Align C4-dicarboxylate TRAP transporter large permease protein DctM (characterized)
to candidate WP_092057789.1 BQ4888_RS13540 TRAP transporter large permease
Query= SwissProt::Q9HU16 (427 letters) >NCBI__GCF_900111775.1:WP_092057789.1 Length = 433 Score = 277 bits (709), Expect = 4e-79 Identities = 156/422 (36%), Positives = 244/422 (57%), Gaps = 6/422 (1%) Query: 3 ILFLFLLLFLLMFIGVPIAVSLGLSGALTILLFSPDSVRSLAIKLFETSEHYTLLAIPFF 62 IL L + LF M +G +A+ LGL+G ++ F + LA +++T Y L IP F Sbjct: 11 ILLLVIGLFSRMPVGFVMAI-LGLAGFSFVVTFDA-GLNLLARDIWDTFSSYGLTVIPLF 68 Query: 63 LLSGAFMTTGGVARRLIDFANACVGHIRGGLAIAAVLACMLFAALSGSSPATVAAVGSIA 122 + G G++RRL A +G+ GGLA+A + AC F+ +SGS+ AT A + ++ Sbjct: 69 VFMGQVAYQSGISRRLYHAAYVMLGNRPGGLALATIGACAGFSTISGSTNATAATMATVT 128 Query: 123 IAGMVRSGYPQAFGAGIVCNAGTLGILIPPSIVMVVYAAATETSVGKLFIAGVVPGLLLG 182 I M R Y AG V G+LGILIPPS++ +VY TE S+GKLF AG++PG+LL Sbjct: 129 IPEMQRRRYDMGLAAGTVAAGGSLGILIPPSVIFIVYGIITEQSIGKLFAAGILPGILLC 188 Query: 183 LILMVVIYIVARVKK--LPAMPRVSLREWLASARKALWGLLLMVIILGGIYSGAFTPTEA 240 + + I + R+ PA P+ SL+ L S + L+L V+++GGI+ G FTPTEA Sbjct: 189 TLFFITIMVRVRLNPALAPAGPKTSLKRKLRSFAGIIETLILFVLVMGGIFLGFFTPTEA 248 Query: 241 AAVAAVYSAFVALFVYRDMRLSECPKVLLESGKLTIMLMFIIANAMLFAHVLTTEQIPQS 300 AAV A + +ALF R + + L ++ +++ M+M I+ A++F + ++P Sbjct: 249 AAVGAFLTIVLALF-RRRLSWQGFIQALRDTTRISCMVMMIVTGAVIFGKFMAITRVPFE 307 Query: 301 IASWVTELGLSPWMFLLVVNIVLLIAGNFMEPSAIILILAPIFFPIAMELGIDPIHLGII 360 +A WV L L P+ + ++ ++ L G FM+ A+I++ PIFFP+ LG DPI G++ Sbjct: 308 LAGWVGSLPLPPYAIMALIILIYLFGGCFMDSLAMIMLTVPIFFPVVQTLGFDPIWFGVV 367 Query: 361 MVVNMEIGLITPPVGLNLFVTSAVT-GMPLGATIRAALPWLMILLVFLIIVTYIPAVSLA 419 +V+ E+G+ITPPVG+N++V + +PL R P+L+ LL I+ P ++L Sbjct: 368 IVLVTEMGVITPPVGINVYVVHGIAKDIPLHTIFRGVFPYLLALLACTGILLLFPQLALF 427 Query: 420 LP 421 LP Sbjct: 428 LP 429 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: 506 Number of extensions: 24 Number of successful extensions: 4 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: 433 Length adjustment: 32 Effective length of query: 395 Effective length of database: 401 Effective search space: 158395 Effective search space used: 158395 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