Align C4-dicarboxylate TRAP transporter large permease protein DctM (characterized)
to candidate WP_092350793.1 BLU87_RS16285 TRAP transporter large permease
Query= SwissProt::Q9HU16 (427 letters) >NCBI__GCF_900107645.1:WP_092350793.1 Length = 428 Score = 323 bits (827), Expect = 8e-93 Identities = 165/421 (39%), Positives = 258/421 (61%), Gaps = 5/421 (1%) Query: 9 LLFLLMFIG-----VPIAVSLGLSGALTILLFSPDSVRSLAIKLFETSEHYTLLAIPFFL 63 LL L + +G VP+ ++L +G ++ + + L+ + + + L+ + FF+ Sbjct: 6 LLILAILLGSLAATVPVFMALFFTGTFGLVYLLGIDPQIVIEVLYRSMDKFALVVVMFFV 65 Query: 64 LSGAFMTTGGVARRLIDFANACVGHIRGGLAIAAVLACMLFAALSGSSPATVAAVGSIAI 123 L G MTTG + +LI AN VG + GGLA+A +LAC F A+SGS+ ATV A+G I Sbjct: 66 LCGNIMTTGSIVEKLIKTANVLVGFLPGGLAMAGILACGFFGAISGSTVATVVAIGGFMI 125 Query: 124 AGMVRSGYPQAFGAGIVCNAGTLGILIPPSIVMVVYAAATETSVGKLFIAGVVPGLLLGL 183 +V + Y + F G++ A LG++IPPSI M++YA + + +LF+ G VPGL++ Sbjct: 126 PALVENDYDEKFSVGVMTTAPILGVVIPPSIAMILYAMVSNDPLEELFLTGFVPGLMIMG 185 Query: 184 ILMVVIYIVARVKKLPAMPRVSLREWLASARKALWGLLLMVIILGGIYSGAFTPTEAAAV 243 + + Y+V + K L + R +L+E L R+++W L L V+I GGIYSG FT EAA V Sbjct: 186 AMSLYAYLVCKKKGLKTIHRPNLKEALPVIRESIWALFLPVLIFGGIYSGMFTANEAAVV 245 Query: 244 AAVYSAFVALFVYRDMRLSECPKVLLESGKLTIMLMFIIANAMLFAHVLTTEQIPQSIAS 303 A Y+ FV +F++RDM+L + +V++ S + L+ I+A A +F LT EQIP IA+ Sbjct: 246 ACFYAFFVEIFIHRDMKLLDVKRVIVSSAVTSATLLIIVAGASVFGEYLTFEQIPNKIAT 305 Query: 304 WVTELGLSPWMFLLVVNIVLLIAGNFMEPSAIILILAPIFFPIAMELGIDPIHLGIIMVV 363 V SPW+FLL VNI+LLI G FM+ + LIL PIF P+ + GI+ +H G++M + Sbjct: 306 AVVSSISSPWVFLLAVNILLLIIGMFMDIISATLILTPIFLPLLNKFGINTMHFGLLMTI 365 Query: 364 NMEIGLITPPVGLNLFVTSAVTGMPLGATIRAALPWLMILLVFLIIVTYIPAVSLALPNW 423 N+ IG TPP+G++L+++ A L +A +P+L+I + L+I+T+ P + L LP W Sbjct: 366 NLGIGYCTPPLGVSLYISGATVNRDLVYVSKAVMPFLLIQIAILLILTFFPDLVLFLPRW 425 Query: 424 L 424 + Sbjct: 426 V 426 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: 478 Number of extensions: 23 Number of successful extensions: 2 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: 428 Length adjustment: 32 Effective length of query: 395 Effective length of database: 396 Effective search space: 156420 Effective search space used: 156420 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 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