Align dicarboxylate TRAP transporter (succinate, fumarate, L-malate, and alpha-ketoglutarate), large permease component (characterized)
to candidate GFF4197 Psest_4270 TRAP transporter, DctM subunit
Query= reanno::PV4:5208943 (465 letters) >FitnessBrowser__psRCH2:GFF4197 Length = 426 Score = 518 bits (1333), Expect = e-151 Identities = 268/459 (58%), Positives = 345/459 (75%), Gaps = 35/459 (7%) Query: 1 MTIATLFISLFLCMLLGMPIAIALGFSSMLTILLFSDDSLASVALKLYESTSEHYTLLAI 60 MTI LF +LF+ M +G+P+A++LG + LTI++FS DS+ S+A+KL+E TSEHYTLLAI Sbjct: 1 MTILFLFAALFVLMFIGVPVAVSLGLAGSLTIMIFSQDSVRSLAIKLFE-TSEHYTLLAI 59 Query: 61 PFFILSSAFLSTGGVARRIIDFAMDSVGHIRGGLAMASVMACMLFAAVSGSSPATVAAIG 120 PFF+L+ AF++TGGVARR+IDFA VGHIRGGLA+ +V+ACMLFAA+SGSSPATVAA+G Sbjct: 60 PFFLLAGAFMTTGGVARRLIDFANACVGHIRGGLAIGAVLACMLFAALSGSSPATVAAVG 119 Query: 121 SIVIVGMVRAGYPEKFAAGVITTSGTLGILIPPSIVMLVYAAATEVSAARMFMAGLIPGL 180 SI I GMVR+GYP+ F AG++ +GTLGILIPPS+VM+VYAAATE S ++FMAG++PG+ Sbjct: 120 SIAIAGMVRSGYPQAFGAGIVCNAGTLGILIPPSVVMVVYAAATETSVGKLFMAGVVPGI 179 Query: 181 MMGLLLMLAIYIVARIKKLPSRPFPGFRPLAISSAKAMGGLALIVIVLGSIYGGIASPTE 240 ++G LM+AIYI+A K LP+ P FR ++ KA+ GL L+VI+LG IY G+ +PTE Sbjct: 180 LLGGALMIAIYIIAVKKNLPALPRASFREWLSAARKAIWGLLLMVIILGGIYSGMFTPTE 239 Query: 241 AAAVACVYAYFIAVFGYRDIGPLKNVSWRDSGEPLIRAILRNLGFMVLAVFKTPADKEIR 300 AAAVA VY+ F+A+F Y+DI S RD + L+ Sbjct: 240 AAAVAAVYSAFVALFVYKDI------SLRDCPKVLL------------------------ 269 Query: 301 HVVRDGAKVSIMLLFIIANAMLFAHVLTTERIPHLIAETIVGMGLPVWGFLIIVNLLLLA 360 + K+SIML+FIIANAMLFAHVLTTE+IP I ++ GL W FL++VN++LL Sbjct: 270 ----ESGKLSIMLMFIIANAMLFAHVLTTEQIPQAITAWVIEAGLQPWMFLLVVNIVLLI 325 Query: 361 AGNFMEPSAILLIMAPILFPIATQLGIDPIHLGIIMVVNMEIGMLTPPVGLNLFVTAGIT 420 AG FMEPSAI+LI+APILFPIA QLGIDPIHLGIIMVVNMEIG++TPPVGLNLFV + +T Sbjct: 326 AGAFMEPSAIILILAPILFPIAIQLGIDPIHLGIIMVVNMEIGLITPPVGLNLFVASAVT 385 Query: 421 GRSMGWVIHSCIPWLALLLFFLALITYIPQISLFLPEYI 459 G + VI + +PWLAL+L FL +ITY+P ISL LP + Sbjct: 386 GMPVTQVIRAVLPWLALMLSFLVIITYVPSISLALPNML 424 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: 676 Number of extensions: 25 Number of successful extensions: 3 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: 426 Length adjustment: 32 Effective length of query: 433 Effective length of database: 394 Effective search space: 170602 Effective search space used: 170602 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