Align D-galacturonate transporter (MFS superfamily) (characterized)
to candidate WP_083458844.1 WG78_RS07235 MFS transporter
Query= reanno::WCS417:GFF828 (454 letters) >NCBI__GCF_001294205.1:WP_083458844.1 Length = 444 Score = 380 bits (975), Expect = e-110 Identities = 190/433 (43%), Positives = 269/433 (62%), Gaps = 15/433 (3%) Query: 5 KPTHVRYLILLMLFLVTTINYADRATIAIAGSSLQKDLGIDAVTLGYIFSAFGWAYVAGQ 64 KPT RYL L+M+F+ I Y DRA +A+A + +QK+ GI +GYIFSAF W Y A Q Sbjct: 22 KPTRRRYLTLVMIFITVVICYVDRANLAVASAHIQKEFGISRAQMGYIFSAFAWTYTACQ 81 Query: 65 IPGGWLLDRFGSKKVYALSIFTWSLFTVLQGYVGEFGVSTAVVALFMLRFMVGLAEAPSF 124 IPGGW LDR GSK Y +++ WS+ T+ QG+ G + +L LR + GL EAP+F Sbjct: 82 IPGGWFLDRVGSKLTYFIAVMGWSVATLFQGFAG------GLASLVGLRAITGLFEAPAF 135 Query: 125 PGNARIVAAWFPTAERGTASAIFNSAQYFATVLFAPLMGWIVYSFGWQHVFIVMGVIGII 184 P N R+V +WFP ER +A + S Q+ PL+ WI S W VFI G +GII Sbjct: 136 PTNNRMVTSWFPEQERASAVGFYTSGQFVGLAFLTPLLIWIQESLSWHWVFIATGAVGII 195 Query: 185 FSLIWLKVIHSPRQHPMINEAEFNHIAANGAMVDMDQ---DKGKGKKTDGPKWDYIRQLL 241 ++L+W V PR+ IN+AE +HIAA G M+D D K +GK T W +L+ Sbjct: 196 WALVWHFVYQPPRKSRGINQAELDHIAAGGGMIDGDAPSTQKSRGKVT-AADW----KLI 250 Query: 242 TNRMMLGVYLGQYCINGITYFFLTWFPVYLVQDRGMTILKAGFIASLPAICGFIGGVLGG 301 NR ++GVY+GQ+ I +FFLTWFP YL Q++ ++ L AGF+ ++P + F+G +L G Sbjct: 251 FNRKLVGVYVGQFAIASTLWFFLTWFPSYLTQEKHVSALTAGFMTTVPFLAAFVGVLLSG 310 Query: 302 VISDYLLRKGHSLTFARKAPIIGGLLISSSIVACNYVDIEWMVVGFMALAFFGKGVGALG 361 +D ++R G S+ FARK PII GLL+S+ I+ NY + ++ MA+AFFG G ++ Sbjct: 311 FAADRMVRAGKSIGFARKLPIISGLLLSTCIIGANYTEDPVWIMTLMAIAFFGNGFASIT 370 Query: 362 WAVVSDTSPKQIAGLSGGLFNTFGNLASITTPIVIGYIISTTGSFKWALVFVGANALVAV 421 W++VS +P ++ GL+GG+FN G L IT P+VIGYI G F AL ++ AL+ Sbjct: 371 WSLVSSLAPLRLIGLTGGVFNFVGGLGGITVPLVIGYIAQDYG-FAPALAYISVVALIGA 429 Query: 422 FSYLVIVGPIKRV 434 SY+ +VG ++RV Sbjct: 430 LSYIFLVGEVRRV 442 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: 725 Number of extensions: 49 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: 444 Length adjustment: 33 Effective length of query: 421 Effective length of database: 411 Effective search space: 173031 Effective search space used: 173031 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