Align Arabinose-proton symporter; Arabinose transporter (characterized)
to candidate Ga0059261_1777 Ga0059261_1777 MFS transporter, sugar porter (SP) family
Query= SwissProt::P96710 (464 letters) >FitnessBrowser__Korea:Ga0059261_1777 Length = 458 Score = 278 bits (712), Expect = 2e-79 Identities = 154/436 (35%), Positives = 250/436 (57%), Gaps = 6/436 (1%) Query: 23 VILISCAAGLGGLLYGYDTAVISGAIGFLKDLYSLSPFMEGLVISSIMIGGVVGVGISGF 82 +IL + A LGGLL+G+DTAVISGA L+ + L+ M G ++S +IG V+G I+G Sbjct: 22 IILSAAGAALGGLLFGFDTAVISGATQALQLQFGLTDAMLGFTVASALIGTVLGSLIAGA 81 Query: 83 LSDRFGRRKILMTAALLFAISAIVSALSQDVSTLIIARIIGGLGIGMGSSLSVTYITEAA 142 +DRFGR+ +++T A+ + +S++ + L+ D++ ++ R +GGL IG S ++ YI E + Sbjct: 82 PADRFGRKGVMLTVAIAYVVSSLGTGLAPDLNAFLVFRFMGGLAIGAASVVTPIYIAEVS 141 Query: 143 PPAIRGSLSSLYQLFTILGISATYFINLAVQRSGTYEWGVHTGWRWMLAYGMVPSVIFFL 202 P RG L ++ QL +LGI + N + +G ++ V WRWM VPS IF L Sbjct: 142 PARFRGRLVAMNQLNIVLGILIAFLSNYII--AGLVQYDV--AWRWMFGIVAVPSTIFLL 197 Query: 203 VLLVVPESPRWLAKAGKTNEALKILTRINGETVAKEELKNIENSLKIEQMGSLSQLFKPG 262 V L++PESPRWLA G+ + A ++ R+ G + EL IE + E+ +LF+ Sbjct: 198 VTLLLPESPRWLAIHGQADRARDVMQRL-GFADPRAELARIELAEAREEAAGKPRLFQRS 256 Query: 263 LRKALVIGILLALFNQVIGMNAITYYGPEIFKMMGFGQNAGFVTTCIVGVVEVIFTVIAV 322 + I +A+FNQ+ G+NA+ YY P IF++ G G ++ + + VG ++FTV A+ Sbjct: 257 HFTPVACAIAIAMFNQLSGINALLYYAPRIFELAGAGADSALLQSIAVGGTNLVFTVAAL 316 Query: 323 LLIDKVGRKKLMSIGSAFMAIFMILIGTSFYFELTSGIMMIVLILGFVAAFCVSVGPITW 382 LID+ GR+ L+ +GS A ++L+G G +++ +LGF+AAF +S G + W Sbjct: 317 FLIDRFGRRPLLFVGSVICAATLLLVGWQLESAKPDGTLILFGLLGFIAAFAMSQGAVIW 376 Query: 383 IMISEIFPNHLRARAAGIATIFLWGANWAIGQFVPMMIDSFGLAYTFWIFAVINILCFLF 442 + ISE+FP+ +R + + + W AI P+ S G + F F + +L L+ Sbjct: 377 VFISEVFPSAVRGKGQALGSTTHWVMAAAITWAFPVFAASVG-GWVFAFFGAMMLLQLLW 435 Query: 443 VVTICPETKNKSLEEI 458 PET +LE++ Sbjct: 436 TWKFMPETNGIALEDM 451 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: 516 Number of extensions: 28 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: 458 Length adjustment: 33 Effective length of query: 431 Effective length of database: 425 Effective search space: 183175 Effective search space used: 183175 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