Align D-galacturonate transporter (MFS superfamily) (characterized)
to candidate H281DRAFT_03857 H281DRAFT_03857 MFS transporter, ACS family, D-galactonate transporter
Query= reanno::WCS417:GFF828 (454 letters) >FitnessBrowser__Burk376:H281DRAFT_03857 Length = 438 Score = 390 bits (1002), Expect = e-113 Identities = 195/434 (44%), Positives = 271/434 (62%), Gaps = 12/434 (2%) Query: 3 ATKPTHVRYLILLMLFLVTTINYADRATIAIAGSSLQKDLGIDAVTLGYIFSAFGWAYVA 62 AT+ T R+ IL +L + T INY DR+ IA S+ +LG++ +G IFSAF W Y A Sbjct: 17 ATRRTRARFQILALLAIGTMINYLDRSVAGIAAPSMSHELGLNPALMGVIFSAFSWTYTA 76 Query: 63 GQIPGGWLLDRFGSKKVYALSIFTWSLFTVLQGYVGEFGVSTAVVALFMLRFMVGLAEAP 122 QIPGG +LDR G++ Y ++ WSLFT LQG ++T ++L ++R ++G+AEAP Sbjct: 77 SQIPGGVMLDRVGTRWTYFFALTLWSLFTGLQG------LATGFISLLIMRLLIGVAEAP 130 Query: 123 SFPGNARIVAAWFPTAERGTASAIFNSAQYFATVLFAPLMGWIVYSFGWQHVFIVMGVIG 182 FP N+R+VA WFP +ER A+ I+ A+Y +PL+ W+ +GW+ +F ++G +G Sbjct: 131 CFPTNSRVVAIWFPQSERARATGIYTFAEYVGLAFLSPLLFWLEQQYGWRALFGIVGTVG 190 Query: 183 IIFSLIWLKVIHSPRQHPMINEAEFNHIAANGAMVDMDQDKGKGKKTDGPKWDYIRQLLT 242 ++F IWL H P Q N AE ++IA G +VD Q K +W I LL Sbjct: 191 VLFGGIWLMRFHEPHQSKSANRAELDYIANGGGVVDGSQ------KATHFRWADIGALLK 244 Query: 243 NRMMLGVYLGQYCINGITYFFLTWFPVYLVQDRGMTILKAGFIASLPAICGFIGGVLGGV 302 R MLG+ +GQ+ N FFLTWFP YLV +R M LK G IA LP I +G + GG Sbjct: 245 RRSMLGICVGQFACNSTNVFFLTWFPTYLVTERHMPWLKVGLIAVLPFIAASVGTLAGGW 304 Query: 303 ISDYLLRKGHSLTFARKAPIIGGLLISSSIVACNYVDIEWMVVGFMALAFFGKGVGALGW 362 ISD +LR+G SL ++RK P+I GLL +SSIV NYV+ V+ + +A+F +G+ AL W Sbjct: 305 ISDSMLRRGISLNWSRKLPVIAGLLAASSIVLANYVESTATVIAILCVAYFAQGMSALAW 364 Query: 363 AVVSDTSPKQIAGLSGGLFNTFGNLASITTPIVIGYIISTTGSFKWALVFVGANALVAVF 422 +VSD +PK + GLSGG+FN F N A I TP+VIG I++ TGSF +AL F+ A L Sbjct: 365 MIVSDIAPKGLLGLSGGIFNLFANAAGIVTPLVIGLIVNATGSFVYALGFISAVTLAGAL 424 Query: 423 SYLVIVGPIKRVVL 436 SY+ +VG IKR+ L Sbjct: 425 SYIFVVGDIKRIEL 438 Lambda K H 0.327 0.142 0.444 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: 651 Number of extensions: 30 Number of successful extensions: 3 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: 454 Length of database: 438 Length adjustment: 32 Effective length of query: 422 Effective length of database: 406 Effective search space: 171332 Effective search space used: 171332 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