Align C4-dicarboxylate TRAP transporter large permease protein DctM (characterized)
to candidate GFF3943 Psest_4013 TRAP transporter, DctM subunit
Query= SwissProt::Q9HU16 (427 letters) >FitnessBrowser__psRCH2:GFF3943 Length = 458 Score = 194 bits (494), Expect = 4e-54 Identities = 137/452 (30%), Positives = 226/452 (50%), Gaps = 35/452 (7%) Query: 1 MTILFLFLLLFLLMFIGVPIAVSLG----LSGALTILLFSPDS--VRSLAIKLFETSEHY 54 M IL + F LM G P+A +LG L + ++ S D + +L ++F + Sbjct: 5 MAILLFISICFALMS-GYPVAFTLGGMALLFAGVGVVTGSFDVGYLHALPNRIFGIMNNQ 63 Query: 55 TLLAIPFFLLSGAFMTTGGVARRLIDFANACVGHIRGGLAIAAVLACMLFAALSGSSPAT 114 T+LA+P F+ G + VA L++ + G +RGGLAI+ + L AA +G AT Sbjct: 64 TMLAVPLFVFMGVMLEKSRVAEDLLESMSRLFGTMRGGLAISVCVVGALLAASTGIVGAT 123 Query: 115 VAAVGSIAIAGMVRSGYPQAFGAGIVCNAGTLGILIPPSIVMVVYA-------------- 160 V +G +A+ M+R GY A G + GTLG +IPPSI++V+ Sbjct: 124 VVTMGLLALPTMLRRGYDPAIATGTLAATGTLGQIIPPSIILVLLGDVMSSAFQQAQLKM 183 Query: 161 ---AATETSVGKLFIAGVVPGLLLGLILMVVIYIVA----RVKKLPAMPRVSLR--EWLA 211 + SVG LF+ ++PGLL L+ M ++Y++A + KKLPA+P+ L EW Sbjct: 184 GIFSPKTVSVGDLFVGALIPGLL--LVGMYILYLIAVAIFQPKKLPALPQEELGPIEWGK 241 Query: 212 SARKALWGLLLMVIILGGIYSGAFTPTEAAAVAAVYSAFVALFVYRDMRLSECPKVLLES 271 L L L+ +LG I +G TPTEAAA+ A+ + +++ + ++ +V + Sbjct: 242 LIGSLLPPLALITAVLGSILAGYATPTEAAAIGALGATLLSI-AKGQLNFTQLKQVAFGT 300 Query: 272 GKLTIMLMFIIANAMLFAHVLTTEQIPQSIASWVTELGLSPWMFLLVVNIVLLIAGNFME 331 ++T M+ I+ A LF+ V I + L LVV +V+ + G ++ Sbjct: 301 TEITSMVFLILIGASLFSLVFRGFGGEVLIEDALHSLPGGVLGAFLVVMLVIFLLGFILD 360 Query: 332 PSAIILILAPIFFPIAMELGIDPIHLGIIMVVNMEIGLITPPVGLNLFVTSAVT--GMPL 389 II ++ PI PI + +G+DP+ LG++ +N++ +TPP G +LF VT +P Sbjct: 361 FIEIIFVVVPIVGPILLAMGLDPVWLGVMFAINLQTSFLTPPFGFSLFYLRGVTPRSVPT 420 Query: 390 GATIRAALPWLMILLVFLIIVTYIPAVSLALP 421 + LP++ I + L++ P + LP Sbjct: 421 SVMYKGVLPFIAIQIGMLVVAYMWPGIVTWLP 452 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: 522 Number of extensions: 31 Number of successful extensions: 7 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: 458 Length adjustment: 32 Effective length of query: 395 Effective length of database: 426 Effective search space: 168270 Effective search space used: 168270 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 17 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