Align Arabinose-proton symporter; Arabinose transporter (characterized)
to candidate AO356_27270 AO356_27270 MFS transporter
Query= SwissProt::P96710 (464 letters) >FitnessBrowser__pseudo5_N2C3_1:AO356_27270 Length = 472 Score = 281 bits (718), Expect = 4e-80 Identities = 155/442 (35%), Positives = 251/442 (56%), Gaps = 11/442 (2%) Query: 26 ISCAAGLGGLLYGYDTAVISGAIGFLKDLYSLSPFMEGLVISSIMIGGVVGVGISGFLSD 85 I+ A GGLL+G+DT VI+GA+ ++KD L+PF EGLV S+++IG ++G SG LSD Sbjct: 31 ITWIATFGGLLFGFDTGVINGALLYMKDDLGLTPFTEGLVASALLIGAMMGALFSGRLSD 90 Query: 86 RFGRRKILMTAALLFAISAIVSALSQDVSTLIIARIIGGLGIGMGSSLSVTYITEAAPPA 145 GRR+I++ A++F + A+ AL+ ++ ++ AR GL +G S + Y+ E AP + Sbjct: 91 LKGRRRIILFLAVVFFLGALACALAPTLNVMVAARFTLGLAVGGASVVVPAYLAEMAPSS 150 Query: 146 IRGSLSSLYQLFTILGISATYFINLAVQRSGTYEWGVHTGWRWMLAYGMVPSVIFFLVLL 205 IRG + + +L + G + N + + GV WRWMLA +P+V +L +L Sbjct: 151 IRGRIITRNELMIVTGQFLAFTTNATLGNLFSDLDGV---WRWMLALATLPAVALWLGML 207 Query: 206 VVPESPRWLAKAGKTNEALKILTRINGETVAKEELKNIENSLKIEQM---GSLSQLFKPG 262 +PESPRWLA G+ E L++L + E AK E++ I + E+ G L + G Sbjct: 208 YMPESPRWLATKGRFREGLEVLKLVREEYYAKAEMEAITQQISNERFIKKGGWRDLSQKG 267 Query: 263 LRKALVIGILLALFNQVIGMNAITYYGPEIFKMMGFGQNAGFVTTCIVGVVEVIFTVIAV 322 R+ +IGI +A+ +Q+ G+N+I Y+G +I G Q + + + GV+ + T + + Sbjct: 268 ARRIFLIGIGIAVTSQLTGVNSIMYFGTQILTEAGLEQRSALIANVVNGVISIGATFVGI 327 Query: 323 LLIDKVGRKKLMSIGSAFMAIFMILIGTSFYFELTSGIMMIVLILGFVAAFCVS----VG 378 L+D+VGR+ +M +G + ++LIG F + + +LILG +A F S +G Sbjct: 328 ALLDRVGRRPMMLLGFTGTTLSLLLIGLVSVF-VDPSVTRAMLILGAMAMFLASMQGLIG 386 Query: 379 PITWIMISEIFPNHLRARAAGIATIFLWGANWAIGQFVPMMIDSFGLAYTFWIFAVINIL 438 P W++++EIFP +R G+A W N IG F P ++ + G+ TF++F +L Sbjct: 387 PAFWVLLAEIFPMRIRGGCMGMAIAAFWLTNVMIGMFFPSLVATIGIGQTFFVFVGAGLL 446 Query: 439 CFLFVVTICPETKNKSLEEIEK 460 FV PET+ +LEEIE+ Sbjct: 447 SLTFVAVWVPETRGSTLEEIEQ 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: 518 Number of extensions: 27 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