Align dicarboxylate TRAP transporter (succinate, fumarate, L-malate, and alpha-ketoglutarate), large permease component (characterized)
to candidate WP_086508845.1 BZY95_RS04845 TRAP transporter large permease
Query= reanno::PV4:5208943 (465 letters) >NCBI__GCF_002151265.1:WP_086508845.1 Length = 424 Score = 318 bits (814), Expect = 3e-91 Identities = 172/457 (37%), Positives = 268/457 (58%), Gaps = 35/457 (7%) Query: 3 IATLFISLFLCMLLGMPIAIALGFSSMLTILLFSDDSLASVALKLYESTSEHYTLLAIPF 62 I L F +LLG+PI +L F+ L I F + V ++++ + +++L+AIPF Sbjct: 2 ITALLPIFFAVLLLGLPIFASLAFAVFLAIDFFGTTNPVIVPMRMFTGMN-NFSLMAIPF 60 Query: 63 FILSSAFLSTGGVARRIIDFAMDSVGHIRGGLAMASVMACMLFAAVSGSSPATVAAIGSI 122 FIL++ + GG++ R+I+ A VG + GGLA A+V++C+LF A+SGSSPATV AIGSI Sbjct: 61 FILAAELMRIGGLSGRLIELAKALVGWVPGGLAAATVLSCLLFGAISGSSPATVVAIGSI 120 Query: 123 VIVGMVRAGYPEKFAAGVITTSGTLGILIPPSIVMLVYAAATEVSAARMFMAGLIPGLMM 182 + +V AGY ++FA G+I T+GTLG ++PPSI +++Y + T S R+F AGL+P +++ Sbjct: 121 MFPALVAAGYDKRFAIGLIATAGTLGPIVPPSIALIIYGSVTGTSVGRLFAAGLLPAILI 180 Query: 183 GLLLMLAIYIVARIKKLPSRPFPGFRPLAISSAKAMGGLALIVIVLGSIYGGIASPTEAA 242 LL+ + + K PFP R +A + A GL L VI+LG IY GI +PTE+A Sbjct: 181 ASLLIAYCMVYSSFKGYARAPFPTLREIAAAVKSAAWGLGLPVILLGGIYSGIFTPTESA 240 Query: 243 AVACVYAYFIAVFGYRDIGPLKNVSWRDSGEPLIRAILRNLGFMVLAVFKTPADKEIRHV 302 AVAC+Y F+ + YR IG WR+ + LRN G Sbjct: 241 AVACMYGLFVGMVVYRTIG------WRE-----LLGTLRNSGL----------------- 272 Query: 303 VRDGAKVSIMLLFIIANAMLFAHVLTTERIPHLIAETIVGMGLPVWGFLIIVNLLLLAAG 362 S LL I A A F+ +L P +A ++ + + + N++++ AG Sbjct: 273 ------TSATLLLITAGASAFSWLLAITGTPTQLASQVLSLTDHPVQVMALFNVVMIVAG 326 Query: 363 NFMEPSAILLIMAPILFPIATQLGIDPIHLGIIMVVNMEIGMLTPPVGLNLFVTAGITGR 422 F++ ++ +++++P+L PIA Q+G+DP+H GII +VN +GM+TPPVGLNLFV I+ Sbjct: 327 FFLDSASAIIVLSPLLQPIAAQVGVDPVHFGIITLVNFSVGMITPPVGLNLFVAMAISRM 386 Query: 423 SMGWVIHSCIPWLALLLFFLALITYIPQISLFLPEYI 459 S+ V +CIP + ++ L ++TY+P S ++P I Sbjct: 387 SLLEVFRACIPLIVMMFIALIVLTYVPWFSTWVPSLI 423 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: 585 Number of extensions: 29 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: 424 Length adjustment: 32 Effective length of query: 433 Effective length of database: 392 Effective search space: 169736 Effective search space used: 169736 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