Align dicarboxylate TRAP transporter (succinate, fumarate, L-malate, and alpha-ketoglutarate), large permease component (characterized)
to candidate 3608435 Dshi_1832 TRAP dicarboxylate transporter, DctM subunit (RefSeq)
Query= reanno::PV4:5208943 (465 letters) >FitnessBrowser__Dino:3608435 Length = 446 Score = 233 bits (593), Expect = 1e-65 Identities = 144/476 (30%), Positives = 247/476 (51%), Gaps = 56/476 (11%) Query: 3 IATLFISLFLCMLLGMPIAIALGFSSMLTILLFSDDSLASVALKLYESTSEHYTLLAIPF 62 I LF +L+G PI +ALG S++++ L ++ + V + S + L+A+P Sbjct: 6 ILILFGGFLTLLLIGAPITVALGVSTLISFLYLGENPIKFVQIAFTSVGS--FPLMALPA 63 Query: 63 FILSSAFLSTGGVARRIIDFAMDSVGHIRGGLAMASVMACMLFAAVSGSSPATVAAIGSI 122 FIL+ A + G++RR+I+ A G GG++ A+V AC+ F A+SGS PAT AA+G + Sbjct: 64 FILAGALMEASGLSRRLINVAESFAGPFTGGMSAATVFACLFFGAISGSGPATTAAVGML 123 Query: 123 VIVGMVRAGYPEKFAAGVITTSGTLGILIPPSIVMLVYAAAT-----------------E 165 +I M++ GY +++ + +SG LGI+IPPSI ++++ A Sbjct: 124 MIPAMIQRGYGRSYSSAITASSGGLGIVIPPSIPLIIFGIAALGMPAPPEAVEKFGTFQT 183 Query: 166 VSAARMFMAGLIPGLMMGLLLMLAIYIVARIKKLPSRPFPGFRPLAISSAKAMGGLALI- 224 VS ++F+AG +P ++ L+L YI+A+ K G+ I G AL+ Sbjct: 184 VSIPKLFIAGFMPAFLIAGSLLLMNYILAK-KHGYKGSAEGWSARQIWCELYRGFWALMA 242 Query: 225 -VIVLGSIYGGIASPTEAAAVACVYAYFIAVFGYRDIGPLKNVSWRDSGEPLIRAILRNL 283 +++LG IY G +PTEAA VA Y + YR++ SW+ Sbjct: 243 PLVILGGIYSGFFTPTEAAIVAIFYTLVVGTVIYREL------SWQ-------------- 282 Query: 284 GFMVLAVFKTPADKEIRHVVRDGAKVSIMLLFIIANAMLFAHVLTTERIPHLIAETIVGM 343 ++ + ++ +L I+ A +F +L +IP +IA ++ + Sbjct: 283 --------------KLFTALETTTWLTGRVLLIMFTATVFGRLLVENQIPAVIANGMLSI 328 Query: 344 GLPVWGFLIIVNLLLLAAGNFMEPSAILLIMAPILFPIATQLGIDPIHLGIIMVVNMEIG 403 ++ +V L LL G FME A +LI+ P++ P+A +GIDPIH G++MV + IG Sbjct: 329 TDNIYIIWTLVILFLLFVGMFMETLATILILVPVMLPVAYSVGIDPIHFGVVMVCCLGIG 388 Query: 404 MLTPPVGLNLFVTAGITGRSMGWVIHSCIPWLALLLFFLALITYIPQISLFLPEYI 459 TPP+G NLF+ +GI+ S+ + + +P+ + + +I ++P+I+L+LP + Sbjct: 389 FQTPPLGENLFIASGISNISIERISVAALPFAFINTVAIFIIAFVPEITLWLPRLL 444 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: 587 Number of extensions: 31 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: 446 Length adjustment: 33 Effective length of query: 432 Effective length of database: 413 Effective search space: 178416 Effective search space used: 178416 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