Align Major myo-inositol transporter, IolT1, of 456 aas (characterized)
to candidate Ga0059261_1777 Ga0059261_1777 MFS transporter, sugar porter (SP) family
Query= TCDB::E1WAV3 (456 letters) >FitnessBrowser__Korea:Ga0059261_1777 Length = 458 Score = 256 bits (655), Expect = 8e-73 Identities = 144/438 (32%), Positives = 242/438 (55%), Gaps = 21/438 (4%) Query: 1 MGGILFGYDTAVISGAIGSLTSYFHLSPAETGWAVSCVVVGCVIGSFSAGYLSKRFGRKK 60 +GG+LFG+DTAVISGA +L F L+ A G+ V+ ++G V+GS AG + RFGRK Sbjct: 31 LGGLLFGFDTAVISGATQALQLQFGLTDAMLGFTVASALIGTVLGSLIAGAPADRFGRKG 90 Query: 61 SLMVSALLFTISAVGTSLSYTFTHFVIYRIIGGLAVGLAATVSPMYMSEVSPKNMRGRAL 120 ++ A+ + +S++GT L+ F+++R +GGLA+G A+ V+P+Y++EVSP RGR + Sbjct: 91 VMLTVAIAYVVSSLGTGLAPDLNAFLVFRFMGGLAIGAASVVTPIYIAEVSPARFRGRLV 150 Query: 121 SMQQFAIVFGQILIFYVNYKIASIAADTWLIELGWRYMFAAGIIPCILFCILVFLIPESP 180 +M Q IV G ++ F NY IA + ++ WR+MF +P +F ++ L+PESP Sbjct: 151 AMNQLNIVLGILIAFLSNYIIAGLVQ----YDVAWRWMFGIVAVPSTIFLLVTLLLPESP 206 Query: 181 RWMMMIGREEETLKILTKISNEEHARHLLADIKTSLQNDQLNAHQKLNYRDGNVRFILIL 240 RW+ + G+ + ++ ++ + R LA I+ + ++ +L R + Sbjct: 207 RWLAIHGQADRARDVMQRLGFAD-PRAELARIELAEAREEAAGKPRLFQRSHFTPVACAI 265 Query: 241 GCMIAMLQQVTGVNVMMYYAPIVLKDVTGSAQEALFQTIWIGVIQLIGSIIGAMIMDKMG 300 IAM Q++G+N ++YYAP + + A AL Q+I +G L+ ++ ++D+ G Sbjct: 266 A--IAMFNQLSGINALLYYAPRIFELAGAGADSALLQSIAVGGTNLVFTVAALFLIDRFG 323 Query: 301 RLSLMRKGTIGSIIGLLLTSWALYS-QATGYFALFGMLFFMIFYALSWGVGAWVLISEIF 359 R L+ G++ LLL W L S + G LFG+L F+ +A+S G WV ISE+F Sbjct: 324 RRPLLFVGSVICAATLLLVGWQLESAKPDGTLILFGLLGFIAAFAMSQGAVIWVFISEVF 383 Query: 360 PNRMRSQGMSISVGFMWMANFLVSQFFPMINENPYLLSHFHGAFPMWIFAI---CCIFSY 416 P+ +R +G ++ W+ ++ FP+ F + W+FA + Sbjct: 384 PSAVRGKGQALGSTTHWVMAAAITWAFPV----------FAASVGGWVFAFFGAMMLLQL 433 Query: 417 FFICRYLPETKGISLEKM 434 + +++PET GI+LE M Sbjct: 434 LWTWKFMPETNGIALEDM 451 Lambda K H 0.329 0.141 0.436 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: 579 Number of extensions: 25 Number of successful extensions: 6 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: 456 Length of database: 458 Length adjustment: 33 Effective length of query: 423 Effective length of database: 425 Effective search space: 179775 Effective search space used: 179775 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 (21.8 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