Align D-galacturonate transporter (MFS superfamily) (characterized)
to candidate BWI76_RS13565 BWI76_RS13565 MFS transporter
Query= reanno::WCS417:GFF828 (454 letters) >FitnessBrowser__Koxy:BWI76_RS13565 Length = 436 Score = 443 bits (1140), Expect = e-129 Identities = 212/435 (48%), Positives = 300/435 (68%), Gaps = 6/435 (1%) Query: 2 QATKPTHVRYLILLMLFLVTTINYADRATIAIAGSSLQKDLGIDAVTLGYIFSAFGWAYV 61 Q K ++VRY ILL LFL T NYADRAT+++ + K+LG D +G FS FG +YV Sbjct: 3 QQLKRSNVRYGILLFLFLATVFNYADRATLSVVAPIMSKELGFDPEAMGLAFSVFGISYV 62 Query: 62 AGQIPGGWLLDRFGSKKVYALSIFTWSLFTVLQGYVGEFGVSTAVVALFMLRFMVGLAEA 121 QIPGGWLLD++GS+ VY ++ WS+ T+ QG + F ++ +VAL +LR M+G EA Sbjct: 63 IMQIPGGWLLDKYGSRLVYGCALIGWSIVTMFQGTIYMF--ASPLVALVILRLMMGAIEA 120 Query: 122 PSFPGNARIVAAWFPTAERGTASAIFNSAQYFATVLFAPLMGWIVYSFGWQHVFIVMGVI 181 P+FP N+R+ WFP ERG ++++ +AQY + + PLM I+++ W +VF +G I Sbjct: 121 PAFPANSRLSVQWFPNKERGFVTSVYQAAQYISLGIITPLMTIILHNLSWHYVFYYIGAI 180 Query: 182 GIIFSLIWLKVIHSPRQHPMINEAEFNHIAANGAMVDMDQDKGKGKKTDGPKWDYIRQLL 241 G++ + WL + P HP IN+ E ++I G ++ K + K T I+ + Sbjct: 181 GVVLGIFWLVKVRDPSHHPKINQQELDYIREGGGEPELGTKKTQQKLTLAQ----IKSVC 236 Query: 242 TNRMMLGVYLGQYCINGITYFFLTWFPVYLVQDRGMTILKAGFIASLPAICGFIGGVLGG 301 NRMM+GVY+GQ+C+ IT+FFLTWFP YL Q +GM+ILK GF+AS+PAI GFIGG+LGG Sbjct: 237 VNRMMIGVYIGQFCVTSITWFFLTWFPTYLYQAKGMSILKVGFVASIPAIAGFIGGLLGG 296 Query: 302 VISDYLLRKGHSLTFARKAPIIGGLLISSSIVACNYVDIEWMVVGFMALAFFGKGVGALG 361 V SD+LL++G+SLT ARK P+I G+L+S IV NY E +V+ M++AFF KG G LG Sbjct: 297 VFSDWLLKRGYSLTTARKLPVICGMLLSCVIVVANYTTSEVVVIAAMSVAFFAKGFGNLG 356 Query: 362 WAVVSDTSPKQIAGLSGGLFNTFGNLASITTPIVIGYIISTTGSFKWALVFVGANALVAV 421 W V+SDTSPK++ G++GG+FN GNLASI TP+VIG II+ T SF +A+++VG+ ++ + Sbjct: 357 WCVLSDTSPKEMLGIAGGVFNMCGNLASIITPLVIGVIIANTHSFDYAILYVGSMGVLGL 416 Query: 422 FSYLVIVGPIKRVVL 436 FSYL IVGP+ R+ L Sbjct: 417 FSYLFIVGPLDRLTL 431 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: 692 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: 436 Length adjustment: 32 Effective length of query: 422 Effective length of database: 404 Effective search space: 170488 Effective search space used: 170488 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