Align dicarboxylate TRAP transporter (succinate, fumarate, L-malate, and alpha-ketoglutarate), large permease component (characterized)
to candidate WP_028583145.1 G494_RS0101755 C4-dicarboxylate ABC transporter permease
Query= reanno::PV4:5208943 (465 letters) >NCBI__GCF_000429965.1:WP_028583145.1 Length = 444 Score = 226 bits (576), Expect = 1e-63 Identities = 157/471 (33%), Positives = 244/471 (51%), Gaps = 54/471 (11%) Query: 1 MTIATLFISLFLCMLLGMPIAIALGFSSMLTILLFS----------DDSLASVALKLYES 50 +TIA LF +FL +L G+ I +L S + +LLF D +A ++ S Sbjct: 8 LTIA-LFGIMFLLLLSGLWIGFSLMASGLAGMLLFQLNLPPTISIWDKIGGLLANSIWNS 66 Query: 51 TSEHYTLLAIPFFILSSAFLSTGGVARRIIDFAMDSVGHIRGGLAMASVMACMLFAAVSG 110 T+ ++L A+P FIL L ++ R+++ + +I G L +V+AC LFAAVSG Sbjct: 67 TNS-WSLTALPLFILMGEILYRTQISTRLLNGLQPWLANIPGRLLHINVVACSLFAAVSG 125 Query: 111 SSPATVAAIGSIVIVGMVRAGYPEKFAAGVITTSGTLGILIPPSIVMLVYAAATEVSAAR 170 SS AT A +G I + + + GY A G + +GTLG LIPPS++M++Y ++ S + Sbjct: 126 SSAATTATVGKITLDELSKRGYDRGIAIGSLAGAGTLGFLIPPSLIMIIYGILSDTSIGK 185 Query: 171 MFMAGLIPGLMMGLLLMLAIYIVARIKKLPS-----RPFPGFRPLAISSAKAMGGLALIV 225 +F+AG+IPGL+ L AIYIV R P+ FR SS + L LIV Sbjct: 186 LFIAGIIPGLL--LASAYAIYIVIRALLNPAVMPEEEEHYTFREKLRSSRELFPVLLLIV 243 Query: 226 IVLGSIYGGIASPTEAAAVACVYAYFIAVFGYRDIGPLKNVSWRDSGEPLIRAILRNLGF 285 IVLG IY GI +PTEAAA+ V A+ +A++ RNL Sbjct: 244 IVLGGIYLGITTPTEAAAIGVVGAFGLALW------------------------FRNL-- 277 Query: 286 MVLAVFKTPADKEIRHVVRDGAKVSIMLLFIIANAMLFAHVLTTERIPHLIAETIVGMGL 345 LA F R V K + M+ FII A + V+ I ++ I G+GL Sbjct: 278 -TLANF--------REAVLSAVKTTSMISFIIVGAAFLSQVVGFVGIARALSLYISGLGL 328 Query: 346 PVWGFLIIVNLLLLAAGNFMEPSAILLIMAPILFPIATQLGIDPIHLGIIMVVNMEIGML 405 + +++V ++ L G ++ +I+++ PI+ PI G +P+ GI +V +E+ + Sbjct: 329 SPYLLIVVVAVMYLILGMILDGISIVVMTLPIVLPIIVAAGFEPLWFGIFLVFMVELSQI 388 Query: 406 TPPVGLNLFVTAGITGRSMGWVIHSCIPWLALLLFFLALITYIPQISLFLP 456 TPPVG ++FV GI+G +G ++ + P+ +++ + LIT P+I FLP Sbjct: 389 TPPVGFSIFVIEGISGERVGNILKATFPFFLIMILMVILITAAPEIVSFLP 439 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: 572 Number of extensions: 35 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: 465 Length of database: 444 Length adjustment: 33 Effective length of query: 432 Effective length of database: 411 Effective search space: 177552 Effective search space used: 177552 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 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