Align Myo-Inositol uptake porter, IolT1 (Km=0.2mM) (characterized)
to candidate WP_007700669.1 AFK65_RS04490 sugar porter family MFS transporter
Query= TCDB::Q8NTX0 (491 letters) >NCBI__GCF_001277175.1:WP_007700669.1 Length = 501 Score = 389 bits (998), Expect = e-112 Identities = 208/459 (45%), Positives = 297/459 (64%), Gaps = 9/459 (1%) Query: 19 PLTEGPYRKRLFYVALVATFGGLLFGYDTGVINGALNPMTRELGLTAFTEGVVTSSLLFG 78 P ++ P + +A++AT GGLLFGYDTGVI+GAL M EL LT T G+VTSSLLFG Sbjct: 15 PNSDAPTAPFVKVIAIIATLGGLLFGYDTGVISGALLFMGSELHLTPLTTGLVTSSLLFG 74 Query: 79 AAAGAMFFGRISDNWGRRKTIISLAVAFFVGTMICVFAPSFAVMVVGRVLLGLAVGGAST 138 AA GA+ G +++ GR+K II LAV F +G + AP + M+ R++LG+AVGGA+ Sbjct: 75 AAFGALLAGHMANAAGRKKIIIYLAVIFAIGAIGTAMAPDVSWMIFFRLVLGVAVGGAAA 134 Query: 139 VVPVYLAELAPFEIRGSLAGRNELMIVVGQLAAFVINAIIGNVFGHHDGVWRYMLAIAAI 198 VPVY+AE+AP RG L ELMIV GQL A++ NA ++G + WR+MLA+A + Sbjct: 135 TVPVYIAEIAPANKRGQLVTLQELMIVSGQLLAYISNASFHELWG-GESTWRWMLAVATL 193 Query: 199 PAIALFFGMLRVPESPRWLVERGRIDEARAVLETIRPLERAHAEVADVEHLAREEHAVSE 258 PA+ L+FGM+ +P++PRW +GR+ EAR VL+ R E E+ ++E + A + Sbjct: 194 PAVLLWFGMMFMPDTPRWYAMKGRLAEARRVLDRTRRPEDVEWELMEIEETLEAQRAQGK 253 Query: 259 KSMGLREILSSKWLVRILLVGIGLGVAQQLTGINSIMYYGQVVLIEAGFSENAALIANVA 318 LRE+L + WL ++ ++GIG+ V QQ+TG+N+IMYY VL G S+NAAL+A VA Sbjct: 254 PR--LRELL-TPWLFKLFMIGIGIAVIQQMTGVNTIMYYAPTVLTAVGMSDNAALVATVA 310 Query: 319 PGVIAVVGAFIALWMMDRINRRTTLITGYSLTTISHVLIGIASVAFP-----VGDPLRPY 373 GV++V+ F+ +WM+ +I RRT + G T V IG S P D LR Y Sbjct: 311 NGVVSVLMTFVGIWMLGKIGRRTMTMIGQFGCTACLVFIGAVSYLLPETVNGQPDALRGY 370 Query: 374 VILTLVVVFVGSMQTFLNVATWVMLSELFPLAMRGFAIGISVFFLWIANAFLGLFFPTIM 433 ++L +++F+ Q L+ TW++LSE+FP +RG +G +VF +WIAN + LFFP ++ Sbjct: 371 MVLAGMLMFLCFQQGALSPVTWLLLSEIFPTRLRGIFMGGAVFSMWIANFLISLFFPILL 430 Query: 434 EAVGLTGTFFMFAGIGVVALIFIYTQVPETRGRTLEEID 472 VGL+GTFF+FA G+V F+ VPETR R+LE+I+ Sbjct: 431 AWVGLSGTFFIFAAFGIVGATFVIKCVPETRNRSLEQIE 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: 645 Number of extensions: 24 Number of successful extensions: 4 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: 501 Length adjustment: 34 Effective length of query: 457 Effective length of database: 467 Effective search space: 213419 Effective search space used: 213419 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 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