Align D-fructose transporter, sugar porter family (characterized)
to candidate WP_008629477.1 C943_RS15175 sugar porter family MFS transporter
Query= reanno::Korea:Ga0059261_1777 (458 letters) >NCBI__GCF_000330725.2:WP_008629477.1 Length = 447 Score = 374 bits (961), Expect = e-108 Identities = 208/438 (47%), Positives = 291/438 (66%), Gaps = 13/438 (2%) Query: 21 AIILSAAGAALGGLLFGFDTAVISGATQALQLQFGLTDAMLGFTVASALIGTVLGSLIAG 80 A+ LS AALGG LFGFDTAVISGA + +Q + L D G VA AL GTVLG+L+ G Sbjct: 7 ALFLSIT-AALGGFLFGFDTAVISGAERDIQNLWELDDWSHGLAVAMALYGTVLGALLGG 65 Query: 81 APADRFGRKGVMLTVAIAYVVSSLGTGLAPDLNAFLVFRFMGGLAIGAASVVTPIYIAEV 140 PAD++GRK ++ + I Y VS+LG+ L D+ +F+ +RF+GGL +GA+SVV P+YI+E+ Sbjct: 66 IPADKYGRKVTLIWIGIFYFVSALGSALVDDVYSFMFYRFIGGLGVGASSVVAPMYISEI 125 Query: 141 SPARFRGRLVAMNQLNIVLGILIAFLSNYIIAGLVQYDVAWRWMFGIVAVPSTIFLLVTL 200 +PA+ RG+LVA+ Q NIV GIL+A+ SNY+I G D AWRWM G+ A+P+ I+ ++ L Sbjct: 126 APAKSRGQLVALYQFNIVFGILMAYFSNYLI-GTANLDEAWRWMLGVEAIPALIYSILIL 184 Query: 201 LLPESPRWLAIHGQ-ADRARDVMQRLGFADPRAELARIELA-EAREEAAGK---PRLFQR 255 +P+SPRWL Q AR+++ R DP I+LA E + GK LF Sbjct: 185 KVPKSPRWLIAKKQDYQTAREILTR---TDPEGVDEAIKLAIEESKSIKGKTSVAALFD- 240 Query: 256 SHFTPVA-CAIAIAMFNQLSGINALLYYAPRIFELAGAGADSALLQSIAVGGTNLVFTVA 314 S F ++ A +A FNQ+SGINA++Y+APRIFE AG + AL +I +G NL+ T+A Sbjct: 241 SRFRKISFFAFLMAFFNQMSGINAIIYFAPRIFESAGISTEDALFSTIGIGVINLIATMA 300 Query: 315 ALFLIDRFGRRPLLFVGSVICAATLLLVGWQLESAKPDGTLILFGLLGFIAAFAMSQGAV 374 L+LID+ GR+ L+++GSV +L L+ + L+ + + FIA+ A+ QG+V Sbjct: 301 GLYLIDKLGRKKLMYIGSVGYIISLSLMAYSYFGGMISSNLLPYFVFVFIASHAIGQGSV 360 Query: 375 IWVFISEVFPSAVRGKGQALGSTTHWVMAAAITWAFPVFAASVG-GWVFAFFGAMMLLQL 433 IWVFI+E+FP+ +R GQ+LGS THW++AA I FP FA + G G +FAFF MM+LQL Sbjct: 361 IWVFIAEIFPNELRAFGQSLGSFTHWILAALIANVFPFFANTFGAGSIFAFFALMMVLQL 420 Query: 434 LWTWKFMPETNGIALEDM 451 LW MPET G +LE++ Sbjct: 421 LWVAFRMPETKGKSLEEI 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: 618 Number of extensions: 41 Number of successful extensions: 7 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: 447 Length adjustment: 33 Effective length of query: 425 Effective length of database: 414 Effective search space: 175950 Effective search space used: 175950 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 24 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