Align C4-dicarboxylate TRAP transporter large permease protein DctM (characterized)
to candidate WP_011842435.1 RSPH17029_RS17920 TRAP transporter large permease
Query= SwissProt::Q9HU16 (427 letters) >NCBI__GCF_000015985.1:WP_011842435.1 Length = 430 Score = 311 bits (797), Expect = 2e-89 Identities = 168/425 (39%), Positives = 262/425 (61%), Gaps = 3/425 (0%) Query: 4 LFLFLLLFLLMFIGVPIAVSLGLSGALTILLFSPDSVRSLAIKLFETSEHYTLLAIPFFL 63 + L L L + +GVP+AVS+GL+ A+ ++ + + + + + ++A+P F+ Sbjct: 5 IILTLAFVLFLILGVPVAVSIGLA-AVAGMIVAGIPLSYVVQAAYSAVNDFLIIAVPMFV 63 Query: 64 LSGAFMTTGGVARRLIDFANACVGHIRGGLAIAAVLACMLFAALSGSSPATVAAVGSIAI 123 L+G M GG+ +RLI F+ VG GGLA ++AC FAA+SGS PAT AA+GSI I Sbjct: 64 LAGVLMEKGGLTQRLIAFSRTLVGRSPGGLASVTIVACTFFAAISGSGPATAAAIGSIMI 123 Query: 124 AGMVRSGYPQAFGAGIVCNAGTLGILIPPSIVMVVYAAATETSVGKLFIAGVVPGLLLGL 183 M++ GY ++F A I NAG +G++IPPSI M++Y E S+ LFIAGV+PGL+L + Sbjct: 124 PTMIKEGYHKSFAAAITSNAGGIGVVIPPSIPMIIYGITAEVSITGLFIAGVIPGLMLAV 183 Query: 184 ILMVVI-YIVARVKKLPAMPR-VSLREWLASARKALWGLLLMVIILGGIYSGAFTPTEAA 241 L V YI + A P SL+ A+A +A W LL +IILGGIY+G FT TEA+ Sbjct: 184 ALTAVSRYISTKRGYAVANPEGRSLKRIGAAAWEARWALLAPIIILGGIYTGIFTVTEAS 243 Query: 242 AVAAVYSAFVALFVYRDMRLSECPKVLLESGKLTIMLMFIIANAMLFAHVLTTEQIPQSI 301 VA +Y+ FV +F+YR + L + + +LT +++F++ + L VLT Q+PQ Sbjct: 244 IVAVLYALFVGIFIYRTITLPGFIDSMSYAVRLTGVVLFVLVSGRLLGRVLTIFQVPQEF 303 Query: 302 ASWVTELGLSPWMFLLVVNIVLLIAGNFMEPSAIILILAPIFFPIAMELGIDPIHLGIIM 361 ++++ +P + +L++ +L+ G +ME ++IL P+ P+A+ GIDPI GI+ Sbjct: 304 SAFMIATFDNPVVLVLLIIALLIFVGMWMETLTQLIILTPLLLPVAVSAGIDPIQFGIMF 363 Query: 362 VVNMEIGLITPPVGLNLFVTSAVTGMPLGATIRAALPWLMILLVFLIIVTYIPAVSLALP 421 V+ EIG TPP+G+NLFV S ++ + +AALP + +V L++VT+IP +SL LP Sbjct: 364 VIACEIGYSTPPLGVNLFVASEISNETVERVSKAALPLIAAEIVVLLLVTFIPQLSLFLP 423 Query: 422 NWLGM 426 +G+ Sbjct: 424 RLMGL 428 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: 515 Number of extensions: 28 Number of successful extensions: 5 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 1 Length of query: 427 Length of database: 430 Length adjustment: 32 Effective length of query: 395 Effective length of database: 398 Effective search space: 157210 Effective search space used: 157210 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 10 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