Query 036312
Match_columns 305
No_of_seqs 147 out of 805
Neff 3.9
Searched_HMMs 46136
Date Fri Mar 29 11:24:19 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/036312.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/036312hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PTZ00458 acyl CoA binding prot 100.0 3.4E-31 7.4E-36 212.6 10.3 86 149-241 3-88 (90)
2 cd00435 ACBP Acyl CoA binding 100.0 2.5E-30 5.4E-35 204.6 9.5 85 147-240 1-85 (85)
3 PF00887 ACBP: Acyl CoA bindin 100.0 3.4E-30 7.3E-35 202.2 8.4 87 147-240 1-87 (87)
4 KOG0817 Acyl-CoA-binding prote 100.0 4.2E-28 9.1E-33 208.9 11.5 94 145-247 3-96 (142)
5 COG4281 ACB Acyl-CoA-binding p 99.9 1.1E-23 2.4E-28 166.3 8.1 84 147-239 2-85 (87)
6 KOG3878 Protein involved in ma 99.1 1.4E-10 3E-15 112.9 8.1 96 137-242 26-124 (469)
7 smart00295 B41 Band 4.1 homolo 97.0 0.0045 9.8E-08 53.0 8.6 85 146-240 98-203 (207)
8 PF00373 FERM_M: FERM central 96.7 0.0079 1.7E-07 48.0 7.4 85 146-240 10-122 (126)
9 KOG3530 FERM domain protein EH 79.8 4.1 8.9E-05 43.3 6.2 63 173-235 121-195 (616)
10 KOG3529 Radixin, moesin and re 35.1 1.7E+02 0.0037 31.4 8.2 87 145-240 105-211 (596)
11 PHA02650 hypothetical protein; 34.7 45 0.00098 27.2 3.1 20 7-26 55-74 (81)
12 COG3065 Slp Starvation-inducib 33.0 45 0.00098 31.0 3.2 66 11-77 10-78 (191)
13 PHA02819 hypothetical protein; 29.4 57 0.0012 26.0 2.8 19 7-25 52-70 (71)
14 PHA02844 putative transmembran 28.6 48 0.001 26.7 2.3 19 7-25 54-72 (75)
15 PRK14759 potassium-transportin 28.2 97 0.0021 20.9 3.3 20 6-25 4-24 (29)
16 PHA03054 IMV membrane protein; 27.3 53 0.0011 26.3 2.3 19 7-25 54-72 (72)
17 KOG4261 Talin [Cytoskeleton] 26.8 1.1E+02 0.0023 34.5 5.1 64 172-235 227-303 (1003)
18 PHA02975 hypothetical protein; 25.7 80 0.0017 25.1 3.0 19 7-25 50-68 (69)
19 PRK11677 hypothetical protein; 25.6 73 0.0016 27.9 3.0 22 4-25 3-24 (134)
20 COG0841 AcrB Cation/multidrug 23.3 1E+02 0.0022 35.0 4.3 30 2-31 454-483 (1009)
21 TIGR00256 D-tyrosyl-tRNA(Tyr) 22.7 1.1E+02 0.0023 27.3 3.5 36 188-237 78-115 (145)
22 PF05552 TM_helix: Conserved T 21.8 1.6E+02 0.0034 21.1 3.7 23 8-30 18-40 (53)
23 cd00563 Dtyr_deacylase D-Tyros 21.4 1.1E+02 0.0025 27.1 3.5 38 188-239 78-117 (145)
24 PF04049 APC8: Anaphase promot 21.3 1.2E+02 0.0025 26.3 3.5 29 148-187 87-115 (142)
25 PF11674 DUF3270: Protein of u 21.3 1.3E+02 0.0027 24.9 3.5 17 13-29 64-80 (90)
26 PRK00753 psbL photosystem II r 20.9 1.1E+02 0.0023 21.9 2.6 16 4-19 20-35 (39)
27 PF00873 ACR_tran: AcrB/AcrD/A 20.2 84 0.0018 34.7 2.9 29 2-30 458-486 (1021)
No 1
>PTZ00458 acyl CoA binding protein; Provisional
Probab=99.97 E-value=3.4e-31 Score=212.62 Aligned_cols=86 Identities=29% Similarity=0.638 Sum_probs=80.5
Q ss_pred HHHHHHHHHHhhhhcccccCCCCCCCChHHHHHHHHHhhhhhcCCCCCCCCCccChhhhHHHHHHHHcCCCCHHHHHHHH
Q 036312 149 NVFATAVKFVEVSESQSESGKKRDDALSDVHMELYALHKIATEGPCRDPQPMPLMLSARSKWNAWQKLGNMNPEEAMERY 228 (305)
Q Consensus 149 e~Fe~Avk~Vk~~~~~~~s~p~~~~ls~D~kL~LYALYKQAT~GdCn~~kPg~~D~vgRaKWdAWkkLgGMSkEEAmk~Y 228 (305)
+.|++|+.+|+ +.+...+++++++|+|||||||||+|||+.++||+|++++|+||+||++++|||+++||++|
T Consensus 3 ~~F~~A~~~v~-------~~~~~~~~s~d~~L~lYalyKQAt~G~c~~~~P~~~d~~~raKw~AW~~l~~ms~~eA~~~Y 75 (90)
T PTZ00458 3 DLFEECVSFIN-------SLPKTVNLSVEIKLDLYKYYKQSTVGNCNIKEPSMFKYQDRKKYEAWKSIENLNREDAKKRY 75 (90)
T ss_pred HHHHHHHHHHH-------hCCCCCCCCHHHHHHHHHHHhhhccCCCCCCCCCcccHHHHHHHHHHHHcCCCCHHHHHHHH
Confidence 46999999998 34445689999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHhhcccccc
Q 036312 229 VALLSDRVPDWKE 241 (305)
Q Consensus 229 IeLV~el~P~W~~ 241 (305)
|+++.+++|.|..
T Consensus 76 I~l~~~l~~~w~~ 88 (90)
T PTZ00458 76 VEIVTELFPNWEK 88 (90)
T ss_pred HHHHHHHhhcccc
Confidence 9999999999984
No 2
>cd00435 ACBP Acyl CoA binding protein (ACBP) binds thiol esters of long fatty acids and coenzyme A in a one-to-one binding mode with high specificity and affinity. Acyl-CoAs are important intermediates in fatty lipid synthesis and fatty acid degradation and play a role in regulation of intermediary metabolism and gene regulation. The suggested role of ACBP is to act as a intracellular acyl-CoA transporter and pool former. ACBPs are present in a large group of eukaryotic species and several tissue-specific isoforms have been detected.
Probab=99.97 E-value=2.5e-30 Score=204.65 Aligned_cols=85 Identities=31% Similarity=0.597 Sum_probs=79.7
Q ss_pred HHHHHHHHHHHHhhhhcccccCCCCCCCChHHHHHHHHHhhhhhcCCCCCCCCCccChhhhHHHHHHHHcCCCCHHHHHH
Q 036312 147 LENVFATAVKFVEVSESQSESGKKRDDALSDVHMELYALHKIATEGPCRDPQPMPLMLSARSKWNAWQKLGNMNPEEAME 226 (305)
Q Consensus 147 LEe~Fe~Avk~Vk~~~~~~~s~p~~~~ls~D~kL~LYALYKQAT~GdCn~~kPg~~D~vgRaKWdAWkkLgGMSkEEAmk 226 (305)
|++.|++|+.+|+ + +...++++++|+|||||||||+|||+.++|++||+++|+||+||++++|||+++||+
T Consensus 1 ~~~~F~~A~~~v~-------~--~~~~~~~~~~L~lYalyKQAt~G~~~~~~P~~~d~~~~~K~~AW~~l~~ms~~eA~~ 71 (85)
T cd00435 1 LQEEFEAAAEKVK-------K--LKTKPSNEEKLQLYSLYKQATVGDCNTERPGMFDLKGRAKWDAWNSLKGMSKEDAMK 71 (85)
T ss_pred ChHHHHHHHHHHH-------h--CCCCcCHHHHHHHHHHHHHhccCCCCCCCCCcccHhhHHHHHHHHHcCCCCHHHHHH
Confidence 4578999999998 2 236899999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHhhccccc
Q 036312 227 RYVALLSDRVPDWK 240 (305)
Q Consensus 227 ~YIeLV~el~P~W~ 240 (305)
.||+++++++|.|.
T Consensus 72 ~YV~~~~~l~~~~~ 85 (85)
T cd00435 72 AYIAKVEELIAKYA 85 (85)
T ss_pred HHHHHHHHHhhccC
Confidence 99999999999983
No 3
>PF00887 ACBP: Acyl CoA binding protein; InterPro: IPR000582 Acyl-CoA-binding protein (ACBP) is a small (10 Kd) protein that binds medium- and long-chain acyl-CoA esters with very high affinity and may function as an intracellular carrier of acyl-CoA esters []. ACBP is also known as diazepam binding inhibitor (DBI) or endozepine (EP) because of its ability to displace diazepam from the benzodiazepine (BZD) recognition site located on the GABA type A receptor. It is therefore possible that this protein also acts as a neuropeptide to modulate the action of the GABA receptor []. ACBP is a highly conserved protein of about 90 residues that is found in all four eukaryotic kingdoms, Animalia, Plantae, Fungi and Protista, and in some eubacterial species []. Although ACBP occurs as a completely independent protein, intact ACB domains have been identified in a number of large, multifunctional proteins in a variety of eukaryotic species. These include large membrane-associated proteins with N-terminal ACB domains, multifunctional enzymes with both ACB and peroxisomal enoyl-CoA Delta(3), Delta(2)-enoyl-CoA isomerase domains, and proteins with both an ACB domain and ankyrin repeats (IPR002110 from INTERPRO) []. The ACB domain consists of four alpha-helices arranged in a bowl shape with a highly exposed acyl-CoA-binding site. The ligand is bound through specific interactions with residues on the protein, most notably several conserved positive charges that interact with the phosphate group on the adenosine-3'phosphate moiety, and the acyl chain is sandwiched between the hydrophobic surfaces of CoA and the protein []. Other proteins containing an ACB domain include: Endozepine-like peptide (ELP) (gene DBIL5) from mouse []. ELP is a testis-specific ACBP homologue that may be involved in the energy metabolism of the mature sperm. MA-DBI, a transmembrane protein of unknown function which has been found in mammals. MA-DBI contains a N-terminal ACB domain. DRS-1 [], a human protein of unknown function that contains a N-terminal ACB domain and a C-terminal enoyl-CoA isomerase/hydratase domain. ; GO: 0000062 fatty-acyl-CoA binding; PDB: 2CB8_A 2FJ9_A 2LBB_A 1ST7_A 3EPY_B 2FDQ_C 1NTI_A 1HB8_A 1ACA_A 1NVL_A ....
Probab=99.96 E-value=3.4e-30 Score=202.18 Aligned_cols=87 Identities=40% Similarity=0.738 Sum_probs=76.8
Q ss_pred HHHHHHHHHHHHhhhhcccccCCCCCCCChHHHHHHHHHhhhhhcCCCCCCCCCccChhhhHHHHHHHHcCCCCHHHHHH
Q 036312 147 LENVFATAVKFVEVSESQSESGKKRDDALSDVHMELYALHKIATEGPCRDPQPMPLMLSARSKWNAWQKLGNMNPEEAME 226 (305)
Q Consensus 147 LEe~Fe~Avk~Vk~~~~~~~s~p~~~~ls~D~kL~LYALYKQAT~GdCn~~kPg~~D~vgRaKWdAWkkLgGMSkEEAmk 226 (305)
|++.|..|+++|+ +.+....++++++|+|||||||||+|||+.++|+++|+.+|+||+||++++|||+++||+
T Consensus 1 Le~~F~~A~~~v~-------~~~~~~~~~~~~~L~LYalyKQAt~Gd~~~~~P~~~d~~~~~K~~AW~~l~gms~~eA~~ 73 (87)
T PF00887_consen 1 LEEEFEAAVEFVS-------NLPKKSQLSNDDKLELYALYKQATHGDCDTPRPGFFDIEGRAKWDAWKALKGMSKEEAMR 73 (87)
T ss_dssp HHHHHHHHHHHHH-------HSSSCSTS-HHHHHHHHHHHHHHHTSS--S-CTTTTCHHHHHHHHHHHTTTTTHHHHHHH
T ss_pred CHHHHHHHHHHHH-------hccccCCCCHHHHHHHHHHHHHHHhCCCcCCCCcchhHHHHHHHHHHHHccCCCHHHHHH
Confidence 7899999999999 333335899999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHhhccccc
Q 036312 227 RYVALLSDRVPDWK 240 (305)
Q Consensus 227 ~YIeLV~el~P~W~ 240 (305)
+||+++++++|.|.
T Consensus 74 ~Yi~~v~~~~~~~~ 87 (87)
T PF00887_consen 74 EYIELVEELIPKYE 87 (87)
T ss_dssp HHHHHHHHHHHHH-
T ss_pred HHHHHHHHHHHhcC
Confidence 99999999999883
No 4
>KOG0817 consensus Acyl-CoA-binding protein [Lipid transport and metabolism]
Probab=99.95 E-value=4.2e-28 Score=208.95 Aligned_cols=94 Identities=33% Similarity=0.582 Sum_probs=86.2
Q ss_pred chHHHHHHHHHHHHhhhhcccccCCCCCCCChHHHHHHHHHhhhhhcCCCCCCCCCccChhhhHHHHHHHHcCCCCHHHH
Q 036312 145 SELENVFATAVKFVEVSESQSESGKKRDDALSDVHMELYALHKIATEGPCRDPQPMPLMLSARSKWNAWQKLGNMNPEEA 224 (305)
Q Consensus 145 seLEe~Fe~Avk~Vk~~~~~~~s~p~~~~ls~D~kL~LYALYKQAT~GdCn~~kPg~~D~vgRaKWdAWkkLgGMSkEEA 224 (305)
..+...|+.|+..++ + +...++++++|+|||||||||+|||+.++||+||+++|+||+||+++||||+++|
T Consensus 3 ~~~~~~Fe~a~~~~~-------~--l~~~p~~ee~L~lYglyKQAt~G~~~~~kPg~~d~~~k~Kw~AW~~l~~~s~~eA 73 (142)
T KOG0817|consen 3 ATLEAKFEAAAEAVK-------N--LKKKPSNEELLKLYGLYKQATVGDCNTPKPGFFDEEGKAKWQAWNSLGGMSKEEA 73 (142)
T ss_pred chHHHHHHHHHHHHH-------h--cccCCCHHHHHHHHHHHHhhccCCCCCCCCchhhHHHHHHHHHHHhcCCCCHHHH
Confidence 457889999999999 3 3456999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHHhhccccccccccCC
Q 036312 225 MERYVALLSDRVPDWKEENYHVN 247 (305)
Q Consensus 225 mk~YIeLV~el~P~W~~~~~~~~ 247 (305)
|+.||+++.+++|.|........
T Consensus 74 ~~~Yv~~~~~l~~~~~~~~~~~~ 96 (142)
T KOG0817|consen 74 MEAYVEKVEELIPKYGAEAETEE 96 (142)
T ss_pred HHHHHHHHHHHHHHhhccccccc
Confidence 99999999999999997755443
No 5
>COG4281 ACB Acyl-CoA-binding protein [Lipid metabolism]
Probab=99.90 E-value=1.1e-23 Score=166.25 Aligned_cols=84 Identities=26% Similarity=0.409 Sum_probs=78.2
Q ss_pred HHHHHHHHHHHHhhhhcccccCCCCCCCChHHHHHHHHHhhhhhcCCCCCCCCCccChhhhHHHHHHHHcCCCCHHHHHH
Q 036312 147 LENVFATAVKFVEVSESQSESGKKRDDALSDVHMELYALHKIATEGPCRDPQPMPLMLSARSKWNAWQKLGNMNPEEAME 226 (305)
Q Consensus 147 LEe~Fe~Avk~Vk~~~~~~~s~p~~~~ls~D~kL~LYALYKQAT~GdCn~~kPg~~D~vgRaKWdAWkkLgGMSkEEAmk 226 (305)
+...|++|..-|+ + +..+|+++.+|+|||||||+++||.+..+||+||++||+||+||..|+|.|+++|.+
T Consensus 2 ~s~~Feqa~~dV~-------~--L~~kP~~d~LLkLYAL~KQ~s~GD~~~ekPG~~d~~gr~K~eAW~~LKGksqedA~q 72 (87)
T COG4281 2 LSTRFEQAQTDVK-------E--LSEKPSNDELLKLYALFKQGSVGDNDGEKPGFFDIVGRYKYEAWAGLKGKSQEDARQ 72 (87)
T ss_pred hhhHHHHHHHHHH-------H--hccCCCcHHHHHHHHHHHhccccccCCCCCCccccccchhHHHHhhccCccHHHHHH
Confidence 5678999999999 2 357899999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHhhcccc
Q 036312 227 RYVALLSDRVPDW 239 (305)
Q Consensus 227 ~YIeLV~el~P~W 239 (305)
+||.+|+++...+
T Consensus 73 eYialVeeLkak~ 85 (87)
T COG4281 73 EYIALVEELKAKY 85 (87)
T ss_pred HHHHHHHHHHhhc
Confidence 9999999997654
No 6
>KOG3878 consensus Protein involved in maintenance of Golgi structure and ER-Golgi transport [Intracellular trafficking, secretion, and vesicular transport]
Probab=99.12 E-value=1.4e-10 Score=112.88 Aligned_cols=96 Identities=27% Similarity=0.463 Sum_probs=85.8
Q ss_pred CCccccccchHHHHHHHHHHHHhhhhcccccCCCCCCCChHHHHHHHHHhhhhhcCCCCCC-CC--CccChhhhHHHHHH
Q 036312 137 DDWEGIERSELENVFATAVKFVEVSESQSESGKKRDDALSDVHMELYALHKIATEGPCRDP-QP--MPLMLSARSKWNAW 213 (305)
Q Consensus 137 dd~Egie~seLEe~Fe~Avk~Vk~~~~~~~s~p~~~~ls~D~kL~LYALYKQAT~GdCn~~-kP--g~~D~vgRaKWdAW 213 (305)
.+| |-+ |++.|..|+.|.+. +..+...++.+++|+|-+|.||+..||+|+. .| |+||+.|+.+..+|
T Consensus 26 ~~w-Gf~---LeElY~LA~~fyKe------~~GKa~h~~YEd~lKLial~kQv~~Gp~n~d~~p~~G~lDv~GnDr~~~W 95 (469)
T KOG3878|consen 26 EKW-GFP---LEELYRLAFTFYKE------NSGKAIHLSYEDNLKLIALKKQVALGPFNTDRAPALGVLDVIGNDRQQHW 95 (469)
T ss_pred HHh-CCC---HHHHHHHHHHHHHh------ccCCccCCChhhhhhhhhhHhhhhcCCCCcccCcccceeecccChHHHHH
Confidence 467 555 99999999999993 3335678999999999999999999999974 34 89999999999999
Q ss_pred HHcCCCCHHHHHHHHHHHHHhhccccccc
Q 036312 214 QKLGNMNPEEAMERYVALLSDRVPDWKEE 242 (305)
Q Consensus 214 kkLgGMSkEEAmk~YIeLV~el~P~W~~~ 242 (305)
..||.||+++||..||.|++.+++.|...
T Consensus 96 ~~LG~~sre~AM~~FV~Lldr~C~~F~~y 124 (469)
T KOG3878|consen 96 QLLGEISREQAMEGFVDLLDRMCSAFRPY 124 (469)
T ss_pred HHHhcccHHHHHHHHHHHHHhcchhhhhH
Confidence 99999999999999999999999998876
No 7
>smart00295 B41 Band 4.1 homologues. Also known as ezrin/radixin/moesin (ERM) protein domains. Present in myosins, ezrin, radixin, moesin, protein tyrosine phosphatases. Plasma membrane-binding domain. These proteins play structural and regulatory roles in the assembly and stabilization of specialized plasmamembrane domains. Some PDZ domain containing proteins bind one or more of this family. Now includes JAKs.
Probab=96.98 E-value=0.0045 Score=53.05 Aligned_cols=85 Identities=20% Similarity=0.199 Sum_probs=63.8
Q ss_pred hHHHHHHHHHHHHhhhhcccccCCCCCCCChHHHHHHHHHhhhhhcCCCCCCC-------------CC-ccCh-------
Q 036312 146 ELENVFATAVKFVEVSESQSESGKKRDDALSDVHMELYALHKIATEGPCRDPQ-------------PM-PLML------- 204 (305)
Q Consensus 146 eLEe~Fe~Avk~Vk~~~~~~~s~p~~~~ls~D~kL~LYALYKQAT~GdCn~~k-------------Pg-~~D~------- 204 (305)
.+.--|.++..-+. ++. -+.+.++...|-||.-|+..|+++.+. |. ..+-
T Consensus 98 ~~~~ly~Q~~~di~-------~g~--~~~~~~~~~~Laal~~q~~~gd~~~~~~~~~~~~~~~~~lP~~~~~~~~~~~~~ 168 (207)
T smart00295 98 RLNLLYLQVRNDIL-------EGR--LPCPEEEALLLAALALQAEFGDYDEELHVLLKELSLKRFLPKQLLDSEKRTLKE 168 (207)
T ss_pred HHHHHHHHHHHHHH-------cCc--cCCCHHHHHHHHHHHHHHHhcCCChHhcCCccccccceeCChhhhhhccccHHH
Confidence 36677888888887 332 356789999999999999999998532 11 1110
Q ss_pred hhhHHHHHHHHcCCCCHHHHHHHHHHHHHhhccccc
Q 036312 205 SARSKWNAWQKLGNMNPEEAMERYVALLSDRVPDWK 240 (305)
Q Consensus 205 vgRaKWdAWkkLgGMSkEEAmk~YIeLV~el~P~W~ 240 (305)
....--++|+++.|||+.+||.+||+++.++ |.|.
T Consensus 169 ~~~~i~~~~~~~~~~s~~~a~~~yl~~~~~l-p~fG 203 (207)
T smart00295 169 WRERIVSLHKELIGLSPEEAKLKYLELAEKL-PTYG 203 (207)
T ss_pred HHHHHHHHHHHcCCCCHHHHHHHHHHHhccc-cccC
Confidence 1222358899999999999999999999987 7665
No 8
>PF00373 FERM_M: FERM central domain; InterPro: IPR019748 The FERM domain (F for 4.1 protein, E for ezrin, R for radixin and M for moesin) is a widespread protein module involved in localising proteins to the plasma membrane []. FERM domains are found in a number of cytoskeletal-associated proteins that associate with various proteins at the interface between the plasma membrane and the cytoskeleton. The FERM domain is located at the N terminus of the majority of FERM-containing proteins [, ], which includes: Band 4.1, which links the spectrin-actin cytoskeleton of erythrocytes to the plasma membrane. Ezrin, a component of the undercoat of the microvilli plasma membrane. Moesin, which is probably involved in binding major cytoskeletal structures to the plasma membrane. Radixin, which is involved in the binding of the barbed end of actin filaments to the plasma membrane in the undercoat of the cell- to-cell adherens junction. Talin, a cytoskeletal protein concentrated in regions of cell-substratum contact and, in lymphocytes, of cell-cell contacts. Filopodin, a slime mold protein that binds actin and which is involved in the control of cell motility and chemotaxis. Merlin (or schwannomin). Protein NBL4. Unconventional myosins X, VIIa and XV, which are mutated in congenital deafness. Focal-adhesion kinases (FAKs), cytoplasmic protein tyrosine kinases involved in signalling through integrins. Janus tyrosine kinases (JAKs), cytoplasmic tyrosine kinases that are non-covalently associated with the cytoplasmic tails of receptors for cytokines or polypeptidic hormones. Non-receptor tyrosine-protein kinase TYK2. Protein-tyrosine phosphatases PTPN3 and PTPN4, enzyme that appear to act at junctions between the membrane and the cytoskeleton. Protein-tyrosine phosphatases PTPN14 and PTP-D1, PTP-RL10 and PTP2E. Caenorhabditis elegans protein phosphatase ptp-1. Ezrin, moesin, and radixin are highly related proteins (ERM protein family), but the other proteins in which the FERM domain is found do not share any region of similarity outside of this domain. ERM proteins are made of three domains, the FERM domain, a central helical domain and a C-terminal tail domain, which binds F-actin. The amino-acid sequence of the FERM domain is highly conserved among ERM proteins and is responsible for membrane association by direct binding to the cytoplasmic domain or tail of integral membrane proteins. ERM proteins are regulated by an intramolecular association of the FERM and C-terminal tail domains that masks their binding sites for other molecules. For cytoskeleton-membrane cross-linking, the dormant molecules becomes activated and the FERM domain attaches to the membrane by binding specific membrane proteins, while the last 34 residues of the tail bind actin filaments. Aside from binding to membranes, the activated FERM domain of ERM proteins can also bind the guanine nucleotide dissociation inhibitor of Rho GTPase (RhoDGI), which suggests that in addition to functioning as a cross-linker, ERM proteins may influence Rho signalling pathways. The crystal structure of the FERM domain reveals that it is composed of three structural modules (F1, F2, and F3) that together form a compact clover-shaped structure []. The FERM domain has also been called the amino-terminal domain, the 30kDa domain, 4.1N30, the membrane-cytoskeletal-linking domain, the ERM-like domain, the ezrin-like domain of the band 4.1 superfamily, the conserved N-terminal region, and the membrane attachment domain [].; PDB: 4DXA_B 2EMS_A 2ZPY_A 1J19_A 2D10_B 2D11_B 1GC6_A 2D2Q_A 2EMT_A 2YVC_A ....
Probab=96.70 E-value=0.0079 Score=47.98 Aligned_cols=85 Identities=21% Similarity=0.282 Sum_probs=60.3
Q ss_pred hHHHHHHHHHHHHhhhhcccccCCCCCCCChHHHHHHHHHhhhhhcCCCCCCC---CCcc-------------C------
Q 036312 146 ELENVFATAVKFVEVSESQSESGKKRDDALSDVHMELYALHKIATEGPCRDPQ---PMPL-------------M------ 203 (305)
Q Consensus 146 eLEe~Fe~Avk~Vk~~~~~~~s~p~~~~ls~D~kL~LYALYKQAT~GdCn~~k---Pg~~-------------D------ 203 (305)
.+.--|.++..-|- .+. -+.+.++-++|-||.-|+..|+++... .+.+ -
T Consensus 10 ~~~lly~Q~~~~vl-------~g~--~~~~~e~a~~LAAl~~q~~~gd~~~~~~~~~~~~~~~~~~~~~~~~iP~~~~~~ 80 (126)
T PF00373_consen 10 TRHLLYLQARRDVL-------QGR--LPCSEEDAIKLAALQLQAEYGDYNSEQEHSSGYIDPEIKEFQLENFIPKAPKLI 80 (126)
T ss_dssp HHHHHHHHHHHHHH-------TTS--STS-HHHHHHHHHHHHHHHHTSSTTTTTSSTTTTTGSHHCTCGHGTSSHHHHHH
T ss_pred HHHHHHHHHHHHHH-------cCc--CCCCHHHHHHHHHHHHHHHhcCCCcccccCcccccccccchhhhhhhhhhHHHH
Confidence 46677888888887 333 378999999999999999999998321 1111 1
Q ss_pred -hhhhHHH-----HHHHHcCCCCHHHHHHHHHHHHHhhccccc
Q 036312 204 -LSARSKW-----NAWQKLGNMNPEEAMERYVALLSDRVPDWK 240 (305)
Q Consensus 204 -~vgRaKW-----dAWkkLgGMSkEEAmk~YIeLV~el~P~W~ 240 (305)
......| ..|+++.|||+.+||..||+++.++ |.|.
T Consensus 81 ~~~~~~~~~~~I~~~~~~l~~~s~~~a~~~fl~~~~~~-p~yG 122 (126)
T PF00373_consen 81 KKMKQKEWEKRILEQHKKLRGMSPEEAKLQFLQICQSL-PTYG 122 (126)
T ss_dssp CCSTHHHHHHHHHHHHHHTTT--HHHHHHHHHHHHCTS-TTTT
T ss_pred hhhhHHHHHHHHHHHHHHhhCCCHHHHHHHHHHHHhcC-CCCC
Confidence 0122223 8899999999999999999999874 6554
No 9
>KOG3530 consensus FERM domain protein EHM2 [General function prediction only]
Probab=79.78 E-value=4.1 Score=43.29 Aligned_cols=63 Identities=14% Similarity=0.064 Sum_probs=49.0
Q ss_pred CCChHHHHHHHHHhhhhhcCCCCCCC--CCc---cChh-------hhHHHHHHHHcCCCCHHHHHHHHHHHHHhh
Q 036312 173 DALSDVHMELYALHKIATEGPCRDPQ--PMP---LMLS-------ARSKWNAWQKLGNMNPEEAMERYVALLSDR 235 (305)
Q Consensus 173 ~ls~D~kL~LYALYKQAT~GdCn~~k--Pg~---~D~v-------gRaKWdAWkkLgGMSkEEAmk~YIeLV~el 235 (305)
+-+-+.-.+|=||-=|+-.|||+..+ |+. |.++ ..+=.+-||.|+|+++.+|+-.|+..++-+
T Consensus 121 ~Cp~~~AaeLaAl~lQsELGDYn~~~Ht~~yVSefRf~p~Qte~LE~~I~e~hK~~rGqspaqAElnyLnkAkwL 195 (616)
T KOG3530|consen 121 YCPFETAAELAALILQSELGDYNEEEHTGGYVSEFRFLPNQTEELEERIFELHKELRGQSPAQAELNYLNKAKWL 195 (616)
T ss_pred CCchhhHHHHHHHHHHHHhcCCChhhccccceeeeEecccccHHHHHHHHHHHHHhcCCCHHHHHHHHHhhhhhh
Confidence 34667777888888899999999864 322 3332 334478999999999999999999998754
No 10
>KOG3529 consensus Radixin, moesin and related proteins of the ERM family [General function prediction only]
Probab=35.14 E-value=1.7e+02 Score=31.45 Aligned_cols=87 Identities=18% Similarity=0.181 Sum_probs=57.2
Q ss_pred chHHHHHHHHHHHHhhhhcccccCCCCCCCChHHHHHHHHHhhhhhcCCCCCC--CCCccC------------h-hhhHH
Q 036312 145 SELENVFATAVKFVEVSESQSESGKKRDDALSDVHMELYALHKIATEGPCRDP--QPMPLM------------L-SARSK 209 (305)
Q Consensus 145 seLEe~Fe~Avk~Vk~~~~~~~s~p~~~~ls~D~kL~LYALYKQAT~GdCn~~--kPg~~D------------~-vgRaK 209 (305)
..+...|-.+++---. + .....++++.-.|-+|-=||.+||.+.. +.+.++ . ....+
T Consensus 105 ~~t~~Lffl~vk~~il------~--~~i~~~~E~~~~las~~vqa~~gdy~~~~~~~~~l~~~~~lP~~~~~q~~~s~~~ 176 (596)
T KOG3529|consen 105 DITQHLFFLQVKEAIL------S--DEIYCPPETSVLLASYAVQAKYGDYDKETHKVGRLAGDRLLPQRVLDQHKMTPDM 176 (596)
T ss_pred HHHHHHHHHHHHHHHh------c--cCCCCCchHHHHHHHHHHHHHhccccchhhhhhccccCcccchhhhhhccccHHH
Confidence 3345556555554331 1 2456788999999999999999987631 111111 1 13344
Q ss_pred H-----HHHHHcCCCCHHHHHHHHHHHHHhhccccc
Q 036312 210 W-----NAWQKLGNMNPEEAMERYVALLSDRVPDWK 240 (305)
Q Consensus 210 W-----dAWkkLgGMSkEEAmk~YIeLV~el~P~W~ 240 (305)
| .=|....||.+++||-+|..++.+ ++-|.
T Consensus 177 ~e~ri~~~~~~~~~~~re~a~leylki~qd-le~yg 211 (596)
T KOG3529|consen 177 WEDRIKEWYAEHRGMTREEAMLEYLKIAQD-LEMYG 211 (596)
T ss_pred HHHHHHHHHHHHHhhhhhhHHHHHHHHhcc-ccccc
Confidence 4 347888999999999999999999 44444
No 11
>PHA02650 hypothetical protein; Provisional
Probab=34.72 E-value=45 Score=27.19 Aligned_cols=20 Identities=30% Similarity=0.565 Sum_probs=16.8
Q ss_pred HHHHHHHHHHHHHHHHHHHH
Q 036312 7 LVLTALIALLFSYLMAKLVS 26 (305)
Q Consensus 7 ~~~t~~~a~~fsfl~aklvs 26 (305)
+++.++++++|.||.-|++-
T Consensus 55 ~i~~v~i~~l~~flYLK~~~ 74 (81)
T PHA02650 55 LIFSLIIVALFSFFVFKGYT 74 (81)
T ss_pred HHHHHHHHHHHHHHHHHHhc
Confidence 46778889999999999873
No 12
>COG3065 Slp Starvation-inducible outer membrane lipoprotein [Cell envelope biogenesis, outer membrane]
Probab=33.03 E-value=45 Score=31.00 Aligned_cols=66 Identities=18% Similarity=0.307 Sum_probs=45.3
Q ss_pred HHHHHHHHHHHHHHHHHH--HccCCCccccchhcccccCcchhHHhhhhcccc-cccccccccccccccc
Q 036312 11 ALIALLFSYLMAKLVSFA--MSGAGDSASASVVEDLKDVDDDVIMEELQFGAK-MNVGILENQHRVEPVQ 77 (305)
Q Consensus 11 ~~~a~~fsfl~aklvs~~--~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~v~ 77 (305)
..+...++||++--+++- .-+.++.+.++... +..++.-.+-.++|||-| +++-...+++|+|+++
T Consensus 10 ~~l~~~laflLsgC~tiPk~l~g~~~~s~~s~~~-~~~~~~~~~gq~aR~GGkVvnv~n~~~rTrlEi~s 78 (191)
T COG3065 10 GALIGTLAFLLSGCVTIPKALKGESPTSQQSLVR-VMSQPQLYVGQQARFGGKVVNVINQKGRTRLEIAS 78 (191)
T ss_pred HHHHHHHHHHHhhcccCChhhcCCCCcchhheee-eccCCcccccceeeeCcEEEEEecCCCcEEEEEEe
Confidence 344567788888777763 33344333333333 445567778899999999 7899999999999854
No 13
>PHA02819 hypothetical protein; Provisional
Probab=29.35 E-value=57 Score=26.03 Aligned_cols=19 Identities=16% Similarity=0.397 Sum_probs=16.0
Q ss_pred HHHHHHHHHHHHHHHHHHH
Q 036312 7 LVLTALIALLFSYLMAKLV 25 (305)
Q Consensus 7 ~~~t~~~a~~fsfl~aklv 25 (305)
+++.++++++|.||.-|++
T Consensus 52 ~l~~~~~~~~~~flYLK~~ 70 (71)
T PHA02819 52 GLVTIVFVIIFIIFYLKVI 70 (71)
T ss_pred HHHHHHHHHHHHHHHHHhc
Confidence 4677888999999999986
No 14
>PHA02844 putative transmembrane protein; Provisional
Probab=28.64 E-value=48 Score=26.69 Aligned_cols=19 Identities=21% Similarity=0.439 Sum_probs=16.0
Q ss_pred HHHHHHHHHHHHHHHHHHH
Q 036312 7 LVLTALIALLFSYLMAKLV 25 (305)
Q Consensus 7 ~~~t~~~a~~fsfl~aklv 25 (305)
+++.++++++|.||.-|++
T Consensus 54 ~i~~v~~~~~~~flYLK~~ 72 (75)
T PHA02844 54 TIIFVVFATFLTFLYLKAV 72 (75)
T ss_pred HHHHHHHHHHHHHHHHhee
Confidence 4677888999999999986
No 15
>PRK14759 potassium-transporting ATPase subunit F; Provisional
Probab=28.17 E-value=97 Score=20.88 Aligned_cols=20 Identities=35% Similarity=0.574 Sum_probs=13.7
Q ss_pred HHHHHHHHHH-HHHHHHHHHH
Q 036312 6 DLVLTALIAL-LFSYLMAKLV 25 (305)
Q Consensus 6 e~~~t~~~a~-~fsfl~aklv 25 (305)
|..+.+++|+ ||.||++-|+
T Consensus 4 ~~~l~~~va~~L~vYL~~ALl 24 (29)
T PRK14759 4 DYSLAGAVSLGLLIYLTYALL 24 (29)
T ss_pred HHHHHHHHHHHHHHHHHHHHh
Confidence 4555566555 8899988764
No 16
>PHA03054 IMV membrane protein; Provisional
Probab=27.29 E-value=53 Score=26.29 Aligned_cols=19 Identities=42% Similarity=0.670 Sum_probs=15.5
Q ss_pred HHHHHHHHHHHHHHHHHHH
Q 036312 7 LVLTALIALLFSYLMAKLV 25 (305)
Q Consensus 7 ~~~t~~~a~~fsfl~aklv 25 (305)
+++.++++++|.||.-|++
T Consensus 54 ~l~~v~~~~l~~flYLK~~ 72 (72)
T PHA03054 54 IFFIVLILLLLIYLYLKVV 72 (72)
T ss_pred HHHHHHHHHHHHHHHHhcC
Confidence 5677888899999998874
No 17
>KOG4261 consensus Talin [Cytoskeleton]
Probab=26.79 E-value=1.1e+02 Score=34.47 Aligned_cols=64 Identities=17% Similarity=0.202 Sum_probs=45.0
Q ss_pred CCCChHHHHHHHHHhhhhhcCCCCCCCCCc-cC-----hh-------hhHHHHHHHHcCCCCHHHHHHHHHHHHHhh
Q 036312 172 DDALSDVHMELYALHKIATEGPCRDPQPMP-LM-----LS-------ARSKWNAWQKLGNMNPEEAMERYVALLSDR 235 (305)
Q Consensus 172 ~~ls~D~kL~LYALYKQAT~GdCn~~kPg~-~D-----~v-------gRaKWdAWkkLgGMSkEEAmk~YIeLV~el 235 (305)
.+++.+.--+|-|+--|...||.+..+|+. +| +. .+.-+.+-+.+++||-.+|+-+|+.+...+
T Consensus 227 hpv~~~kA~e~a~~qshiq~g~~~~~k~k~~ld~kd~lpk~y~k~k~ekKif~~~k~~~~~sei~ak~~y~k~~r~l 303 (1003)
T KOG4261|consen 227 HPVSFEKACEFAGFQSHIQFGPHNEDKHKGFLDLKDFLPKEYVKQKGEKKIFQAHKNCGGMSEIDAKVKYVKLARSL 303 (1003)
T ss_pred CchhHHHHHHHhccccccccCCchhhccccchhccccChHHHhccccchhhhhhhhhhcchhHHHHHHHHHHHhccc
Confidence 345666666666666677777766655543 22 11 233388999999999999999999998765
No 18
>PHA02975 hypothetical protein; Provisional
Probab=25.72 E-value=80 Score=25.12 Aligned_cols=19 Identities=21% Similarity=0.480 Sum_probs=15.8
Q ss_pred HHHHHHHHHHHHHHHHHHH
Q 036312 7 LVLTALIALLFSYLMAKLV 25 (305)
Q Consensus 7 ~~~t~~~a~~fsfl~aklv 25 (305)
+++.++++++|.||.-|++
T Consensus 50 ~i~~v~~~~~~~flYLK~~ 68 (69)
T PHA02975 50 FIIFITCIAVFTFLYLKLM 68 (69)
T ss_pred HHHHHHHHHHHHHHHHHhh
Confidence 4667888899999999986
No 19
>PRK11677 hypothetical protein; Provisional
Probab=25.55 E-value=73 Score=27.89 Aligned_cols=22 Identities=0% Similarity=0.144 Sum_probs=15.1
Q ss_pred HHHHHHHHHHHHHHHHHHHHHH
Q 036312 4 VQDLVLTALIALLFSYLMAKLV 25 (305)
Q Consensus 4 ~~e~~~t~~~a~~fsfl~aklv 25 (305)
|.-.+++++|+++++|+++++.
T Consensus 3 W~~a~i~livG~iiG~~~~R~~ 24 (134)
T PRK11677 3 WEYALIGLVVGIIIGAVAMRFG 24 (134)
T ss_pred HHHHHHHHHHHHHHHHHHHhhc
Confidence 5556667777777777777753
No 20
>COG0841 AcrB Cation/multidrug efflux pump [Defense mechanisms]
Probab=23.28 E-value=1e+02 Score=34.96 Aligned_cols=30 Identities=30% Similarity=0.466 Sum_probs=27.3
Q ss_pred hhHHHHHHHHHHHHHHHHHHHHHHHHHHcc
Q 036312 2 ELVQDLVLTALIALLFSYLMAKLVSFAMSG 31 (305)
Q Consensus 2 e~~~e~~~t~~~a~~fsfl~aklvs~~~~~ 31 (305)
++++++++|+.+|+++|.++|-.++=+++.
T Consensus 454 ~~f~~f~~tia~a~~~S~~vAltltP~L~a 483 (1009)
T COG0841 454 ELFRQFAITIAVAMLLSLLVALTLTPALCA 483 (1009)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 689999999999999999999999888774
No 21
>TIGR00256 D-tyrosyl-tRNA(Tyr) deacylase. This homodimeric enzyme appears able to cleave any D-amino acid (and glycine, which does not have distinct D/L forms) from charged tRNA. The name reflects characterization with respect to D-Tyr on tRNA(Tyr) as established in the literature, but substrate specificity seems much broader.
Probab=22.69 E-value=1.1e+02 Score=27.26 Aligned_cols=36 Identities=17% Similarity=0.099 Sum_probs=27.4
Q ss_pred hhh-cCCC-CCCCCCccChhhhHHHHHHHHcCCCCHHHHHHHHHHHHHhhcc
Q 036312 188 IAT-EGPC-RDPQPMPLMLSARSKWNAWQKLGNMNPEEAMERYVALLSDRVP 237 (305)
Q Consensus 188 QAT-~GdC-n~~kPg~~D~vgRaKWdAWkkLgGMSkEEAmk~YIeLV~el~P 237 (305)
|.| .|+| .+.||++.+ .|+++.|+..|-.++.++-.
T Consensus 78 QFTL~a~~~KG~rPsF~~--------------a~~~~~A~~ly~~fv~~l~~ 115 (145)
T TIGR00256 78 QFTLAADTKKGMRPSFSK--------------GASPDRAEELYEYFVELCRE 115 (145)
T ss_pred CCcccccCCCCCCCCccc--------------cCCHHHHHHHHHHHHHHHHh
Confidence 555 3677 567898644 47899999999999988863
No 22
>PF05552 TM_helix: Conserved TM helix; InterPro: IPR008910 This alignment represents a conserved transmembrane helix as well as some flanking sequence. It is often found in association with a Mechanosensitive (MS) channel IPR006685 from INTERPRO.; PDB: 2VV5_F 2OAU_E.
Probab=21.84 E-value=1.6e+02 Score=21.14 Aligned_cols=23 Identities=22% Similarity=0.450 Sum_probs=18.2
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHc
Q 036312 8 VLTALIALLFSYLMAKLVSFAMS 30 (305)
Q Consensus 8 ~~t~~~a~~fsfl~aklvs~~~~ 30 (305)
++.+++-+++++++||+|+-.+.
T Consensus 18 iv~AilIl~vG~~va~~v~~~~~ 40 (53)
T PF05552_consen 18 IVGAILILIVGWWVAKFVRKLVR 40 (53)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHHHHHHHH
Confidence 45677778899999999987665
No 23
>cd00563 Dtyr_deacylase D-Tyrosyl-tRNAtyr deacylases; a class of tRNA-dependent hydrolases which are capable of hydrolyzing the ester bond of D-Tyrosyl-tRNA reducing the level of cellular D-Tyrosine while recycling the peptidyl-tRNA; found in bacteria and in eukaryotes but not in archea; beta barrel-like fold structure; forms homodimers in which two surface cavities serve as the active site for tRNA binding
Probab=21.36 E-value=1.1e+02 Score=27.05 Aligned_cols=38 Identities=13% Similarity=0.038 Sum_probs=28.7
Q ss_pred hhh-cCCC-CCCCCCccChhhhHHHHHHHHcCCCCHHHHHHHHHHHHHhhcccc
Q 036312 188 IAT-EGPC-RDPQPMPLMLSARSKWNAWQKLGNMNPEEAMERYVALLSDRVPDW 239 (305)
Q Consensus 188 QAT-~GdC-n~~kPg~~D~vgRaKWdAWkkLgGMSkEEAmk~YIeLV~el~P~W 239 (305)
|.| .|+| .+.||++.. .|+++.|+..|-.++..+-..+
T Consensus 78 QFTL~~~~~KG~rP~F~~--------------a~~~e~A~~ly~~fv~~l~~~~ 117 (145)
T cd00563 78 QFTLYADTKKGRRPSFSA--------------AAPPDKAEPLYESFVELLREKG 117 (145)
T ss_pred ccccccccCCCCCCCccc--------------cCCHHHHHHHHHHHHHHHHHcC
Confidence 555 3677 567898654 4789999999999999886544
No 24
>PF04049 APC8: Anaphase promoting complex subunit 8 / Cdc23 ; InterPro: IPR007192 The anaphase-promoting complex is composed of eight protein subunits, including BimE (APC1), CDC27 (APC3), CDC16 (APC6), and CDC23 (APC8). This entry is for CDC23.; GO: 0030071 regulation of mitotic metaphase/anaphase transition, 0005680 anaphase-promoting complex
Probab=21.34 E-value=1.2e+02 Score=26.30 Aligned_cols=29 Identities=10% Similarity=0.128 Sum_probs=21.0
Q ss_pred HHHHHHHHHHHhhhhcccccCCCCCCCChHHHHHHHHHhh
Q 036312 148 ENVFATAVKFVEVSESQSESGKKRDDALSDVHMELYALHK 187 (305)
Q Consensus 148 Ee~Fe~Avk~Vk~~~~~~~s~p~~~~ls~D~kL~LYALYK 187 (305)
-+.|.+|+.+++. ..-+...-|+||+.|-
T Consensus 87 ~kEy~RaA~~L~~-----------~~s~~~~FL~lYs~YL 115 (142)
T PF04049_consen 87 CKEYDRAAHVLKD-----------CKSPKALFLRLYSRYL 115 (142)
T ss_pred hhHHHHHHHHHcc-----------CCCchHHHHHHHHHHH
Confidence 4569999999982 2234466899999884
No 25
>PF11674 DUF3270: Protein of unknown function (DUF3270); InterPro: IPR021688 This family of proteins with unknown function appears to be restricted to Streptococcus.
Probab=21.31 E-value=1.3e+02 Score=24.92 Aligned_cols=17 Identities=24% Similarity=0.589 Sum_probs=9.4
Q ss_pred HHHHHHHHHHHHHHHHH
Q 036312 13 IALLFSYLMAKLVSFAM 29 (305)
Q Consensus 13 ~a~~fsfl~aklvs~~~ 29 (305)
++-++||++|-++|+|.
T Consensus 64 l~t~~Af~~Ai~~Sl~~ 80 (90)
T PF11674_consen 64 LNTFWAFPLAILISLAI 80 (90)
T ss_pred hhHHHHHHHHHHHHHHH
Confidence 34455556666666654
No 26
>PRK00753 psbL photosystem II reaction center L; Provisional
Probab=20.88 E-value=1.1e+02 Score=21.91 Aligned_cols=16 Identities=31% Similarity=0.503 Sum_probs=11.4
Q ss_pred HHHHHHHHHHHHHHHH
Q 036312 4 VQDLVLTALIALLFSY 19 (305)
Q Consensus 4 ~~e~~~t~~~a~~fsf 19 (305)
.--|++..++|+|||-
T Consensus 20 y~GlLlifvl~vLFss 35 (39)
T PRK00753 20 YLGLLLVFVLGILFSS 35 (39)
T ss_pred HHHHHHHHHHHHHHHh
Confidence 3456777888888873
No 27
>PF00873 ACR_tran: AcrB/AcrD/AcrF family; InterPro: IPR001036 The Escherichia coli acrA and acrB genes encode a multi-drug efflux system that is believed to protect the bacterium against hydrophobic inhibitors []. The E. coli AcrB protein is a transporter that is energized by proton-motive force and that shows the widest substrate specificity among all known multidrug pumps, ranging from most of the currently used antibiotics, disinfectants, dyes, and detergents to simple solvents. The structure of ligand-free AcrB shows that it is a homotrimer of 110kDa per subunit. Each subunit contains 12 transmembrane helices and two large periplasmic domains (each exceeding 300 residues) between helices 1 and 2, and helices 7 and 8. X-ray analysis of the overexpressed AcrB protein demonstrated that the three periplasmic domains form, in the centre, a funnel-like structure and a connected narrow (or closed) pore. The pore is opened to the periplasm through three vestibules located at subunit interfaces. These vestibules were proposed to allow direct access of drugs from the periplasm as well as the outer leaflet of the cytoplasmic membrane. The three transmembrane domains of AcrB protomers form a large, 30A-wide central cavity that spans the cytoplasmic membrane and extends to the cytoplasm X-ray crystallographic structures of the trimeric AcrB pump from E. coli with four structurally diverse ligands demonstrated that three molecules of ligand bind simultaneously to the extremely large central cavity of 5000 cubic angstroms, primarily by hydrophobic, aromatic stacking and van der Waals interactions. Each ligand uses a slightly different subset of AcrB residues for binding. The bound ligand molecules often interact with each other, stabilising the binding. ; GO: 0005215 transporter activity, 0006810 transport, 0016020 membrane; PDB: 2V50_B 1T9U_A 2HRT_B 3NOC_A 3NOG_A 4DX7_A 1OYD_A 3AOB_A 1T9V_A 4DX6_B ....
Probab=20.17 E-value=84 Score=34.75 Aligned_cols=29 Identities=34% Similarity=0.450 Sum_probs=25.1
Q ss_pred hhHHHHHHHHHHHHHHHHHHHHHHHHHHc
Q 036312 2 ELVQDLVLTALIALLFSYLMAKLVSFAMS 30 (305)
Q Consensus 2 e~~~e~~~t~~~a~~fsfl~aklvs~~~~ 30 (305)
++++.|.+|+++||++|+++|-++-=+++
T Consensus 458 ~~~~~l~~~v~~al~~Sllval~~~P~l~ 486 (1021)
T PF00873_consen 458 QFFRPLALTVIIALIASLLVALTLVPALA 486 (1021)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHTTHHHHH
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHhhhhhh
Confidence 47899999999999999999998766555
Done!