Align C4-dicarboxylate TRAP transporter large permease protein DctM (characterized)
to candidate GFF762 PGA1_c07760 TRAP transporter, subunit DctM
Query= SwissProt::Q9HU16 (427 letters) >FitnessBrowser__Phaeo:GFF762 Length = 442 Score = 248 bits (633), Expect = 3e-70 Identities = 143/422 (33%), Positives = 244/422 (57%), Gaps = 8/422 (1%) Query: 5 FLFLLLFL-LMFIGVPIAVSLGLSGALTILLFSPD-SVRSLAIKLFETSEHYTLLAIPFF 62 +L ++LF+ L+ + VP+ ++G + A+T+L+ S D + ++ LF + + L A+P F Sbjct: 17 YLPVILFVALIALAVPVWAAIG-AAAITMLVMSGDLPLSAIGESLFTGIDAFALTAVPLF 75 Query: 63 LLSGAFMTTGGVARRLIDFANACVGHIRGGLAIAAVLACMLFAALSGSSPATVAAVGSIA 122 +L+G + G++++ +D A A RGG A VL C +FAA+SGS A AAVG + Sbjct: 76 ILTGDVLVRTGLSKKFLDVAEALTCWTRGGFGSATVLVCGMFAAISGSDAAGAAAVGRMT 135 Query: 123 IAGMVRSGYPQAFGAGIVCNAGTLGILIPPSIVMVVYAAATETSVGKLFIAGVVPGLLLG 182 IA +V SGYP+ + +V GILIPPSI ++ S LF+A ++PG+ + Sbjct: 136 IARLVESGYPRPYACALVAAGACTGILIPPSIAYIIIGLVLGISASTLFLAALIPGIAIL 195 Query: 183 LILMVVIYIVARVKKLPAMPRVSLREWLASARKAL----WGLLLMVIILGGIYSGAFTPT 238 + ++V I+ R+ + L EWL + ++L + ++ II GI+SG TPT Sbjct: 196 VSILVTNIIMNRLYTYETGGNMGLGEWLGNLGQSLKSGWYAFIVPGIIFYGIFSGRLTPT 255 Query: 239 EAAAVAAVYSAFVALFVYRDMRLSECPKVLLESGKLTIMLMFIIANAMLFAHVLTTEQIP 298 EA A A V + + F+ ++L++ P +L+ S K+ +++ IIA + A L +P Sbjct: 256 EAGATAVVVTILMG-FLLGTLKLADFPAMLVSSAKVNGVILPIIAFSAPLAEALAIMGVP 314 Query: 299 QSIASWVTELGLSPWMFLLVVNIVLLIAGNFMEPSAIILILAPIFFPIAMELGIDPIHLG 358 Q + VT L P + +L++ +L+ AG ME + I+ILAPI P+A +G++ I Sbjct: 315 QGFVTAVTGLTDDPSILILLMICILIAAGCVMETTPNIVILAPILKPLADNIGMNEIQFC 374 Query: 359 IIMVVNMEIGLITPPVGLNLFVTSAVTGMPLGATIRAALPWLMILLVFLIIVTYIPAVSL 418 I+M+ + +G ITPP+GLNLFV S +TG + A+P+++ +L+ ++++ Y+PA+S Sbjct: 375 IMMITALGVGFITPPLGLNLFVVSGITGESILKIAARAIPFVLTMLIVVLLIAYLPAIST 434 Query: 419 AL 420 L Sbjct: 435 TL 436 Lambda K H 0.330 0.144 0.425 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: 470 Number of extensions: 30 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: 427 Length of database: 442 Length adjustment: 32 Effective length of query: 395 Effective length of database: 410 Effective search space: 161950 Effective search space used: 161950 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 (21.9 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