Align C4-dicarboxylate TRAP transporter large permease protein DctM (characterized)
to candidate 1937061 b3578 predicted transporter (NCBI)
Query= SwissProt::Q9HU16 (427 letters) >FitnessBrowser__Keio:1937061 Length = 425 Score = 295 bits (756), Expect = 1e-84 Identities = 153/424 (36%), Positives = 249/424 (58%) Query: 1 MTILFLFLLLFLLMFIGVPIAVSLGLSGALTILLFSPDSVRSLAIKLFETSEHYTLLAIP 60 M +L L + IG+PIA +L L GA + V+ +A L ++ ++LLAIP Sbjct: 1 MAVLIFLGCLLGGIAIGLPIAWALLLCGAALMFWLDMFDVQIMAQTLVNGADSFSLLAIP 60 Query: 61 FFLLSGAFMTTGGVARRLIDFANACVGHIRGGLAIAAVLACMLFAALSGSSPATVAAVGS 120 FF+L+G M GG+++R++D VGH GGL VLA M+ A+LSGS+ A AAV + Sbjct: 61 FFVLAGEIMNAGGLSKRIVDLPMKLVGHKPGGLGYVGVLAAMIMASLSGSAVADTAAVAA 120 Query: 121 IAIAGMVRSGYPQAFGAGIVCNAGTLGILIPPSIVMVVYAAATETSVGKLFIAGVVPGLL 180 + + M + YP AG++ + G + +IPPSI +++ ++ S+ KLF+AG+ PG++ Sbjct: 121 LLVPMMRSANYPVNRAAGLIASGGIIAPIIPPSIPFIIFGVSSGLSISKLFMAGIAPGMM 180 Query: 181 LGLILMVVIYIVARVKKLPAMPRVSLREWLASARKALWGLLLMVIILGGIYSGAFTPTEA 240 +G LM+ + A LP + +++E S +W L L VII+GG SG FTPTEA Sbjct: 181 MGATLMLTWWWQASRLNLPRQQKATMQEIWHSFVSGIWALFLPVIIIGGFRSGLFTPTEA 240 Query: 241 AAVAAVYSAFVALFVYRDMRLSECPKVLLESGKLTIMLMFIIANAMLFAHVLTTEQIPQS 300 AVAA Y+ FVA +YR+M + VL+ + K T ++MF++A+A + A ++T ++P Sbjct: 241 GAVAAFYALFVATVIYREMTFATLWHVLIGAAKTTSVVMFLVASAQVSAWLITIAELPMM 300 Query: 301 IASWVTELGLSPWMFLLVVNIVLLIAGNFMEPSAIILILAPIFFPIAMELGIDPIHLGII 360 ++ + L SP + +V+ + +LI G M+ + +LIL P+ P+ E GIDPI+ G++ Sbjct: 301 VSDLLQPLVDSPRLLFIVIMVAILIVGMVMDLTPTVLILTPVLMPLVKEAGIDPIYFGVM 360 Query: 361 MVVNMEIGLITPPVGLNLFVTSAVTGMPLGATIRAALPWLMILLVFLIIVTYIPAVSLAL 420 ++N IGLITPP+G L V S V + +R P++++L L++ +IP + + Sbjct: 361 FIINCSIGLITPPIGNVLNVISGVAKLKFDDAVRGVFPYVLVLYSLLVVFVFIPDLIILP 420 Query: 421 PNWL 424 W+ Sbjct: 421 LKWI 424 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: 465 Number of extensions: 14 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: 425 Length adjustment: 32 Effective length of query: 395 Effective length of database: 393 Effective search space: 155235 Effective search space used: 155235 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