Align D-galacturonate transporter (MFS superfamily) (characterized)
to candidate GFF33 PS417_00170 glucarate transporter
Query= reanno::WCS417:GFF828 (454 letters) >FitnessBrowser__WCS417:GFF33 Length = 435 Score = 400 bits (1029), Expect = e-116 Identities = 188/432 (43%), Positives = 283/432 (65%), Gaps = 11/432 (2%) Query: 6 PTHVRYLILLMLFLVTTINYADRATIAIAGSSLQKDLGIDAVTLGYIFSAFGWAYVAGQI 65 PT R+ I+++LF+ INY DR+ ++IA +L +LGID V +G IFSAFGW Y A QI Sbjct: 15 PTRKRFFIMVLLFITVVINYLDRSNLSIAAPALTSELGIDPVHVGLIFSAFGWTYAAMQI 74 Query: 66 PGGWLLDRFGSKKVYALSIFTWSLFTVLQGYVGEFGVSTAVVALFMLRFMVGLAEAPSFP 125 PGGWL+DR + +Y ++ WS+ TV+ G+ F +ALF+LR VG EAP++P Sbjct: 75 PGGWLVDRVPPRILYTAALLLWSIATVMLGFAASF------IALFVLRMAVGALEAPAYP 128 Query: 126 GNARIVAAWFPTAERGTASAIFNSAQYFATVLFAPLMGWIVYSFGWQHVFIVMGVIGIIF 185 N+R+V WFP ER TA ++ S Q+ P++ W+ ++FGW VF+ G +GI++ Sbjct: 129 INSRVVTTWFPERERATAIGVYTSGQFVGLAFLTPVLAWLQHAFGWHMVFVATGGVGIVW 188 Query: 186 SLIWLKVIHSPRQHPMINEAEFNHIAANGAMVDMDQDKGKGKKTDGPKWDYIRQLLTNRM 245 ++IW V P++ N AE + I G +VDM + K + W + +L+ R Sbjct: 189 AVIWYAVYREPKEFKGANTAEIDLIREGGGLVDMQEKAAKAPFS----WVDLGIVLSKRK 244 Query: 246 MLGVYLGQYCINGITYFFLTWFPVYLVQDRGMTILKAGFIASLPAICGFIGGVLGGVISD 305 + G+YLGQ+C+N +FFLTWFP YLV+ RGM +K+G +ASLP + F+G + G+ SD Sbjct: 245 LWGIYLGQFCLNSTLWFFLTWFPTYLVKYRGMDFIKSGLLASLPFLAAFVGVLCSGIFSD 304 Query: 306 YLLRKGHSLTFARKAPIIGGLLISSSIVACNYVDIEWMVVGFMALAFFGKGVGALGWAVV 365 +L+R+G S+ FARK PIIGGLLIS++I+ NYVD V+ F+A+AFFG G+ ++ W++V Sbjct: 305 WLIRRGASVGFARKLPIIGGLLISTAIIGANYVDSTAWVIAFLAVAFFGNGLASITWSLV 364 Query: 366 SDTSPKQIAGLSGGLFNTFGNLASITTPIVIGYIISTTGSFKWALVFVGANALVAVFSYL 425 S +P ++ GL+GG+FN GNL++I TPIVIG++ S SF A+ ++ AL+ SY+ Sbjct: 365 STLAPARLLGLTGGVFNFIGNLSAIATPIVIGFLAS-GDSFAPAITYIAVLALLGALSYV 423 Query: 426 VIVGPIKRVVLK 437 ++VG ++R+ LK Sbjct: 424 LLVGKVERIELK 435 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: 698 Number of extensions: 40 Number of successful extensions: 4 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: 435 Length adjustment: 32 Effective length of query: 422 Effective length of database: 403 Effective search space: 170066 Effective search space used: 170066 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