Align dicarboxylate TRAP transporter (succinate, fumarate, L-malate, and alpha-ketoglutarate), large permease component (characterized)
to candidate Dsui_1262 Dsui_1262 TRAP transporter, DctM subunit
Query= reanno::PV4:5208943 (465 letters) >FitnessBrowser__PS:Dsui_1262 Length = 488 Score = 175 bits (443), Expect = 3e-48 Identities = 132/462 (28%), Positives = 216/462 (46%), Gaps = 53/462 (11%) Query: 6 LFISLFLCMLLGMPIAIALGFSSMLTILLFSDDSLASVALKLYESTSEHY-------TLL 58 +F +L L +L G P+A AL + M + F L + L+++ E TLL Sbjct: 12 MFGALVLFLLFGYPVAFALAANGM--VFGFIGMELGLLHPALFQALPERVFGIMANDTLL 69 Query: 59 AIPFFILSSAFLSTGGVARRIIDFAMDSVGHIRGGLAMASVMACMLFAAVSGSSPATVAA 118 AIPFF L G+A ++D G +RGGLA A + L AA +G A+V + Sbjct: 70 AIPFFTFMGLVLERSGMAEDLLDTIGQLFGPMRGGLAYAVIFVGALLAATTGVVAASVIS 129 Query: 119 IGSIVIVGMVRAGYPEKFAAGVITTSGTLGILIPPSIVMLVYAAATEVSAARMFMAGLIP 178 +G I + M+R GY ++ A+GVI SGTL +IPPS+V+++ A S M+ ++P Sbjct: 130 MGLISLPIMLRYGYDKRLASGVIAASGTLAQIIPPSLVLIIMADQLGKSVGDMYEGAMVP 189 Query: 179 GLMMGLLLMLAIYIVARIK-------KLPSRPFPGFRPLAISSAKAMGGLALIVIVLGSI 231 GL++ L + + I+ IK L +R G + L + L LI +VLG+I Sbjct: 190 GLILTSLYVGYVVILTLIKPNAAPALPLEARSLRGAKLLMRVLTSLVPPLVLIFLVLGTI 249 Query: 232 YGGIASPTEAAAVACVYAYFIAVFGYRDIGPLKNVSWRDSGEPLIRAILRNLGFMVLAVF 291 + GIA+PTE A+ A +A+ R + +++ Sbjct: 250 FMGIATPTEGGAMGASGALILALMRKR---------------------------LSVSLL 282 Query: 292 KTPADKEIRHVVRDGAKVSIMLLFIIANAMLFAHVLTTERIPHLIAETIVGMGLPVWGFL 351 K D AK+S ++FI+ + +F V + + + GFL Sbjct: 283 KQAMDTT--------AKLSSFVVFILVGSTVFGLVFRAVNGDLWVEHLLTSLPGGQLGFL 334 Query: 352 IIVNLLLLAAGNFMEPSAILLIMAPILFPIATQLGIDPIHLGIIMVVNMEIGMLTPPVGL 411 I+VN+L+ F++ + I+ P+L P+A +LGID I G+++ VNM+ + PP G Sbjct: 335 IVVNILVFVLAFFLDFFELSFIIVPLLGPVAEKLGIDLIWFGVLLGVNMQTSFMHPPFGF 394 Query: 412 NLFVTAGITGRSMGW--VIHSCIPWLALLLFFLALITYIPQI 451 LF + S+ + +P++ + + +ALI P I Sbjct: 395 ALFYLRSVAPASIKTTDIYWGAVPFVCIQIIMVALIIIFPGI 436 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: 567 Number of extensions: 30 Number of successful extensions: 3 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 465 Length of database: 488 Length adjustment: 33 Effective length of query: 432 Effective length of database: 455 Effective search space: 196560 Effective search space used: 196560 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