Align C4-dicarboxylate TRAP transporter large permease protein DctM (characterized)
to candidate WP_092057792.1 BQ4888_RS13555 TRAP transporter large permease
Query= SwissProt::Q9HU16 (427 letters) >NCBI__GCF_900111775.1:WP_092057792.1 Length = 431 Score = 319 bits (817), Expect = 1e-91 Identities = 168/419 (40%), Positives = 253/419 (60%), Gaps = 2/419 (0%) Query: 5 FLFLLLFLLMFIG--VPIAVSLGLSGALTILLFSPDSVRSLAIKLFETSEHYTLLAIPFF 62 +L +L LL + VP+ ++L +G L + R + L+ + + + L+ + FF Sbjct: 5 YLIILAVLLGALATTVPVFMALFFTGLLGLSWLMGIDPRIVIEVLYRSMDKFALIVVLFF 64 Query: 63 LLSGAFMTTGGVARRLIDFANACVGHIRGGLAIAAVLACMLFAALSGSSPATVAAVGSIA 122 +L G MTTG + +LI AN VG + GGLA+A +LAC LF A+SGS+ AT A+G Sbjct: 65 VLCGNVMTTGTIVEKLIKTANVLVGCLPGGLAMAGILACGLFGAISGSTVATAVAIGGFM 124 Query: 123 IAGMVRSGYPQAFGAGIVCNAGTLGILIPPSIVMVVYAAATETSVGKLFIAGVVPGLLLG 182 I ++ +GY ++F G++ A LGI+IPPSI M++YA T S+ LF+ G +PG L+ Sbjct: 125 IPALIDNGYDESFSVGVMTTAPILGIVIPPSIAMILYAMVTNDSLEALFLTGFIPGALIM 184 Query: 183 LILMVVIYIVARVKKLPAMPRVSLREWLASARKALWGLLLMVIILGGIYSGAFTPTEAAA 242 L + + + V R K PR +L E +A+ +++ W LLL II GIY G FT EAA Sbjct: 185 LAMSIYAFFVCRAKGYAVRPRPTLAEAVATLKESFWALLLPAIIFIGIYGGIFTANEAAV 244 Query: 243 VAAVYSAFVALFVYRDMRLSECPKVLLESGKLTIMLMFIIANAMLFAHVLTTEQIPQSIA 302 VA Y+ FV + ++RDMRL + KV++ S + L+ I+A A +F LT EQIP IA Sbjct: 245 VACFYAFFVEIVIHRDMRLRDVKKVIVASAITSATLLIIVAGASVFGEYLTFEQIPDKIA 304 Query: 303 SWVTELGLSPWMFLLVVNIVLLIAGNFMEPSAIILILAPIFFPIAMELGIDPIHLGIIMV 362 + V SPW+FLL VNI+LL+ G FM+ + LIL PIF P+ + G+D +H G++M Sbjct: 305 NGVVGNIQSPWVFLLAVNILLLVIGMFMDIISATLILTPIFLPLLAKFGVDTMHFGLLMT 364 Query: 363 VNMEIGLITPPVGLNLFVTSAVTGMPLGATIRAALPWLMILLVFLIIVTYIPAVSLALP 421 +N+ IG TPP+G++L+++ A L RA P+LMI ++ L++ T+ P + L LP Sbjct: 365 INLGIGYCTPPLGVSLYISGATVNRDLLYVSRAVFPFLMIQILLLLLFTFWPDLVLLLP 423 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: 465 Number of extensions: 18 Number of successful extensions: 1 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: 431 Length adjustment: 32 Effective length of query: 395 Effective length of database: 399 Effective search space: 157605 Effective search space used: 157605 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 Apr 09 2024. 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