Align dicarboxylate TRAP transporter (succinate, fumarate, L-malate, and alpha-ketoglutarate), large permease component (characterized)
to candidate WP_041098416.1 SUTH_RS08115 TRAP transporter large permease
Query= reanno::PV4:5208943 (465 letters) >NCBI__GCF_000828635.1:WP_041098416.1 Length = 438 Score = 189 bits (480), Expect = 2e-52 Identities = 128/409 (31%), Positives = 207/409 (50%), Gaps = 45/409 (11%) Query: 55 YTLLAIPFFILSSAFLSTGGVARRIIDFAMDSVGHIRGGLAMASVMACMLFAAVSGSSPA 114 Y L +P F+L F + GG+++ + +GH RGG+AMA+V AC F A+ GSS A Sbjct: 60 YDLSVVPLFLLMGQFATHGGLSKALFRAGNTLIGHWRGGMAMAAVGACAGFGAICGSSLA 119 Query: 115 TVAAIGSIVIVGMVRAGYPEKFAAGVITTSGTLGILIPPSIVMLVYAAATEVSAARMFMA 174 T A +G + + + Y + A I GTLGILIPPS+ +++YA TE + A++F++ Sbjct: 120 TAATMGQVALPELRSHKYSGRLATAAIAAGGTLGILIPPSVPLVIYAILTEQNIAKLFVS 179 Query: 175 GLIPGLMMGLLLMLAIYIVARI--KKLPSRPFPGFRPLAISSAKAMGGLALIVIVLGSIY 232 IPGL+ ML I I+AR+ P+ + + + L + +V+G IY Sbjct: 180 AFIPGLIAMGGYMLVIAIMARVDPTSAPAGDRATWGERLAALVETWPVLLIFTVVIGGIY 239 Query: 233 GGIASPTEAAAVACVYAYFIAVFGYRDIGPLKNVSWRDSGEPLIRAILRNLGFMVLAVFK 292 GG +PTEAA++ + GY V+W+ G LR GF+ Sbjct: 240 GGFFTPTEAASIGTL------ATGY--------VAWKSGG-------LRKHGFI------ 272 Query: 293 TPADKEIRHVVRDGAKVSIMLLFIIANAMLFAHVLTTERIPHLIAETIVGMGLPVWGFLI 352 V A+ + M+ I+ A + L ++P +++ +VG+GL L Sbjct: 273 --------ECVYGTAQATGMIFLILLGADIMNVFLALTQMPAELSKWVVGLGLSPLLVLF 324 Query: 353 IVNLLLLAAGNFMEPSAILLIMAPILFPIATQL---GID----PIHLGIIMVVNMEIGML 405 ++ + L G M+ +++L+ PI FPI L G+D I GI+ ++ +EIGM+ Sbjct: 325 VILCIYLVLGCIMDSLSMILLTVPIFFPIIMGLDFWGLDAEAKAIWFGILTLMAVEIGMI 384 Query: 406 TPPVGLNLFVTAGIT-GRSMGWVIHSCIPWLALLLFFLALITYIPQISL 453 TPPVGLN+F+ + + SM +P+LA +AL+ ++P I+L Sbjct: 385 TPPVGLNVFIISSMAKDTSMKETFIGIVPFLASDFLRIALLVFVPSIAL 433 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: 583 Number of extensions: 28 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: 465 Length of database: 438 Length adjustment: 33 Effective length of query: 432 Effective length of database: 405 Effective search space: 174960 Effective search space used: 174960 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 Apr 09 2024. 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