Align Major myo-inositol transporter IolT (characterized)
to candidate CA265_RS23325 CA265_RS23325 MFS transporter
Query= SwissProt::O34718 (473 letters) >FitnessBrowser__Pedo557:CA265_RS23325 Length = 443 Score = 270 bits (691), Expect = 6e-77 Identities = 153/454 (33%), Positives = 259/454 (57%), Gaps = 17/454 (3%) Query: 1 MNKQGNQMSFLRTIILVSTFGGLLFGYDTGVLNGALPYMGEPDQLNLNAFTEGLVTSSLL 60 M++ +++ I L++ GG LFG+D V++G+LP++ + Q L + EG T SL Sbjct: 1 MSQSKFNTAYITFISLLAAGGGYLFGFDFAVISGSLPFLEK--QFQLTPYWEGFATGSLA 58 Query: 61 FGAALGAVFGGRMSDFNGRRKNILFLAVIFFISTIGCTFAPNVTVMIISRFVLGIAVGGA 120 GA +G + G +SD GR+ ++ A +F S++ APN I+SRF GI VG A Sbjct: 59 LGAMVGCLIAGYVSDAYGRKPGLMIAAFVFLASSLAMAMAPNRDFFIVSRFFSGIGVGMA 118 Query: 121 SVTVPAYLAEMSPVESRGRMVTQNELMIVSGQLLAFVFNAILGTTMGDNSHVWRFMLVIA 180 S+ P Y+AE++P + RGR+V N+L IV G L+ + N L T D WR+M + Sbjct: 119 SMLSPMYIAELAPPKFRGRLVAINQLTIVLGILITNLINYTLRNTGED---AWRWMFGLG 175 Query: 181 SLPALFLFFGMIRMPESPRWLVSKGRKEDALRVLKKIRDEKRAAAELQEIEFAFKKEDQL 240 ++P+ G+ +PESPRWLV KG+ E AL+VL KI + + AA L+ IE +++ + Sbjct: 176 AIPSGIFLIGISILPESPRWLVQKGKNEKALKVLNKIGNHEFAADALKNIEQTLQRKSNV 235 Query: 241 E-KATFKDLSVPWVRRIVFIGLGIAIVQQITGVNSIMYYGTEILRNSGFQTEAALIGNIA 299 E ++ F + P V IG+G+AI QQ G+N++ Y ++ + G + L+ + Sbjct: 236 EHESIFNKMYFP----AVMIGIGLAIFQQFCGINTVFNYAPKLFESIGTSQDDQLLQTVF 291 Query: 300 NGVISVLATFVGIWLLGRVGRRPMLMTGLIGTTTALLLIGIFSLVLEGSPALPYVVLSLT 359 G ++V+ T ++L+ ++GR+P+++ G G A+L + I L+ GS + + +LS Sbjct: 292 IGAVNVIFTISAMFLVDKIGRKPLMLIGAGG--LAVLYVLISQLLASGSTMVSWFLLSAI 349 Query: 360 VTFLAFQQGAISPVTWLMLSEIFPLRLRGLGMGVTVFCLWMVNFAVSFTFPILLAAIGLS 419 + +++PVTW+++SEIFP ++R + CLW F + FTFPIL + Sbjct: 350 GVYAV----SLAPVTWVLISEIFPNKVRVKATTWAILCLWGAYFVLVFTFPILFDWL-KE 404 Query: 420 TTFFIFVGLGICSVLFVKRFLPETKGLSLEQLEE 453 + F+I+ + + + +F+ ETKG +LE++E+ Sbjct: 405 SIFYIYAAICTLGCIGIWKFVKETKGKTLEEIED 438 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: 552 Number of extensions: 32 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: 473 Length of database: 443 Length adjustment: 33 Effective length of query: 440 Effective length of database: 410 Effective search space: 180400 Effective search space used: 180400 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