Align C4-dicarboxylate TRAP transporter large permease protein DctM (characterized)
to candidate WP_086509695.1 BZY95_RS09470 TRAP transporter large permease
Query= SwissProt::Q9HU16 (427 letters) >NCBI__GCF_002151265.1:WP_086509695.1 Length = 419 Score = 341 bits (875), Expect = 2e-98 Identities = 171/411 (41%), Positives = 271/411 (65%), Gaps = 5/411 (1%) Query: 6 LFLLLFLLMFIGVPIAVSLGLSGALTILLFSPDSVRSLAI--KLFETSEHYTLLAIPFFL 63 LFLL F M +GVPIA+++G S T+L + V + + ++F+ + L+A+P F+ Sbjct: 5 LFLLFFAFMLLGVPIALAIGAS---TLLALNAQGVPLMVVTQQMFQGINSFALVAVPMFI 61 Query: 64 LSGAFMTTGGVARRLIDFANACVGHIRGGLAIAAVLACMLFAALSGSSPATVAAVGSIAI 123 L+G M G V+ +L+DFA++ G ++GGL++ +V A M FAA+SGS AT AAVGS + Sbjct: 62 LAGDLMAQGKVSEKLVDFADSLFGFLKGGLSLVSVGAGMFFAAISGSGAATTAAVGSSLV 121 Query: 124 AGMVRSGYPQAFGAGIVCNAGTLGILIPPSIVMVVYAAATETSVGKLFIAGVVPGLLLGL 183 + R GY A A ++ +GT+G++IPPS+ M++YA + SV KLF+ G+VPG+L+G+ Sbjct: 122 PELKRKGYDPASAASLIAASGTIGVVIPPSVPMIIYAVVAQQSVSKLFLNGIVPGILMGI 181 Query: 184 ILMVVIYIVARVKKLPAMPRVSLREWLASARKALWGLLLMVIILGGIYSGAFTPTEAAAV 243 L + A + P +SL + + A WGL+ VIILGGI+SG FTP+EAA V Sbjct: 182 GLAAIAITQAYRRNYPRGTALSLATIWRTFKSASWGLMTPVIILGGIFSGIFTPSEAAVV 241 Query: 244 AAVYSAFVALFVYRDMRLSECPKVLLESGKLTIMLMFIIANAMLFAHVLTTEQIPQSIAS 303 A Y+ V+LFVYRD+ L + ++L+ S T ++M +IA + + + L++ Q+P +IA Sbjct: 242 AVNYALLVSLFVYRDLSLGDVYRILIRSAITTAVIMLVIATSAVLSWTLSSWQVPGTIAQ 301 Query: 304 WVTELGLSPWMFLLVVNIVLLIAGNFMEPSAIILILAPIFFPIAMELGIDPIHLGIIMVV 363 V L +P++ +L++ V+L+ G F+E ++ ++IL P+ P+ ++LGIDPIH GII+V+ Sbjct: 302 TVLSLSTNPYVIMLLIVAVILLTGVFIETASALIILTPVLLPLVLQLGIDPIHFGIIIVM 361 Query: 364 NMEIGLITPPVGLNLFVTSAVTGMPLGATIRAALPWLMILLVFLIIVTYIP 414 + IG+ITPPV +NL+V S+VT +PL RA LP+L+ L+ L++V Y+P Sbjct: 362 GLAIGMITPPVAINLYVASSVTQLPLERITRAILPYLLGLIGVLLLVVYVP 412 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: 489 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: 419 Length adjustment: 32 Effective length of query: 395 Effective length of database: 387 Effective search space: 152865 Effective search space used: 152865 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: 50 (23.9 bits)
This GapMind analysis is from Sep 24 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