Align D-fructose transporter, sugar porter family (characterized)
to candidate Echvi_2805 Echvi_2805 MFS transporter, sugar porter (SP) family
Query= reanno::Korea:Ga0059261_1777 (458 letters) >FitnessBrowser__Cola:Echvi_2805 Length = 448 Score = 383 bits (984), Expect = e-111 Identities = 202/436 (46%), Positives = 289/436 (66%), Gaps = 10/436 (2%) Query: 22 IILSAAGAALGGLLFGFDTAVISGATQALQLQFGLTDAMLGFTVASALIGTVLGSLIAGA 81 +I + AALGG LFGFDTAVISGA + +Q ++ L+D G VA AL GTV+G+L G Sbjct: 7 VIFLSIVAALGGFLFGFDTAVISGAERFIQEKWQLSDWTHGMAVAIALYGTVIGALFGGI 66 Query: 82 PADRFGRKGVMLTVAIAYVVSSLGTGLAPDLNAFLVFRFMGGLAIGAASVVTPIYIAEVS 141 PAD++GRK +L + + Y +S+LG+ LAPD+ +F+ FRF+GGL +GA+SVV P+YI+E++ Sbjct: 67 PADKYGRKTSLLWIGVLYFISALGSALAPDVYSFMFFRFIGGLGVGASSVVAPMYISEIA 126 Query: 142 PARFRGRLVAMNQLNIVLGILIAFLSNYIIAGLVQYDVAWRWMFGIVAVPSTIFLLVTLL 201 PA+ RG LVA+ Q NIV GIL+A+ SNY+I + + +WRWM G+ A+P+ I+ L+++ Sbjct: 127 PAKNRGVLVALYQFNIVFGILMAYFSNYLIE-MADLNESWRWMMGMEAIPALIYTLLSIR 185 Query: 202 LPESPRWL-AIHGQADRARDVMQRLGFADPRA--ELARIELAEAREE--AAGKPRLFQRS 256 +P+SPRWL A H + + A ++++ DP E + + E E G LF+ S Sbjct: 186 VPKSPRWLIAHHNKVEEATQILRK---TDPEGVDEAIHLAIEERNREKIKVGFAVLFKHS 242 Query: 257 HFTPVACAIAIAMFNQLSGINALLYYAPRIFELAGAGADSALLQSIAVGGTNLVFTVAAL 316 H AI IA+FNQLSGINA++Y+APR+FE+AG SALL +I +G N++ T+ L Sbjct: 243 HLKTTLLAIMIALFNQLSGINAIIYFAPRVFEMAGIDQKSALLSTIGIGVVNMIATMIGL 302 Query: 317 FLIDRFGRRPLLFVGSVICAATLLLVGWQLESAKPDGTLILFGLLGFIAAFAMSQGAVIW 376 +LIDR GR+ L+ +GS+ +LLL+ + + + + FIA+ A+ QG+VIW Sbjct: 303 YLIDRIGRKKLMVIGSIGYIISLLLMAYSFSGGVINSGYLPLFVFVFIASHAVGQGSVIW 362 Query: 377 VFISEVFPSAVRGKGQALGSTTHWVMAAAITWAFPVFAASVG-GWVFAFFGAMMLLQLLW 435 VFISEVFP+ R GQ++G THW++AA I FP FA S G +F FF MM LQLLW Sbjct: 363 VFISEVFPNETRAFGQSIGCFTHWILAAVIANVFPFFANSFGPASIFGFFAVMMGLQLLW 422 Query: 436 TWKFMPETNGIALEDM 451 MPET G +LE++ Sbjct: 423 VLTKMPETKGRSLEEI 438 Lambda K H 0.327 0.139 0.420 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: 616 Number of extensions: 34 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: 458 Length of database: 448 Length adjustment: 33 Effective length of query: 425 Effective length of database: 415 Effective search space: 176375 Effective search space used: 176375 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