Align dicarboxylate TRAP transporter (succinate, fumarate, L-malate, and alpha-ketoglutarate), large permease component (characterized)
to candidate H281DRAFT_05326 H281DRAFT_05326 TRAP transporter, DctM subunit
Query= reanno::PV4:5208943 (465 letters) >FitnessBrowser__Burk376:H281DRAFT_05326 Length = 450 Score = 227 bits (578), Expect = 7e-64 Identities = 149/481 (30%), Positives = 239/481 (49%), Gaps = 57/481 (11%) Query: 1 MTIATLFISLFLCMLLGMPIAIALGFSSMLTILLFSDDSLASVALKLYESTSEHYTLLAI 60 M +A L IS + ++LG+P++ ALG S +LT L + A+ A++ S ++ LA+ Sbjct: 1 MELALLSISFIVFLVLGVPVSFALGLSCVLTYLY--EGLPAATAMQSMISGMNAFSFLAV 58 Query: 61 PFFILSSAFLSTGGVARRIIDFAMDSVGHIRGGLAMASVMACMLFAAVSGSSPATVAAIG 120 PFFI S + GG+A RI+ FA +VGH RGGL MA+V+AC LF VSGS A +A+G Sbjct: 59 PFFIFSGELMLHGGIADRILRFAQATVGHFRGGLGMANVVACTLFGGVSGSPTADTSAMG 118 Query: 121 SIVIVGMVRAGYPEKFAAGVITTSGTLGILIPPSIVMLVYAAATE-------------VS 167 +VI M R GY +A V T S G L+P S M++YA A + VS Sbjct: 119 GVVIPLMKREGYSAAYAVNVTTHSSLAGALMPTSTNMIIYAFAAQGITGTLNGVPMSGVS 178 Query: 168 AARMFMAGLIPGLMMGLLLMLAIYIVARIKKLPSRP--------FPGFRPLAISSAKAMG 219 + +GL+P L + +++A Y A P RP FPG+ +A + A+ Sbjct: 179 IGDLLFSGLLPVLWVMGFVLIAAYWQAVRYGYPRRPDGSTALQRFPGWMAVARTFLGALP 238 Query: 220 GLALIVIVLGSIYGGIASPTEAAAVACVYAYFIAVFGYRDIGPLKNVSWRDSGEPLIRAI 279 GL +I I+L + GIA+ TEAAA+A Y+ + V YR + Sbjct: 239 GLMVIAIILVCVAKGIATATEAAAIAVAYSLVLTVVVYRSM------------------T 280 Query: 280 LRNLGFMVLAVFKTPADKEIRHVVRDGAKVSIMLLFIIANAMLFAHVLTTERIPHLIAET 339 L+ L F + AK + ++L +I + + + + IP I Sbjct: 281 LKKLSF----------------ALSKAAKTTGVVLLLIGVSNMLRYQMAYLEIPDAIEHM 324 Query: 340 IVGMGLPVWGFLIIVNLLLLAAGNFMEPSAILLIMAPILFPIATQLGIDPIHLGIIMVVN 399 + G W L+ +N++ + G F++ +A +LI P+ P+A G+ P+ GI++++N Sbjct: 325 LDGATSIPWLMLLYINIIQVFLGTFVDMAAHILITTPLFLPMAMHSGVGPVQFGIMILLN 384 Query: 400 MEIGMLTPPVGLNLFVTAGITGRSMGWVIHSCIPWLALLLFFLALITYIPQISLFLPEYI 459 +G++ PP+G F+ I S+G P+ + + ++TY+P S +LP I Sbjct: 385 CALGLVHPPIGSVQFIGCAIGNVSIGETTKVAWPYYLAIFSAINIVTYVPMFSTWLPSVI 444 Query: 460 D 460 + Sbjct: 445 N 445 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: 558 Number of extensions: 34 Number of successful extensions: 6 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: 450 Length adjustment: 33 Effective length of query: 432 Effective length of database: 417 Effective search space: 180144 Effective search space used: 180144 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