Align Arabinose-proton symporter; Arabinose transporter (characterized)
to candidate Echvi_2810 Echvi_2810 MFS transporter, sugar porter (SP) family
Query= SwissProt::P96710 (464 letters) >FitnessBrowser__Cola:Echvi_2810 Length = 450 Score = 246 bits (628), Expect = 1e-69 Identities = 153/429 (35%), Positives = 225/429 (52%), Gaps = 12/429 (2%) Query: 32 LGGLLYGYDTAVISGAIGFLKDLYSLSPFMEGLVISSIMIGG-VVGVGISGFLSDRFGRR 90 L G L+G+DTAVISGA LK L+ S + G I S+ + G V+G + G GR+ Sbjct: 14 LTGFLFGFDTAVISGANLPLKALWQTSDWFHGFFIMSVALWGTVIGALLGGIPCHHLGRK 73 Query: 91 KILMTAALLFAISAIVSALSQDVSTLIIARIIGGLGIGMGSSLSVTYITEAAPPAIRGSL 150 L ++F +SA+ +AL+ D R +GG+ IG S + TY++E + RG Sbjct: 74 NTLFWIGVMFLVSALGTALATDPFVFSFYRFVGGVAIGASSIAAPTYVSEISQAYQRGRR 133 Query: 151 SSLYQLFTILGISATYFINLAVQRSGTYEWGVHTGWRWMLAYGMVPSVIFFLVLLVVPES 210 LYQ+ + GI Y N +Q G H WRWMLA ++P++I+ +L +PES Sbjct: 134 VGLYQINIVSGILVAYVSNYLLQGVGD-----HNDWRWMLAAEIIPAIIYLAFILDIPES 188 Query: 211 PRWLAKAGKTNEAL-KILTRINGETVAKEELKNIENSLKIEQMGSLSQLFKPGLRKALVI 269 PRWL K A K+L +I + + L +SL+ ++M +LF R L + Sbjct: 189 PRWLILKQKDESAAQKVLKKITTGKIDQLLLSIKHDSLRSKKM----KLFSAKNRLPLFL 244 Query: 270 GILLALFNQVIGMNAITYYGPEIFKMMGFGQNAGFVTTCIVGVVEVIFTVIAVLLIDKVG 329 ++A+FNQ+ G+N I YY PEI + GF + +G +IFT+I + LIDK G Sbjct: 245 AGIIAIFNQLSGINFILYYAPEIMEKAGFVTTTSLLGAVCIGFTNLIFTLIGMSLIDKTG 304 Query: 330 RKKLMSIGSAFMAIFMILIGTSFYFELTSGIMMIVLILGFVAAFCVSVGPITWIMISEIF 389 RK+LM IGS I + L+ FY + +S + ++ IL F+AA + G + W+ ISEIF Sbjct: 305 RKQLMLIGSMGYIISLGLVSYGFY-DSSSPLFILTSILIFIAAHGIGQGAVIWVFISEIF 363 Query: 390 PNHLRARAAGIATIFLWGANWAIGQFVPMMIDSFGLAYTFWIFAVINILCFLFVVTICPE 449 PN +RA WG I F ++ID+ F +F + IL F+FV PE Sbjct: 364 PNKVRAMGQSFGAGVHWGGAAMITLFGAVLIDTLMPFQIFMVFMALMILQFVFVWRYMPE 423 Query: 450 TKNKSLEEI 458 TK LE + Sbjct: 424 TKGLELENL 432 Lambda K H 0.327 0.142 0.425 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: 562 Number of extensions: 30 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: 464 Length of database: 450 Length adjustment: 33 Effective length of query: 431 Effective length of database: 417 Effective search space: 179727 Effective search space used: 179727 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