Align Myo-Inositol uptake porter, IolT1 (Km=0.2mM) (characterized)
to candidate BWI76_RS03110 BWI76_RS03110 MFS transporter
Query= TCDB::Q8NTX0 (491 letters) >FitnessBrowser__Koxy:BWI76_RS03110 Length = 499 Score = 387 bits (995), Expect = e-112 Identities = 210/464 (45%), Positives = 297/464 (64%), Gaps = 9/464 (1%) Query: 14 SKKLPPLTEGPYRKRLFYVALVATFGGLLFGYDTGVINGALNPMTRELGLTAFTEGVVTS 73 +K P +E P + VAL+AT GGLLFGYDTGVI+GAL M EL LT FT G+VTS Sbjct: 10 NKASGPNSETPTTPFVKVVALIATLGGLLFGYDTGVISGALLFMGTELHLTPFTTGLVTS 69 Query: 74 SLLFGAAAGAMFFGRISDNWGRRKTIISLAVAFFVGTMICVFAPSFAVMVVGRVLLGLAV 133 SLLFGAA GA+ G +++ GR+K I+ LAV F +G + AP M+ R++LG+AV Sbjct: 70 SLLFGAAFGALLSGNLANAAGRKKIILWLAVLFAIGAIGTSMAPDVNWMIFFRLILGVAV 129 Query: 134 GGASTVVPVYLAELAPFEIRGSLAGRNELMIVVGQLAAFVINAIIGNVFGHHDGVWRYML 193 GGA+ VPVY+AE+AP RG L ELMIV GQL A++ NA V+G + WR+ML Sbjct: 130 GGAAATVPVYIAEIAPANKRGQLVTLQELMIVSGQLLAYISNATFHEVWG-GESTWRWML 188 Query: 194 AIAAIPAIALFFGMLRVPESPRWLVERGRIDEARAVLETIRPLERAHAEVADVEHLAREE 253 A+A +PA+ L+FGM+ +P+SPRW +GR+ EAR VLE R + E+ ++ E+ Sbjct: 189 AVATLPAVLLWFGMMFMPDSPRWYAMKGRLAEARRVLERTRHKDDVEWELLEITETLDEQ 248 Query: 254 HAVSEKSMGLREILSSKWLVRILLVGIGLGVAQQLTGINSIMYYGQVVLIEAGFSENAAL 313 + + EI+ + WL ++ ++GIG+ V QQLTG+N+IMYY VL G ++NAAL Sbjct: 249 RNLGKPRFS--EIM-TPWLFKLFMIGIGIAVIQQLTGVNTIMYYAPTVLTSVGMTDNAAL 305 Query: 314 IANVAPGVIAVVGAFIALWMMDRINRRTTLITGYSLTTISHVLIGIASVAFP-----VGD 368 A +A GV++V+ F+ +WM+ +I RR + G T V IG S P D Sbjct: 306 FATIANGVVSVLMTFVGIWMLGKIGRRPMTMIGQFGCTACLVFIGAVSYLLPETVNGQPD 365 Query: 369 PLRPYVILTLVVVFVGSMQTFLNVATWVMLSELFPLAMRGFAIGISVFFLWIANAFLGLF 428 LR Y++L +++F+ Q L+ TW+++SE+FP +RG +G +VF +WIAN + LF Sbjct: 366 ALRAYMVLAGMLLFLSFQQGALSPVTWLLMSEIFPTRLRGIFMGGAVFSMWIANFLISLF 425 Query: 429 FPTIMEAVGLTGTFFMFAGIGVVALIFIYTQVPETRGRTLEEID 472 FP ++ +GL+GTFF+FAGIGV IF+ VPETR R+LE+I+ Sbjct: 426 FPILLAWLGLSGTFFIFAGIGVFGAIFVIKCVPETRHRSLEQIE 469 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: 627 Number of extensions: 25 Number of successful extensions: 5 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: 499 Length adjustment: 34 Effective length of query: 457 Effective length of database: 465 Effective search space: 212505 Effective search space used: 212505 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