Align C4-dicarboxylate TRAP transporter large permease protein DctM (characterized)
to candidate WP_049989147.1 LT39_RS03805 TRAP transporter large permease
Query= SwissProt::Q9HU16 (427 letters) >NCBI__GCF_000784335.1:WP_049989147.1 Length = 431 Score = 273 bits (699), Expect = 6e-78 Identities = 154/431 (35%), Positives = 252/431 (58%), Gaps = 8/431 (1%) Query: 1 MTILFLFLLLFLLMF-IGVPIAVSLGLSGALTILL----FSPDSVRSLAIKLFETSEHYT 55 + ++ LF+L+ L ++ IGVP+A +LGL+ + +L +SP+ V A L ++ + Sbjct: 3 VVLIALFILVLLALYLIGVPVAFALGLTSLILMLTPMVSYSPELV---AQTLVSGADSFV 59 Query: 56 LLAIPFFLLSGAFMTTGGVARRLIDFANACVGHIRGGLAIAAVLACMLFAALSGSSPATV 115 LLAIP FLL+G +M + G+ + DFA +G IRGG+A +LA +LF+ ++G++ A Sbjct: 60 LLAIPLFLLTGLYMNSFGLTSIIFDFAEEMIGPIRGGIAHVNILASILFSGMTGTAAADA 119 Query: 116 AAVGSIAIAGMVRSGYPQAFGAGIVCNAGTLGILIPPSIVMVVYAAATETSVGKLFIAGV 175 A +G+I M +GY + + A + ++ +G +IPPS+ +++Y + S+G LFIAG+ Sbjct: 120 AGLGAIEYEAMQDAGYEKGYSAAVTGSSAIIGPIIPPSVPLIMYGILAQVSIGVLFIAGI 179 Query: 176 VPGLLLGLILMVVIYIVARVKKLPAMPRVSLREWLASARKALWGLLLMVIILGGIYSGAF 235 VPGL++G L+++ A SL + S + A L V+I+GG+ G F Sbjct: 180 VPGLIMGATLLMLCTYYAHSHGYERGTWWSLPDIWESFKTAAPALGTPVLIIGGLLGGFF 239 Query: 236 TPTEAAAVAAVYSAFVALFVYRDMRLSECPKVLLESGKLTIMLMFIIANAMLFAHVLTTE 295 T TEA AVA Y+ FV Y + + + E T L FI+A+A L+ ++ Sbjct: 240 TATEAGAVALFYTLFVGYVFYGGVENGDFVETTYEGVVTTAALTFIVASATLYGFLVRRA 299 Query: 296 QIPQSIASWVTELGLSPWMFLLVVNIVLLIAGNFMEPSAIILILAPIFFPIAMELGIDPI 355 Q+P ++A V + P + LL++ VLLI G ME A I IL P+F P+ GIDPI Sbjct: 300 QLPDALAEAVIGVTGDPTLLLLMIVGVLLIVGLMMETIAAITILTPVFLPVIDVAGIDPI 359 Query: 356 HLGIIMVVNMEIGLITPPVGLNLFVTSAVTGMPLGATIRAALPWLMILLVFLIIVTYIPA 415 H GI+M++ + IGL+TPP G+ LF+ VT + L +R+ +P+ + LL+ L++V +P Sbjct: 360 HFGIVMILTLMIGLLTPPFGIILFILEKVTDVGLERIMRSMVPFYIPLLIILLLVVVLPG 419 Query: 416 VSLALPNWLGM 426 ++L LP ++G+ Sbjct: 420 LTLWLPKFVGL 430 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: 502 Number of extensions: 29 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: 431 Length adjustment: 32 Effective length of query: 395 Effective length of database: 399 Effective search space: 157605 Effective search space used: 157605 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 24 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