Transmembrane proteins

MacAB-like efflux pump, PDB ID: 5xu1

Hydrophobic Thickness	32 Å
Transmembrane segments coordinates	M - Tilt: 1( 15- 37), 2( 290- 313), 3( 339- 365), 4( 382- 405) S - Tilt: 1( 15- 37), 2( 290- 312), 3( 336- 364), 4( 382- 405)
Mean number of residues	23.5
Localization	Bacterial Gram-positive plasma membrane

MacAB-like efflux pump, PDB ID: 5xu1

Omp33 porin, PDB ID: 6gie

Hydrophobic Thickness	25 Å
Transmembrane segments coordinates	A - Tilt:1( 3- 10), 2( 22- 30), 3( 51- 58), 4( 74- 83), 5( 90- 97), 6( 115- 121), 7( 127- 134), 8( 169- 177), 9( 185- 194),10( 200- 206),11( 214- 219),12( 232- 239),13( 246- 251),14( 265- 272)
Mean number of residues	7
Localization	Bacterial Gram-negative outer membrane

Omp33 porin, PDB ID: 6gie

Prediction of transmembrane helices in proteins

TMHMM_M prediction for M chain of MacAB-like efflux pump protein, x-axis is the number of residues, y-axis is TMHMM probability, colors are defined on a figure.

TMHMM_M prediction for S chain of MacAB-like efflux pump protein, x-axis is the number of residues, y-axis is TMHMM probability, colors are defined on a figure.

PHOBIUS prediction for M chain of MacAB-like efflux pump protein, x-axis is the number of residues, y-axis is Phobius posterior probability, colors are defined on a figure.

PHOBIUS prediction for S chain of MacAB-like efflux pump protein, x-axis is the number of residues, y-axis is Phobius posterior probability, colors are defined on a figure.

Both predictions have the same amount of TM helixes, but the number of residues in all of them differs from the OPM real structure. TMHMM and Phobius algorithms use Hidden Markov Models, but the architecture differs.

Structure of HMM in Phobius algorithm

Structure of HMM in TMHMM algorithm

TCDB

Omp33 porin have an accession in TDCB with TC-code: 1.B.1 The General Bacterial Porin (GBP) Family.
OMP порины присутствуют во внешней мембране Грам-отрицательных бактерий, митохондрий и пластид. Они катализируют перенос небольших молекул (<1000 Da) без затрат энергии через внешнюю мембрану бактерий и органелл с разной степенью избирательности.
There is no accession for MacAB-like efflux pump in TDCB, but it partly blasted on proteins with TC-code: 3.A.1 The ATP-binding Cassette (ABC) Superfamily
ABC суперсемейство содержит импортирующие и экскретирующие транспортные белки, внутри этих подгрупп белки довольно близки структурно. ABС суперсемейство коррелирует с субстратной специфичностью и содержит очень много семейств.

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© Gumerov Ruslan, 2017