Align Arabinose-proton symporter; Arabinose transporter (characterized)
to candidate Pf6N2E2_883 Major myo-inositol transporter IolT
Query= SwissProt::P96710 (464 letters) >FitnessBrowser__pseudo6_N2E2:Pf6N2E2_883 Length = 472 Score = 280 bits (716), Expect = 7e-80 Identities = 157/465 (33%), Positives = 257/465 (55%), Gaps = 11/465 (2%) Query: 3 NTPTQLEPNVPVTRSHSMGFVILISCAAGLGGLLYGYDTAVISGAIGFLKDLYSLSPFME 62 NT V + + ++ I+ A GGLL+G+DT VI+GA+ ++KD L+PF E Sbjct: 8 NTADTSAAYVSPEKHQAQRYLQKITWIATFGGLLFGFDTGVINGALLYMKDDLGLTPFTE 67 Query: 63 GLVISSIMIGGVVGVGISGFLSDRFGRRKILMTAALLFAISAIVSALSQDVSTLIIARII 122 GLV S+++IG ++G SG LSD GRR+I++ A++F + A+ AL+ + ++ AR Sbjct: 68 GLVASALLIGAMMGALFSGRLSDLKGRRRIILFLAVVFFLGALACALAPTLDVMVAARFT 127 Query: 123 GGLGIGMGSSLSVTYITEAAPPAIRGSLSSLYQLFTILGISATYFINLAVQRSGTYEWGV 182 GL +G S + Y++E AP +IRG + + +L + G + N + + GV Sbjct: 128 LGLAVGGASVVVPAYLSEMAPSSIRGRIITRNELMIVTGQFLAFTTNATLGNLFSDLDGV 187 Query: 183 HTGWRWMLAYGMVPSVIFFLVLLVVPESPRWLAKAGKTNEALKILTRINGETVAKEELKN 242 WRWMLA +P+V +L +L +PESPRWLA G+ E L++L + E AK E++ Sbjct: 188 ---WRWMLALATLPAVALWLGMLYMPESPRWLATKGRFREGLEVLKLVREEYYAKAEMEA 244 Query: 243 IENSLKIEQM---GSLSQLFKPGLRKALVIGILLALFNQVIGMNAITYYGPEIFKMMGFG 299 I + E+ G L + G R+ +IGI +A+ +Q+ G+N+I Y+G +I G Sbjct: 245 ITQQISNERFIKKGGWRDLSQKGARRIFLIGIGIAVTSQLTGVNSIMYFGTQILTEAGLE 304 Query: 300 QNAGFVTTCIVGVVEVIFTVIAVLLIDKVGRKKLMSIGSAFMAIFMILIGTSFYFELTSG 359 Q + + + G++ + T + + L+D+VGR+ +M +G + ++LIG F + Sbjct: 305 QRSALIANVVNGIISIGATFVGIALLDRVGRRPMMLLGFTGTTLSLLLIGLVSVF-VDPS 363 Query: 360 IMMIVLILGFVAAFCVS----VGPITWIMISEIFPNHLRARAAGIATIFLWGANWAIGQF 415 + +LILG +A F S +GP W++++EIFP +R G+A W N IG F Sbjct: 364 VTRAMLILGAMAMFLASMQGLIGPAFWVLLAEIFPMRIRGGCMGMAIAAFWLTNVMIGMF 423 Query: 416 VPMMIDSFGLAYTFWIFAVINILCFLFVVTICPETKNKSLEEIEK 460 P ++ G+ TF++F +L FV PET+ +LEEIE+ Sbjct: 424 FPSLVAMIGIGQTFFVFVGAGLLSLTFVAVWVPETRGSTLEEIEQ 468 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: 520 Number of extensions: 28 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: 464 Length of database: 472 Length adjustment: 33 Effective length of query: 431 Effective length of database: 439 Effective search space: 189209 Effective search space used: 189209 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