Align C4-dicarboxylate TRAP transporter large permease protein DctM (characterized)
to candidate GFF3978 HP15_3918 trap-type mannitol/chloroaromatic compound transport system, large permease component
Query= SwissProt::Q9HU16 (427 letters) >FitnessBrowser__Marino:GFF3978 Length = 436 Score = 251 bits (640), Expect = 4e-71 Identities = 149/436 (34%), Positives = 245/436 (56%), Gaps = 18/436 (4%) Query: 1 MTILFLFLLLFLLMFIGVPIAVSLGLSGALTILLFSP---DSVRSLAIKLFETSEHYTLL 57 +T+LF LLF L+ +G+P+A LG G + L+ DS +A +++ T +TL+ Sbjct: 6 LTLLFFGSLLFFLL-LGLPLAFVLG--GVSVVFLYFTWGFDSFYMVASQIWGTMGSFTLV 62 Query: 58 AIPFFLLSGAFMTTGGVARRLIDFANACVGHIRGGLAIAAVLACMLFAALSGSSPATVAA 117 AIP F+ + GVAR L + G +RGGLA+ + C +FAA+ G S A V A Sbjct: 63 AIPLFVFMAMILERTGVARDLYRMMHLWCGGLRGGLALGTLGICAVFAAMVGISGAAVVA 122 Query: 118 VGSIAIAGMVRSGYPQAFGAGIVCNAGTLGILIPPSIVMVVYAAATETSVGKLFIAGVVP 177 +G+IA+ M+ GY ++ G++ G GILIPPSI+M++YA T SVGK+F AG++P Sbjct: 123 MGTIALPSMLERGYDKSMALGVINTGGGWGILIPPSILMILYALITGVSVGKMFAAGIMP 182 Query: 178 GLLLGLILMVVIYIVARV----KKLPAMPRVSLREW---LASARKALWGLLLMVIILGGI 230 G+L L+++ IYI+ R + PA+P+ W + R L + ++V++LG I Sbjct: 183 GVL--LMVLTAIYIIVRCHLQPELAPALPKEDRGTWPEKFRALRAVLLPIGVVVMVLGSI 240 Query: 231 YSGAFTPTEAAAVAAVYSAFVALFVYRDMRLSECPKVLLESGKLTIMLMFIIANAMLFAH 290 G TPTEAAA+ V A ++ VYR + S + + + KLT M+M+I+ A F+ Sbjct: 241 IGGITTPTEAAAM-GVLGALISAAVYRQFKWSILKEAAIRTFKLTGMIMWILFAAHAFSA 299 Query: 291 VLTTEQIPQSIASWVTELGLSPWMFLLVVNIVLLIAGNFMEPSAIILILAPIFFPIAMEL 350 + + I + + PW ++ + +++ + ++P I+LI P+F PI L Sbjct: 300 AYQSMGAQELIEGLMNMVPGGPWGIIIAMMVIVFLLAMVLDPVGIMLITLPVFMPIVESL 359 Query: 351 GIDPIHLGIIMVVNMEIGLITPPVGLNLFVTSAVT--GMPLGATIRAALPWLMILLVFLI 408 G DPI GI+ V+NMEIG +TPP G NLF + + + ++ +P++++ +V +I Sbjct: 360 GFDPIWFGILFVINMEIGYMTPPFGFNLFYLKGIVPPSITMKDIYKSIIPFVIVEIVGII 419 Query: 409 IVTYIPAVSLALPNWL 424 ++ P ++ LP+ L Sbjct: 420 LIMVFPEIATWLPDLL 435 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: 525 Number of extensions: 25 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: 436 Length adjustment: 32 Effective length of query: 395 Effective length of database: 404 Effective search space: 159580 Effective search space used: 159580 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