Align D-galacturonate transporter (MFS superfamily) (characterized)
to candidate PfGW456L13_3476 D-glucarate permease
Query= reanno::WCS417:GFF828 (454 letters) >FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_3476 Length = 467 Score = 471 bits (1213), Expect = e-137 Identities = 225/434 (51%), Positives = 308/434 (70%), Gaps = 3/434 (0%) Query: 4 TKPTHVRYLILLMLFLVTTINYADRATIAIAGSSLQKDLGIDAVTLGYIFSAFGWAYVAG 63 TK + R+LIL ++ +V ++ DRA +++AG+ + K+LGI +V +GY+FSAF WAYV Sbjct: 32 TKKSSYRFLILALITIVLALSTGDRAALSVAGTDMSKELGISSVEMGYLFSAFSWAYVIF 91 Query: 64 QIPGGWLLDRFGSKKVYALSIFTWSLFTVLQGYVGEFGVSTAVVALFMLRFMVGLAEAPS 123 IP GWL DR GSK L++ WS FTV+ G V G+ V L LRF++G AE+P Sbjct: 92 LIPSGWLTDRIGSKLSMMLAVVIWSCFTVMMGMVHFIGM--VVPLLLALRFLLGAAESPV 149 Query: 124 FPGNARIVAAWFPTAERGTASAIFNSAQYFATVLFAPLMGWIVYSFGWQHVFIVMGVIGI 183 P + RI+AAWFP++ERG A AIFNSAQY + +F P+MGW+ Y++GW++VFI+MG IG+ Sbjct: 150 GPASGRIIAAWFPSSERGIAGAIFNSAQYLSLAVFTPVMGWLCYTYGWEYVFIIMGAIGL 209 Query: 184 IFSLIWLKVIHSPRQHPMINEAEFNHIAANGAMVDMDQDKGKGKKTD-GPKWDYIRQLLT 242 + IW K + P HP +N E +I A +VD++ K K T G K I QL Sbjct: 210 VIGAIWWKFYYLPIDHPKMNSEELEYIRAGDGLVDLESLKSKAANTGKGMKLGEIGQLFR 269 Query: 243 NRMMLGVYLGQYCINGITYFFLTWFPVYLVQDRGMTILKAGFIASLPAICGFIGGVLGGV 302 +RM++G++L QYCI IT+FF+TWFP+YLV++RG IL+AGFIA++PA+CG +GGV G Sbjct: 270 SRMLVGIFLAQYCITSITWFFMTWFPIYLVKERGFDILQAGFIAAIPALCGLVGGVSSGF 329 Query: 303 ISDYLLRKGHSLTFARKAPIIGGLLISSSIVACNYVDIEWMVVGFMALAFFGKGVGALGW 362 ISD +L+K SL+ ARK PI GLL+S+SI+ CNY + +VV M+LAFFGKG G++GW Sbjct: 330 ISDLILKKTGSLSIARKTPITIGLLLSASIILCNYAESAAVVVVLMSLAFFGKGFGSMGW 389 Query: 363 AVVSDTSPKQIAGLSGGLFNTFGNLASITTPIVIGYIISTTGSFKWALVFVGANALVAVF 422 VV+DT+PK++ G +GG+FN FGN A I TP+VIGYI+ TTGSF AL++VGA+ LVAV Sbjct: 390 TVVADTAPKELIGTTGGVFNAFGNTAGIVTPVVIGYILQTTGSFDGALLYVGAHGLVAVA 449 Query: 423 SYLVIVGPIKRVVL 436 SY +IVG I+R L Sbjct: 450 SYWLIVGKIQRFKL 463 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: 657 Number of extensions: 37 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: 454 Length of database: 467 Length adjustment: 33 Effective length of query: 421 Effective length of database: 434 Effective search space: 182714 Effective search space used: 182714 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