SLE LE++ Sbjct: 414 LLNTALGSYGTFWIYSAICVFGFLFFLRALPETKGKSLETLEKD 457 Lambda K H 0.327 0.142 0.418 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: 580 Number of extensions: 31 Number of successful extensions: 7 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: 473 Length of database: 460 Length adjustment: 33 Effective length of query: 440 Effective length of database: 427 Effective search space: 187880 Effective search space used: 187880 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 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