Align dicarboxylate TRAP transporter (succinate, fumarate, L-malate, and alpha-ketoglutarate), large permease component (characterized)
to candidate 202250 SO3136 C4-dicarboxylate transport protein (NCBI ptt file)
Query= reanno::PV4:5208943 (465 letters) >FitnessBrowser__MR1:202250 Length = 465 Score = 788 bits (2034), Expect = 0.0 Identities = 402/465 (86%), Positives = 432/465 (92%) Query: 1 MTIATLFISLFLCMLLGMPIAIALGFSSMLTILLFSDDSLASVALKLYESTSEHYTLLAI 60 M IATLF LF+CM LGMPIAIALGFSSMLTIL FS+DSLASVALKLYES+SEHYTLLAI Sbjct: 1 MAIATLFCVLFICMFLGMPIAIALGFSSMLTILFFSNDSLASVALKLYESSSEHYTLLAI 60 Query: 61 PFFILSSAFLSTGGVARRIIDFAMDSVGHIRGGLAMASVMACMLFAAVSGSSPATVAAIG 120 PFFILSSAFLSTGGVARRIIDFAMD VGHIRGGLAMASVMACMLFAAVSGSSPATVAAIG Sbjct: 61 PFFILSSAFLSTGGVARRIIDFAMDCVGHIRGGLAMASVMACMLFAAVSGSSPATVAAIG 120 Query: 121 SIVIVGMVRAGYPEKFAAGVITTSGTLGILIPPSIVMLVYAAATEVSAARMFMAGLIPGL 180 SIVIVGMV+AGYPEKFA+GVITTSGTLGILIPPSIVMLVYAAATEVS A++FMAGL+PGL Sbjct: 121 SIVIVGMVKAGYPEKFASGVITTSGTLGILIPPSIVMLVYAAATEVSVAKIFMAGLVPGL 180 Query: 181 MMGLLLMLAIYIVARIKKLPSRPFPGFRPLAISSAKAMGGLALIVIVLGSIYGGIASPTE 240 ++G L+M+ IYIVARIK LPS PFPGF+ L +SSAKA+GGLALI IVLGSIYGG+ASPTE Sbjct: 181 LLGFLIMVVIYIVARIKNLPSIPFPGFKKLGVSSAKAIGGLALIFIVLGSIYGGVASPTE 240 Query: 241 AAAVACVYAYFIAVFGYRDIGPLKNVSWRDSGEPLIRAILRNLGFMVLAVFKTPADKEIR 300 A+AVACVYAYFIAVFGYRDIGPLKNV+WR+ E + AI RNLG MVL + KTP DKEIR Sbjct: 241 ASAVACVYAYFIAVFGYRDIGPLKNVAWRNPNEAIPSAIARNLGHMVLGLIKTPIDKEIR 300 Query: 301 HVVRDGAKVSIMLLFIIANAMLFAHVLTTERIPHLIAETIVGMGLPVWGFLIIVNLLLLA 360 HVVRDGAKVSIMLLFIIANAMLFAHVLTTERIPH+IAE IVGMGLP WGFLIIVNLLLLA Sbjct: 301 HVVRDGAKVSIMLLFIIANAMLFAHVLTTERIPHIIAEYIVGMGLPAWGFLIIVNLLLLA 360 Query: 361 AGNFMEPSAILLIMAPILFPIATQLGIDPIHLGIIMVVNMEIGMLTPPVGLNLFVTAGIT 420 AGNFMEPSAI+LIMAPILFPIATQLGIDPIHLGIIMVVNMEIGMLTPPVGLNLFVT+GIT Sbjct: 361 AGNFMEPSAIVLIMAPILFPIATQLGIDPIHLGIIMVVNMEIGMLTPPVGLNLFVTSGIT 420 Query: 421 GRSMGWVIHSCIPWLALLLFFLALITYIPQISLFLPEYIDKLNGY 465 GR++GWVI S +PWL +L FL LITY+PQISLFLPE +DKLNGY Sbjct: 421 GRNIGWVIQSVLPWLVFMLAFLMLITYVPQISLFLPELLDKLNGY 465 Lambda K H 0.330 0.144 0.424 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: 818 Number of extensions: 17 Number of successful extensions: 1 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: 465 Length of database: 465 Length adjustment: 33 Effective length of query: 432 Effective length of database: 432 Effective search space: 186624 Effective search space used: 186624 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 (21.8 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