Align C4-dicarboxylate TRAP transporter large permease protein DctM (characterized)
to candidate WP_086510167.1 BZY95_RS12010 TRAP transporter large permease
Query= SwissProt::Q9HU16 (427 letters) >NCBI__GCF_002151265.1:WP_086510167.1 Length = 423 Score = 351 bits (901), Expect = e-101 Identities = 182/419 (43%), Positives = 272/419 (64%) Query: 4 LFLFLLLFLLMFIGVPIAVSLGLSGALTILLFSPDSVRSLAIKLFETSEHYTLLAIPFFL 63 L LFLLL +L IGVPIA SLGL+ A+T+ + +A + + + L+AIPFF+ Sbjct: 3 LLLFLLLIVLFVIGVPIAFSLGLASAITVWQGELMPMLIVAQQYITSVNSFPLMAIPFFI 62 Query: 64 LSGAFMTTGGVARRLIDFANACVGHIRGGLAIAAVLACMLFAALSGSSPATVAAVGSIAI 123 L+G M +GG++RRL+DF+N VG + GGLA+ A++ + FAA+SGS AT AA+G+I I Sbjct: 63 LAGYLMQSGGISRRLVDFSNTIVGSMTGGLAMVAIVTSLFFAAISGSGAATTAAIGAILI 122 Query: 124 AGMVRSGYPQAFGAGIVCNAGTLGILIPPSIVMVVYAAATETSVGKLFIAGVVPGLLLGL 183 M+ GY + A +G LG++IPPSI +++Y A SVG +F+AG++PGL++ L Sbjct: 123 PAMIAKGYASGYAAANQAASGALGVIIPPSIPLILYGIAANVSVGDMFVAGILPGLMITL 182 Query: 184 ILMVVIYIVARVKKLPAMPRVSLREWLASARKALWGLLLMVIILGGIYSGAFTPTEAAAV 243 L++ Y AR R S RE + RKAL +L+ VIILGGIY G FTPTEAA + Sbjct: 183 SLLLFAYGYARYHGHGGGERSSWREMFTAGRKALLAILMPVIILGGIYGGIFTPTEAAVI 242 Query: 244 AAVYSAFVALFVYRDMRLSECPKVLLESGKLTIMLMFIIANAMLFAHVLTTEQIPQSIAS 303 A VYS V +YR++ L + +L E+ T +++ II A L+ +L + ++P +++ Sbjct: 243 AVVYSFLVGFVIYREISLKDIVGILQEAAVTTAVVLSIIGAAGLYGRILQSLRVPSMLSN 302 Query: 304 WVTELGLSPWMFLLVVNIVLLIAGNFMEPSAIILILAPIFFPIAMELGIDPIHLGIIMVV 363 +V SP +F+++VN++LL+AG F+E +A ILI PI PIA+ G DP+H GIIMVV Sbjct: 303 FVIGAIDSPLLFIVLVNVLLLMAGMFIEAAAAILIFVPILLPIAVSFGFDPVHFGIIMVV 362 Query: 364 NMEIGLITPPVGLNLFVTSAVTGMPLGATIRAALPWLMILLVFLIIVTYIPAVSLALPN 422 N+ +G+ TPPVGLNLFV S ++ + + + LP++ I+LV L I++ +P +S LP+ Sbjct: 363 NLAMGMFTPPVGLNLFVASQISKVGVARLTWSILPFVAIVLVNLFIISVVPFLSTWLPS 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: 487 Number of extensions: 15 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: 423 Length adjustment: 32 Effective length of query: 395 Effective length of database: 391 Effective search space: 154445 Effective search space used: 154445 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