Align Major myo-inositol transporter, IolT1, of 456 aas (characterized)
to candidate Echvi_2810 Echvi_2810 MFS transporter, sugar porter (SP) family
Query= TCDB::E1WAV3 (456 letters) >FitnessBrowser__Cola:Echvi_2810 Length = 450 Score = 244 bits (623), Expect = 4e-69 Identities = 148/445 (33%), Positives = 238/445 (53%), Gaps = 19/445 (4%) Query: 3 GILFGYDTAVISGAIGSLTSYFHLSPAETGWAVSCVVV-GCVIGSFSAGYLSKRFGRKKS 61 G LFG+DTAVISGA L + + S G+ + V + G VIG+ G GRK + Sbjct: 16 GFLFGFDTAVISGANLPLKALWQTSDWFHGFFIMSVALWGTVIGALLGGIPCHHLGRKNT 75 Query: 62 LMVSALLFTISAVGTSLSYTFTHFVIYRIIGGLAVGLAATVSPMYMSEVSPKNMRGRALS 121 L ++F +SA+GT+L+ F YR +GG+A+G ++ +P Y+SE+S RGR + Sbjct: 76 LFWIGVMFLVSALGTALATDPFVFSFYRFVGGVAIGASSIAAPTYVSEISQAYQRGRRVG 135 Query: 122 MQQFAIVFGQILIFYVNYKIASIAADTWLIELGWRYMFAAGIIPCILFCILVFLIPESPR 181 + Q IV G ++ + NY + + WR+M AA IIP I++ + IPESPR Sbjct: 136 LYQINIVSGILVAYVSNYLLQGVGDHN-----DWRWMLAAEIIPAIIYLAFILDIPESPR 190 Query: 182 WMMMIGREEETL-KILTKISNEEHARHLLADIKTSLQNDQLNAHQKLNYRDGNVRFILIL 240 W+++ ++E K+L KI+ + + LL S+++D L + +K+ R L L Sbjct: 191 WLILKQKDESAAQKVLKKITTGKIDQLLL-----SIKHDSLRS-KKMKLFSAKNRLPLFL 244 Query: 241 GCMIAMLQQVTGVNVMMYYAPIVLKDVTGSAQEALFQTIWIGVIQLIGSIIGAMIMDKMG 300 +IA+ Q++G+N ++YYAP +++ +L + IG LI ++IG ++DK G Sbjct: 245 AGIIAIFNQLSGINFILYYAPEIMEKAGFVTTTSLLGAVCIGFTNLIFTLIGMSLIDKTG 304 Query: 301 RLSLMRKGTIGSIIGLLLTSWALYSQATGYFALFGMLFFMIFYALSWGVGAWVLISEIFP 360 R LM G++G II L L S+ Y ++ F L +L F+ + + G WV ISEIFP Sbjct: 305 RKQLMLIGSMGYIISLGLVSYGFYDSSSPLFILTSILIFIAAHGIGQGAVIWVFISEIFP 364 Query: 361 NRMRSQGMSISVGFMWMANFLVSQFFPMINENPYLLSHFHGAFPMWIFAICCIFSYFFIC 420 N++R+ G S G W +++ F ++ + F +F I + F+ Sbjct: 365 NKVRAMGQSFGAGVHWGGAAMITLFGAVLIDTLMPFQIF------MVFMALMILQFVFVW 418 Query: 421 RYLPETKGISLEKMESVVLAKRRKK 445 RY+PETKG+ LE + S + K +K Sbjct: 419 RYMPETKGLELENLHSKLAQKLYEK 443 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: 583 Number of extensions: 35 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: 456 Length of database: 450 Length adjustment: 33 Effective length of query: 423 Effective length of database: 417 Effective search space: 176391 Effective search space used: 176391 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