Align C4-dicarboxylate TRAP transporter large permease protein DctM (characterized)
to candidate WP_086508845.1 BZY95_RS04845 TRAP transporter large permease
Query= SwissProt::Q9HU16 (427 letters) >NCBI__GCF_002151265.1:WP_086508845.1 Length = 424 Score = 345 bits (886), Expect = 1e-99 Identities = 175/420 (41%), Positives = 267/420 (63%) Query: 3 ILFLFLLLFLLMFIGVPIAVSLGLSGALTILLFSPDSVRSLAIKLFETSEHYTLLAIPFF 62 I L + F ++ +G+PI SL + L I F + + +++F +++L+AIPFF Sbjct: 2 ITALLPIFFAVLLLGLPIFASLAFAVFLAIDFFGTTNPVIVPMRMFTGMNNFSLMAIPFF 61 Query: 63 LLSGAFMTTGGVARRLIDFANACVGHIRGGLAIAAVLACMLFAALSGSSPATVAAVGSIA 122 +L+ M GG++ RLI+ A A VG + GGLA A VL+C+LF A+SGSSPATV A+GSI Sbjct: 62 ILAAELMRIGGLSGRLIELAKALVGWVPGGLAAATVLSCLLFGAISGSSPATVVAIGSIM 121 Query: 123 IAGMVRSGYPQAFGAGIVCNAGTLGILIPPSIVMVVYAAATETSVGKLFIAGVVPGLLLG 182 +V +GY + F G++ AGTLG ++PPSI +++Y + T TSVG+LF AG++P +L+ Sbjct: 122 FPALVAAGYDKRFAIGLIATAGTLGPIVPPSIALIIYGSVTGTSVGRLFAAGLLPAILIA 181 Query: 183 LILMVVIYIVARVKKLPAMPRVSLREWLASARKALWGLLLMVIILGGIYSGAFTPTEAAA 242 +L+ + + K P +LRE A+ + A WGL L VI+LGGIYSG FTPTE+AA Sbjct: 182 SLLIAYCMVYSSFKGYARAPFPTLREIAAAVKSAAWGLGLPVILLGGIYSGIFTPTESAA 241 Query: 243 VAAVYSAFVALFVYRDMRLSECPKVLLESGKLTIMLMFIIANAMLFAHVLTTEQIPQSIA 302 VA +Y FV + VYR + E L SG + L+ I A A F+ +L P +A Sbjct: 242 VACMYGLFVGMVVYRTIGWRELLGTLRNSGLTSATLLLITAGASAFSWLLAITGTPTQLA 301 Query: 303 SWVTELGLSPWMFLLVVNIVLLIAGNFMEPSAIILILAPIFFPIAMELGIDPIHLGIIMV 362 S V L P + + N+V+++AG F++ ++ I++L+P+ PIA ++G+DP+H GII + Sbjct: 302 SQVLSLTDHPVQVMALFNVVMIVAGFFLDSASAIIVLSPLLQPIAAQVGVDPVHFGIITL 361 Query: 363 VNMEIGLITPPVGLNLFVTSAVTGMPLGATIRAALPWLMILLVFLIIVTYIPAVSLALPN 422 VN +G+ITPPVGLNLFV A++ M L RA +P ++++ + LI++TY+P S +P+ Sbjct: 362 VNFSVGMITPPVGLNLFVAMAISRMSLLEVFRACIPLIVMMFIALIVLTYVPWFSTWVPS 421 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: 484 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: 424 Length adjustment: 32 Effective length of query: 395 Effective length of database: 392 Effective search space: 154840 Effective search space used: 154840 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