Query 025004
Match_columns 259
No_of_seqs 114 out of 132
Neff 4.3
Searched_HMMs 46136
Date Fri Mar 29 09:11:17 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/025004.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/025004hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF04505 Dispanin: Interferon- 88.5 0.16 3.4E-06 39.4 0.4 18 234-251 25-43 (82)
2 PF02326 YMF19: Plant ATP synt 58.4 15 0.00033 28.8 3.8 30 205-248 10-39 (86)
3 KOG2927 Membrane component of 55.3 38 0.00083 33.4 6.7 13 237-249 239-251 (372)
4 COG3671 Predicted membrane pro 54.2 55 0.0012 27.8 6.6 47 208-254 70-116 (125)
5 PF02656 DUF202: Domain of unk 51.9 60 0.0013 23.7 5.9 49 82-130 17-70 (73)
6 PF10329 DUF2417: Region of un 46.1 98 0.0021 28.7 7.5 80 168-251 35-123 (232)
7 PF13748 ABC_membrane_3: ABC t 43.5 59 0.0013 30.3 5.7 73 52-133 75-164 (237)
8 PTZ00201 amastin surface glyco 38.9 48 0.001 29.9 4.2 21 222-242 84-104 (192)
9 PHA03283 envelope glycoprotein 37.9 28 0.00062 35.9 2.9 28 106-133 397-431 (542)
10 PF11712 Vma12: Endoplasmic re 37.5 55 0.0012 27.3 4.2 27 166-192 78-104 (142)
11 PF11368 DUF3169: Protein of u 35.8 1.1E+02 0.0024 27.6 6.2 17 202-218 126-142 (248)
12 PF05478 Prominin: Prominin; 34.9 44 0.00094 35.6 3.9 29 207-239 89-117 (806)
13 KOG1935 Membrane protein Patch 33.8 40 0.00088 37.1 3.4 40 209-248 1026-1071(1143)
14 PF02985 HEAT: HEAT repeat; I 28.2 32 0.00068 21.3 1.0 19 45-63 8-26 (31)
15 MTH00169 ATP8 ATP synthase F0 27.5 99 0.0021 23.3 3.7 14 204-217 10-23 (67)
16 PF05961 Chordopox_A13L: Chord 27.3 74 0.0016 24.5 3.0 14 239-252 11-24 (68)
17 PF12326 EOS1: N-glycosylation 26.8 2.1E+02 0.0045 25.0 6.0 43 86-131 51-94 (148)
18 PHA03049 IMV membrane protein; 25.7 82 0.0018 24.2 3.0 12 241-252 13-24 (68)
19 smart00714 LITAF Possible memb 25.5 69 0.0015 23.3 2.5 9 236-244 37-45 (67)
20 PF01534 Frizzled: Frizzled/Sm 25.3 3.2E+02 0.007 26.3 7.7 29 170-198 96-125 (328)
21 TIGR02741 TraQ type-F conjugat 25.2 64 0.0014 25.4 2.3 22 69-94 32-53 (80)
22 PF01036 Bac_rhodopsin: Bacter 24.3 2.7E+02 0.0059 24.6 6.5 126 63-225 72-208 (222)
23 PF10601 zf-LITAF-like: LITAF- 24.1 89 0.0019 23.0 2.9 15 230-244 37-51 (73)
24 PF06814 Lung_7-TM_R: Lung sev 22.9 5.9E+02 0.013 23.3 11.3 122 72-220 45-167 (295)
25 PF02932 Neur_chan_memb: Neuro 22.5 2.4E+02 0.0051 22.1 5.3 12 213-224 33-44 (237)
26 PF02411 MerT: MerT mercuric t 22.3 80 0.0017 26.2 2.6 18 231-248 18-35 (116)
27 PF09125 COX2-transmemb: Cytoc 22.1 51 0.0011 22.7 1.1 22 69-90 11-32 (38)
28 PF08370 PDR_assoc: Plant PDR 21.7 66 0.0014 24.2 1.8 16 206-221 27-43 (65)
29 PRK14010 potassium-transportin 21.5 2E+02 0.0043 30.4 5.8 41 208-249 223-269 (673)
30 PRK14749 hypothetical protein; 20.5 1.7E+02 0.0038 19.2 3.3 23 106-128 4-27 (30)
No 1
>PF04505 Dispanin: Interferon-induced transmembrane protein; InterPro: IPR007593 This family includes the human leukocyte antigen CD225, which is an interferon inducible transmembrane protein, and is associated with interferon induced cell growth suppression [].; GO: 0009607 response to biotic stimulus, 0016021 integral to membrane
Probab=88.54 E-value=0.16 Score=39.37 Aligned_cols=18 Identities=50% Similarity=1.202 Sum_probs=13.3
Q ss_pred HHHHhhHH-HHHHHHHHhh
Q 025004 234 IALCCCLP-CIIAILYAVA 251 (259)
Q Consensus 234 ialCCCLP-cIIaiLyav~ 251 (259)
..+|||+| -|++|.|+..
T Consensus 25 s~l~Cc~PlGi~Ai~~s~k 43 (82)
T PF04505_consen 25 STLCCCWPLGIVAIVYSSK 43 (82)
T ss_pred HHHHHHhhHHHHHheechh
Confidence 34599999 4777878776
No 2
>PF02326 YMF19: Plant ATP synthase F0; InterPro: IPR003319 ATPases (or ATP synthases) are membrane-bound enzyme complexes/ion transporters that combine ATP synthesis and/or hydrolysis with the transport of protons across a membrane. ATPases can harness the energy from a proton gradient, using the flux of ions across the membrane via the ATPase proton channel to drive the synthesis of ATP. Some ATPases work in reverse, using the energy from the hydrolysis of ATP to create a proton gradient. There are different types of ATPases, which can differ in function (ATP synthesis and/or hydrolysis), structure (e.g., F-, V- and A-ATPases, which contain rotary motors) and in the type of ions they transport [, ]. The different types include: F-ATPases (F1F0-ATPases), which are found in mitochondria, chloroplasts and bacterial plasma membranes where they are the prime producers of ATP, using the proton gradient generated by oxidative phosphorylation (mitochondria) or photosynthesis (chloroplasts). V-ATPases (V1V0-ATPases), which are primarily found in eukaryotic vacuoles and catalyse ATP hydrolysis to transport solutes and lower pH in organelles. A-ATPases (A1A0-ATPases), which are found in Archaea and function like F-ATPases (though with respect to their structure and some inhibitor responses, A-ATPases are more closely related to the V-ATPases). P-ATPases (E1E2-ATPases), which are found in bacteria and in eukaryotic plasma membranes and organelles, and function to transport a variety of different ions across membranes. E-ATPases, which are cell-surface enzymes that hydrolyse a range of NTPs, including extracellular ATP. F-ATPases (also known as F1F0-ATPase, or H(+)-transporting two-sector ATPase) (3.6.3.14 from EC) are composed of two linked complexes: the F1 ATPase complex is the catalytic core and is composed of 5 subunits (alpha, beta, gamma, delta, epsilon), while the F0 ATPase complex is the membrane-embedded proton channel that is composed of at least 3 subunits (A-C), nine in mitochondria (A-G, F6, F8). Both the F1 and F0 complexes are rotary motors that are coupled back-to-back. In the F1 complex, the central gamma subunit forms the rotor inside the cylinder made of the alpha(3)beta(3) subunits, while in the F0 complex, the ring-shaped C subunits forms the rotor. The two rotors rotate in opposite directions, but the F0 rotor is usually stronger, using the force from the proton gradient to push the F1 rotor in reverse in order to drive ATP synthesis []. These ATPases can also work in reverse to hydrolyse ATP to create a proton gradient. This entry represents subunit 8 (or ymf19) found in the F0 complex of mitochondrial F-ATPases from plants and algae. This subunit is sometimes found in association and N-terminal to IPR009455 from INTERPRO, in higher plants. Subunit 8 differs in sequence between plants, Metazoa (IPR001421 from INTERPRO) and fungi (IPR009230 from INTERPRO) [, ]. More information about this protein can be found at Protein of the Month: ATP Synthases [].; GO: 0015078 hydrogen ion transmembrane transporter activity, 0015986 ATP synthesis coupled proton transport, 0000276 mitochondrial proton-transporting ATP synthase complex, coupling factor F(o)
Probab=58.44 E-value=15 Score=28.77 Aligned_cols=30 Identities=33% Similarity=0.699 Sum_probs=20.1
Q ss_pred chhHHHHHHHHhhhhHHHHHHHHHHHHHHHHHHhhHHHHHHHHH
Q 025004 205 PRLYWLAVVFLAFDVFFAIFCVVLACLIGIALCCCLPCIIAILY 248 (259)
Q Consensus 205 P~LYwLcivFLAFd~ifvvfcyal~cli~ialCCCLPcIIaiLy 248 (259)
+|.+|+|+.|++|=.+++ -..||-|..+|-
T Consensus 10 sQ~fW~~i~f~~~y~~~~--------------~~~lP~i~~~lk 39 (86)
T PF02326_consen 10 SQYFWLLIFFFFFYIFLV--------------NFILPKISRILK 39 (86)
T ss_pred HHHHHHHHHHHHHHHHHH--------------HHHHHHHHHHHH
Confidence 577899999886544421 346787777663
No 3
>KOG2927 consensus Membrane component of ER protein translocation complex [Intracellular trafficking, secretion, and vesicular transport]
Probab=55.31 E-value=38 Score=33.45 Aligned_cols=13 Identities=31% Similarity=-0.003 Sum_probs=8.4
Q ss_pred HhhHHHHHHHHHH
Q 025004 237 CCCLPCIIAILYA 249 (259)
Q Consensus 237 CCCLPcIIaiLya 249 (259)
=|.|-||++|||-
T Consensus 239 RlILF~I~~il~~ 251 (372)
T KOG2927|consen 239 RLILFGITWILTG 251 (372)
T ss_pred HHHHHHHHHHHhC
Confidence 3556667777764
No 4
>COG3671 Predicted membrane protein [Function unknown]
Probab=54.22 E-value=55 Score=27.83 Aligned_cols=47 Identities=17% Similarity=0.492 Sum_probs=39.7
Q ss_pred HHHHHHHHhhhhHHHHHHHHHHHHHHHHHHhhHHHHHHHHHHhhccc
Q 025004 208 YWLAVVFLAFDVFFAIFCVVLACLIGIALCCCLPCIIAILYAVAGQV 254 (259)
Q Consensus 208 YwLcivFLAFd~ifvvfcyal~cli~ialCCCLPcIIaiLyav~~qe 254 (259)
||+|+.+--.+.++..++..+..++...+-..+=|++.+.|-..||-
T Consensus 70 Fw~~vl~~iIg~Llt~lgiGv~i~~AlgvW~i~Riv~G~~yl~~g~a 116 (125)
T COG3671 70 FWLAVLWWIIGLLLTFLGIGVVILVALGVWYIYRIVIGFKYLNEGKA 116 (125)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCc
Confidence 58888887777777777888888888999999999999999888763
No 5
>PF02656 DUF202: Domain of unknown function (DUF202); InterPro: IPR003807 This entry describes proteins of unknown function.
Probab=51.92 E-value=60 Score=23.68 Aligned_cols=49 Identities=33% Similarity=0.386 Sum_probs=31.9
Q ss_pred HHHHHHHHHHHHHhccCCCCCc---hHHHHHHHhhhhHHHHHHHHH--HHHHHh
Q 025004 82 NSAFVIVSAAMLIITINERPST---RIRLWICGYALQCLVHVVLVW--MEYRRR 130 (259)
Q Consensus 82 nLaqIvaAivVL~lS~~E~P~~---PLr~WIvGYa~gCv~hl~lV~--~rYr~R 130 (259)
.++.+++++.++-....+++.. .--..++|+.+-.+..+.+++ +||+++
T Consensus 17 ~l~l~~~g~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ry~~~ 70 (73)
T PF02656_consen 17 ALALVGVGLALLRFFSLDHPSSSASRRVSKVLGLLLIVLGLLTLIYGIYRYRRR 70 (73)
T ss_pred HHHHHHHHHHHHHhccccccccccchHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 4667777777777776554421 334668898888887777776 445544
No 6
>PF10329 DUF2417: Region of unknown function (DUF2417); InterPro: IPR019431 This entry represents a family of fungal proteins with no known function. In some cases these proteins also contain an alpha/beta hydrolase fold (IPR000073 from INTERPRO).
Probab=46.13 E-value=98 Score=28.67 Aligned_cols=80 Identities=15% Similarity=0.238 Sum_probs=43.4
Q ss_pred hhHHHHhHHHHHHHHHHHHhhheeeeeecCccccccCchhH--H---HHHHHHhhhhHHHHHHHHHH----HHHHHHHHh
Q 025004 168 TSFTKRCESINTMASFLWWIVGFYWVVSGGDLLLQAAPRLY--W---LAVVFLAFDVFFAIFCVVLA----CLIGIALCC 238 (259)
Q Consensus 168 ~~i~k~lesalt~Ff~VWfVVGf~WV~~gg~ss~~daP~LY--w---LcivFLAFd~ifvvfcyal~----cli~ialCC 238 (259)
-+..|-+-.++....++|||+-.+=.|..-....+..+-.+ + ++++-+.++-+| +++| -++++.+|+
T Consensus 35 ir~~r~i~~~~l~i~~iw~v~llvS~F~s~Pg~~~Rg~~F~~~~l~~lsl~~~~~~L~F----f~vpS~~~r~l~~vl~~ 110 (232)
T PF10329_consen 35 IRNLRWILNIFLAINFIWWVLLLVSDFFSPPGFNNRGSGFLDFDLTLLSLITNLFNLWF----FGVPSKLERILNIVLAG 110 (232)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCCCCCCCchHHHHHHHHHHHHHHHHHHh----eecCcHHHHHHHHHHHH
Confidence 35667777788888899999876644432223223333322 3 344444444443 3333 566677776
Q ss_pred hHHHHHHHHHHhh
Q 025004 239 CLPCIIAILYAVA 251 (259)
Q Consensus 239 CLPcIIaiLyav~ 251 (259)
++=.=.-++++|.
T Consensus 111 Lllvdlilil~V~ 123 (232)
T PF10329_consen 111 LLLVDLILILAVP 123 (232)
T ss_pred HHHHHHHHHHhhH
Confidence 6653333344443
No 7
>PF13748 ABC_membrane_3: ABC transporter transmembrane region
Probab=43.47 E-value=59 Score=30.32 Aligned_cols=73 Identities=21% Similarity=0.345 Sum_probs=53.3
Q ss_pred HhhHhHHHH--HHHhhcCCCCCCch----hh------H-----HHHHHHHHHHHHHHHHHhccCCCCCchHHHHHHHhhh
Q 025004 52 LVRETAARE--LEERRADWGYSKPV----VA------L-----DIMWNSAFVIVSAAMLIITINERPSTRIRLWICGYAL 114 (259)
Q Consensus 52 ~vre~aa~~--le~r~~dwaySk~~----v~------L-----elvwnLaqIvaAivVL~lS~~E~P~~PLr~WIvGYa~ 114 (259)
++|+.-|-+ ++.|+.+-..|+.- ++ + .++-++++++.|+++|.. +-.|+-.=.+
T Consensus 75 rIy~~la~~vi~~qr~~~~~~S~i~ARv~lsRE~VdFfE~~lP~lits~vsivga~vmLl~---------~e~~~g~~~l 145 (237)
T PF13748_consen 75 RIYAELAVPVILSQRQQGLSVSTIAARVALSREFVDFFEQHLPTLITSVVSIVGAAVMLLV---------FEFWLGLACL 145 (237)
T ss_pred HHHHHHhHHHHHHHHHhCCChhHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHH---------HHHHHHHHHH
Confidence 456666666 66666666555432 11 1 235789999999999975 4589988888
Q ss_pred hHHHHHHHHHHHHHHhhcc
Q 025004 115 QCLVHVVLVWMEYRRRNTR 133 (259)
Q Consensus 115 gCv~hl~lV~~rYr~Rn~~ 133 (259)
+=++-+.+++.+|-++|.+
T Consensus 146 ~~l~~~~~i~~~f~~~~~~ 164 (237)
T PF13748_consen 146 LILALFLLILPRFARRNYR 164 (237)
T ss_pred HHHHHHHHHHHHHHHHHHH
Confidence 8889999999999888765
No 8
>PTZ00201 amastin surface glycoprotein; Provisional
Probab=38.86 E-value=48 Score=29.86 Aligned_cols=21 Identities=19% Similarity=0.235 Sum_probs=13.0
Q ss_pred HHHHHHHHHHHHHHHHhhHHH
Q 025004 222 AIFCVVLACLIGIALCCCLPC 242 (259)
Q Consensus 222 vvfcyal~cli~ialCCCLPc 242 (259)
.+|.|..++++|+..-||-+|
T Consensus 84 SI~v~~aA~vlg~~~l~cc~~ 104 (192)
T PTZ00201 84 SILVYGAAFVLGLVLLYGCTI 104 (192)
T ss_pred HHHHHHHHHHHHHHHHHccch
Confidence 445888888886664334333
No 9
>PHA03283 envelope glycoprotein E; Provisional
Probab=37.89 E-value=28 Score=35.89 Aligned_cols=28 Identities=32% Similarity=0.578 Sum_probs=19.6
Q ss_pred HHHH-HHhhhhHHHHHHHH------HHHHHHhhcc
Q 025004 106 RLWI-CGYALQCLVHVVLV------WMEYRRRNTR 133 (259)
Q Consensus 106 r~WI-vGYa~gCv~hl~lV------~~rYr~Rn~~ 133 (259)
+-|+ +++.++|++-+.++ |.+||++|++
T Consensus 397 ~~~l~~~~~~~~~~~~~~~~l~vw~c~~~r~~~~~ 431 (542)
T PHA03283 397 RHYLAFLLAIICTCAALLVALVVWGCILYRRSNRK 431 (542)
T ss_pred cccchhHHHHHHHHHHHHHHHhhhheeeehhhcCC
Confidence 5666 78888888665443 5677877766
No 10
>PF11712 Vma12: Endoplasmic reticulum-based factor for assembly of V-ATPase; InterPro: IPR021013 ATPases (or ATP synthases) are membrane-bound enzyme complexes/ion transporters that combine ATP synthesis and/or hydrolysis with the transport of protons across a membrane. ATPases can harness the energy from a proton gradient, using the flux of ions across the membrane via the ATPase proton channel to drive the synthesis of ATP. Some ATPases work in reverse, using the energy from the hydrolysis of ATP to create a proton gradient. There are different types of ATPases, which can differ in function (ATP synthesis and/or hydrolysis), structure (e.g., F-, V- and A-ATPases, which contain rotary motors) and in the type of ions they transport [, ]. The different types include: F-ATPases (F1F0-ATPases), which are found in mitochondria, chloroplasts and bacterial plasma membranes where they are the prime producers of ATP, using the proton gradient generated by oxidative phosphorylation (mitochondria) or photosynthesis (chloroplasts). V-ATPases (V1V0-ATPases), which are primarily found in eukaryotic vacuoles and catalyse ATP hydrolysis to transport solutes and lower pH in organelles. A-ATPases (A1A0-ATPases), which are found in Archaea and function like F-ATPases (though with respect to their structure and some inhibitor responses, A-ATPases are more closely related to the V-ATPases). P-ATPases (E1E2-ATPases), which are found in bacteria and in eukaryotic plasma membranes and organelles, and function to transport a variety of different ions across membranes. E-ATPases, which are cell-surface enzymes that hydrolyse a range of NTPs, including extracellular ATP. V-ATPases (also known as V1V0-ATPase or vacuolar ATPase) (3.6.3.14 from EC) are found in the eukaryotic endomembrane system, and in the plasma membrane of prokaryotes and certain specialised eukaryotic cells. V-ATPases hydrolyse ATP to drive a proton pump, and are involved in a variety of vital intra- and inter-cellular processes such as receptor mediated endocytosis, protein trafficking, active transport of metabolites, homeostasis and neurotransmitter release []. V-ATPases are composed of two linked complexes: the V1 complex (subunits A-H) contains the catalytic core that hydrolyses ATP, while the V0 complex (subunits a, c, c', c'', d) forms the membrane-spanning pore. V-ATPases may have an additional role in membrane fusion through binding to t-SNARE proteins []. The yeast vacuolar proton-translocating ATPase (V-ATPase) is the best characterised member of the V-ATPase family. A total of thirteen genes are required for encoding the subunits of the enzyme complex itself and an additional three for providing factors necessary for the assembly of the whole. Vma12 is one of these latter, all three of which are localised to the endoplasmic reticulum [].
Probab=37.55 E-value=55 Score=27.30 Aligned_cols=27 Identities=11% Similarity=0.203 Sum_probs=21.3
Q ss_pred chhhHHHHhHHHHHHHHHHHHhhheee
Q 025004 166 TRTSFTKRCESINTMASFLWWIVGFYW 192 (259)
Q Consensus 166 ~~~~i~k~lesalt~Ff~VWfVVGf~W 192 (259)
.-+.+.+-+=++..+|+++||..+-.|
T Consensus 78 qls~v~Nilvsv~~~~~~~~~~~~~~~ 104 (142)
T PF11712_consen 78 QLSTVFNILVSVFAVFFAGWYWAGYSF 104 (142)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHhh
Confidence 345778888999999999997777555
No 11
>PF11368 DUF3169: Protein of unknown function (DUF3169); InterPro: IPR021509 Some members in this family of proteins are annotated as membrane proteins however this cannot be confirmed. Currently there is no known function.
Probab=35.79 E-value=1.1e+02 Score=27.64 Aligned_cols=17 Identities=12% Similarity=0.237 Sum_probs=10.1
Q ss_pred ccCchhHHHHHHHHhhh
Q 025004 202 QAAPRLYWLAVVFLAFD 218 (259)
Q Consensus 202 ~daP~LYwLcivFLAFd 218 (259)
.+.+...|..+.|+..-
T Consensus 126 ~~~~~~l~~~i~~~v~~ 142 (248)
T PF11368_consen 126 ISNKSSLFIIIPFLVLL 142 (248)
T ss_pred cCcchHHHHHHHHHHHH
Confidence 45566677767666433
No 12
>PF05478 Prominin: Prominin; InterPro: IPR008795 The prominins are an emerging family of proteins that, among the multispan membrane proteins, display a novel topology. Mouse and Homo sapiens prominin and (Mus musculus) prominin-like 1 (PROML1) are predicted to contain five membrane spanning domains, with an N-terminal domain exposed to the extracellular space followed by four, alternating small cytoplasmic and large extracellular, loops and a cytoplasmic C-terminal domain []. The exact function of prominin is unknown although in humans defects in PROM1, the gene coding for prominin, cause retinal degeneration [].; GO: 0016021 integral to membrane
Probab=34.87 E-value=44 Score=35.58 Aligned_cols=29 Identities=31% Similarity=0.939 Sum_probs=18.6
Q ss_pred hHHHHHHHHhhhhHHHHHHHHHHHHHHHHHHhh
Q 025004 207 LYWLAVVFLAFDVFFAIFCVVLACLIGIALCCC 239 (259)
Q Consensus 207 LYwLcivFLAFd~ifvvfcyal~cli~ialCCC 239 (259)
.||.-+++.++.++|+|+ || ++|+..|||
T Consensus 89 ~~~g~~v~~~i~ll~~il---~P-~vg~~fCcC 117 (806)
T PF05478_consen 89 YEWGFLVCAVIGLLFIIL---MP-LVGLCFCCC 117 (806)
T ss_pred HHHHHHHHHHHHHHHHHH---HH-HHHHHHhcc
Confidence 467777777766665544 44 456677777
No 13
>KOG1935 consensus Membrane protein Patched/PTCH [Signal transduction mechanisms]
Probab=33.82 E-value=40 Score=37.08 Aligned_cols=40 Identities=30% Similarity=0.639 Sum_probs=33.3
Q ss_pred HHHHHHHhhhhH-HHH--HHHHHHHHHHHHHH---hhHHHHHHHHH
Q 025004 209 WLAVVFLAFDVF-FAI--FCVVLACLIGIALC---CCLPCIIAILY 248 (259)
Q Consensus 209 wLcivFLAFd~i-fvv--fcyal~cli~ialC---CCLPcIIaiLy 248 (259)
||-+.+|+|+-| |+| |+++|..++|+-+| |-||.+.++++
T Consensus 1026 ~lgv~MLs~S~FdFvVryFf~~ltvl~~lGv~ngL~~lPVlLS~~G 1071 (1143)
T KOG1935|consen 1026 LLGVLMLSFSEFDFVVRYFFAVLTVLTCLGVLNGLVVLPVLLSLVG 1071 (1143)
T ss_pred HhhHheeccCchhHHHHHHHHHHHHHHHHHHhccchHHHHHHHhcC
Confidence 788888998888 776 88899999999887 78898887764
No 14
>PF02985 HEAT: HEAT repeat; InterPro: IPR000357 The HEAT repeat is a tandemly repeated, 37-47 amino acid long module occurring in a number of cytoplasmic proteins, including the four name-giving proteins huntingtin, elongation factor 3 (EF3), the 65 Kd alpha regulatory subunit of protein phosphatase 2A (PP2A) and the yeast PI3-kinase TOR1 []. Arrays of HEAT repeats consists of 3 to 36 units forming a rod-like helical structure and appear to function as protein-protein interaction surfaces. It has been noted that many HEAT repeat-containing proteins are involved in intracellular transport processes. In the crystal structure of PP2A PR65/A [], the HEAT repeats consist of pairs of antiparallel alpha helices [].; GO: 0005515 protein binding; PDB: 3FGA_A 2PF4_C 2IAE_A 2BKU_D 3EA5_B 3ND2_A 2BPT_A 2NYL_A 2NPP_D 2PKG_B ....
Probab=28.16 E-value=32 Score=21.27 Aligned_cols=19 Identities=37% Similarity=0.266 Sum_probs=14.7
Q ss_pred CCCCCchHhhHhHHHHHHH
Q 025004 45 RGHGPSMLVRETAARELEE 63 (259)
Q Consensus 45 ~~r~ps~~vre~aa~~le~ 63 (259)
++.+|+-.||++|++-+.+
T Consensus 8 ~l~D~~~~VR~~a~~~l~~ 26 (31)
T PF02985_consen 8 LLNDPSPEVRQAAAECLGA 26 (31)
T ss_dssp HHT-SSHHHHHHHHHHHHH
T ss_pred HcCCCCHHHHHHHHHHHHH
Confidence 3578999999999987753
No 15
>MTH00169 ATP8 ATP synthase F0 subunit 8; Provisional
Probab=27.54 E-value=99 Score=23.35 Aligned_cols=14 Identities=7% Similarity=0.508 Sum_probs=10.6
Q ss_pred CchhHHHHHHHHhh
Q 025004 204 APRLYWLAVVFLAF 217 (259)
Q Consensus 204 aP~LYwLcivFLAF 217 (259)
.+|++|++++|.++
T Consensus 10 ~sQ~~Wl~i~f~~l 23 (67)
T MTH00169 10 LTQYIWTLIILFFL 23 (67)
T ss_pred HHHHHHHHHHHHHH
Confidence 36889999877654
No 16
>PF05961 Chordopox_A13L: Chordopoxvirus A13L protein; InterPro: IPR009236 This family consists of A13L proteins from the Chordopoxviruses. A13L or p8 is one of the three most abundant membrane proteins of the intracellular mature Vaccinia virus [].
Probab=27.30 E-value=74 Score=24.51 Aligned_cols=14 Identities=36% Similarity=0.676 Sum_probs=9.5
Q ss_pred hHHHHHHHHHHhhc
Q 025004 239 CLPCIIAILYAVAG 252 (259)
Q Consensus 239 CLPcIIaiLyav~~ 252 (259)
|+-.|-.|+|++=.
T Consensus 11 CVaii~lIlY~iYn 24 (68)
T PF05961_consen 11 CVAIIGLILYGIYN 24 (68)
T ss_pred HHHHHHHHHHHHHh
Confidence 34447788899864
No 17
>PF12326 EOS1: N-glycosylation protein; InterPro: IPR021100 This entry represents a family, containing several predicted transmembrane helices, which includes the fungal N-glycosylation protein EOS1. EOS1 is not essential for cell growth, but is necessary for tolerance to oxidative stress, and appears to be involved the N-glycosylation of cellular proteins [].
Probab=26.84 E-value=2.1e+02 Score=25.01 Aligned_cols=43 Identities=14% Similarity=0.387 Sum_probs=29.5
Q ss_pred HHHHHHHHHhcc-CCCCCchHHHHHHHhhhhHHHHHHHHHHHHHHhh
Q 025004 86 VIVSAAMLIITI-NERPSTRIRLWICGYALQCLVHVVLVWMEYRRRN 131 (259)
Q Consensus 86 IvaAivVL~lS~-~E~P~~PLr~WIvGYa~gCv~hl~lV~~rYr~Rn 131 (259)
|......+.+|- .++|+.||..||+ ++|.+++.-..-.|-.-|
T Consensus 51 i~~t~~~l~ls~~s~d~~~~L~~WI~---Is~~lt~~yivq~~vTSN 94 (148)
T PF12326_consen 51 ICWTLEHLLLSGLSPDPRYPLPAWIL---ISCTLTISYIVQNWVTSN 94 (148)
T ss_pred HHHHHHHHHHHhcCCCccccchHHHH---HHHHHHHHHHHHHHHhcc
Confidence 555666666663 4559999999996 677777776666565544
No 18
>PHA03049 IMV membrane protein; Provisional
Probab=25.69 E-value=82 Score=24.23 Aligned_cols=12 Identities=25% Similarity=0.301 Sum_probs=8.2
Q ss_pred HHHHHHHHHhhc
Q 025004 241 PCIIAILYAVAG 252 (259)
Q Consensus 241 PcIIaiLyav~~ 252 (259)
-.|-.|+|++=.
T Consensus 13 aIi~lIvYgiYn 24 (68)
T PHA03049 13 VIIGLIVYGIYN 24 (68)
T ss_pred HHHHHHHHHHHh
Confidence 337777888864
No 19
>smart00714 LITAF Possible membrane-associated motif in LPS-induced tumor necrosis factor alpha factor (LITAF), also known as PIG7, and other animal proteins.
Probab=25.54 E-value=69 Score=23.28 Aligned_cols=9 Identities=67% Similarity=2.265 Sum_probs=6.0
Q ss_pred HHhhHHHHH
Q 025004 236 LCCCLPCII 244 (259)
Q Consensus 236 lCCCLPcII 244 (259)
.|||+|+.+
T Consensus 37 ~~~~iP~~~ 45 (67)
T smart00714 37 FCCCLPCCL 45 (67)
T ss_pred HHHHHHHhc
Confidence 477888644
No 20
>PF01534 Frizzled: Frizzled/Smoothened family membrane region; InterPro: IPR000539 The frizzled (fz) locus of Drosophila coordinates the cytoskeletons of epidermal cells, producing a parallel array of cuticular hairs and bristles [, ]. In fz mutants, the orientation of individual hairs with respect both to their neighbours and to the organism as a whole is altered. In the wild-type wing, all hairs point towards the distal tip []. In the developing wing, fz has 2 functions: it is required for the proximal-distal transmission of an intracellular polarity signal; and it is required for cells to respond to the polarity signal. Fz produces an mRNA that encodes an integral membrane protein with 7 putative transmembrane (TM) domains. This protein should contain both extracellular and cytoplasmic domains, which could function in the transmission and interpretation of polarity information []. This signature is usually found downstream of the Fz domain (IPR000024 from INTERPRO); GO: 0007166 cell surface receptor linked signaling pathway, 0016020 membrane
Probab=25.35 E-value=3.2e+02 Score=26.29 Aligned_cols=29 Identities=28% Similarity=0.482 Sum_probs=19.6
Q ss_pred HHHHhHHHHHHHHHHHHhhhee-eeeecCc
Q 025004 170 FTKRCESINTMASFLWWIVGFY-WVVSGGD 198 (259)
Q Consensus 170 i~k~lesalt~Ff~VWfVVGf~-WV~~gg~ 198 (259)
++--+-....|-+.+|||+-.+ |..+.|.
T Consensus 96 ~~F~l~Yyf~mAa~~WWviLt~~W~lsa~~ 125 (328)
T PF01534_consen 96 VVFLLLYYFGMAASLWWVILTLTWFLSAGL 125 (328)
T ss_pred hHHHHHHHHHhHHHHHHHHHHHHHHHHhhc
Confidence 3334555556667899998776 8876654
No 21
>TIGR02741 TraQ type-F conjugative transfer system pilin chaperone TraQ. This protein makes a specific interaction with the pilin (TraA) protein to aid its transfer through the inner membrane during the process of F-type conjugative pilus assembly.
Probab=25.21 E-value=64 Score=25.38 Aligned_cols=22 Identities=27% Similarity=0.259 Sum_probs=16.1
Q ss_pred CCCCchhhHHHHHHHHHHHHHHHHHH
Q 025004 69 GYSKPVVALDIMWNSAFVIVSAAMLI 94 (259)
Q Consensus 69 aySk~~v~LelvwnLaqIvaAivVL~ 94 (259)
-|++||+ .|-+++|++.+.||.
T Consensus 32 Vy~~P~m----A~~laeliav~lVl~ 53 (80)
T TIGR02741 32 VYRKPWM----AFFLAELIAVILVLW 53 (80)
T ss_pred HHcChHH----HHHHHHHHHHHHHHh
Confidence 3778875 467888888777765
No 22
>PF01036 Bac_rhodopsin: Bacteriorhodopsin-like protein; InterPro: IPR001425 The bacterial opsins are retinal-binding proteins that provide light- dependent ion transport and sensory functions to a family of halophilic bacteria [, ]. They are integral membrane proteins believed to contain seven transmembrane (TM) domains, the last of which contains the attachment point for retinal (a conserved lysine). There are several classes of these bacterial proteins: they include bacteriorhodopsin and archaerhodopsin, which are light-driven proton pumps; halorhodopsin, a light-driven chloride pump; and sensory rhodopsin, which mediates both photoattractant (in the red) and photophobic (in the UV) responses.; GO: 0005216 ion channel activity, 0006811 ion transport, 0016020 membrane; PDB: 3QBI_B 3QBK_D 3QBL_D 3QBG_B 3AM6_D 1UAZ_B 1E12_A 2JAF_A 2JAG_A 3UG9_A ....
Probab=24.29 E-value=2.7e+02 Score=24.57 Aligned_cols=126 Identities=17% Similarity=0.366 Sum_probs=67.0
Q ss_pred HhhcCCCCCCchhhHHHH-------HHHH-HHHHHHHHHHhc-cCC-CCCchHHHHHHHhhhhHHHHHHHHHHHHHHhhc
Q 025004 63 ERRADWGYSKPVVALDIM-------WNSA-FVIVSAAMLIIT-INE-RPSTRIRLWICGYALQCLVHVVLVWMEYRRRNT 132 (259)
Q Consensus 63 ~r~~dwaySk~~v~Lelv-------wnLa-qIvaAivVL~lS-~~E-~P~~PLr~WIvGYa~gCv~hl~lV~~rYr~Rn~ 132 (259)
-|--||.-.-|.+.+++. .++. .|.+..++++.. -.| -+.. .-| ..|+++|++.+.++|.-+..-++
T Consensus 72 ~RYidW~lT~Plll~~L~~lag~~~~~~~~~i~~~~~mi~~g~~g~~~~~~--~kw-~~~~~~~~~~~~i~y~l~~~~~~ 148 (222)
T PF01036_consen 72 ARYIDWLLTTPLLLLALALLAGASRRLLLFLIAADVVMIVTGLVGALVPGT--YKW-GWFLVSCAAFLYIVYLLFGPLRR 148 (222)
T ss_dssp HHHHHHHHHHHHHHHHHHHHCTTTHHHHHHHHHHHHHHHHHHHHHHHTSHH--HHH-HHHHHHHHHHHHHHHHHHTHHHH
T ss_pred HHHhhHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHhcccH--HHH-HHHHHHHHHHHHHHHHHHHHHHH
Confidence 577788877788766653 2222 222333322222 111 1222 244 67899999999998876643322
Q ss_pred ccCCCccCCCCCCCCCCCCCCccccccccccccchhhHHHHhHHHHHHHHHHHHhhheeeeeecCccccccCchhHHHHH
Q 025004 133 RRVRDDEMGGEDFRDVNNDSEDEEEDGIVYRTSTRTSFTKRCESINTMASFLWWIVGFYWVVSGGDLLLQAAPRLYWLAV 212 (259)
Q Consensus 133 ~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~~~~~~~i~k~lesalt~Ff~VWfVVGf~WV~~gg~ss~~daP~LYwLci 212 (259)
...+ .+.+. +..+..-.+..++|.+-..+|..+.+.... | | .---+
T Consensus 149 ~a~~-----------------------------~~~~~-~~~~~l~~~~~~~W~~YPi~w~l~~~g~~i-~-~--~~~~i 194 (222)
T PF01036_consen 149 AASA-----------------------------VSPSV-GLYNKLRNLTVVLWILYPIVWLLSEGGNGI-D-P--TVEAI 194 (222)
T ss_dssp HHTT-----------------------------STHHH-HHHHHHHHHHHHHHHHHHHHHHHSTTTTSS-C-H--HHHHH
T ss_pred HHHh-----------------------------cCchH-HHHHHHHHHHHHHHHHHHHHHHHhcCCCcC-C-c--hHHHH
Confidence 2100 01222 444555557788899999999985332222 2 2 12344
Q ss_pred HHHhhhhH-HHHHH
Q 025004 213 VFLAFDVF-FAIFC 225 (259)
Q Consensus 213 vFLAFd~i-fvvfc 225 (259)
.|--.|++ .++|+
T Consensus 195 ~y~ilD~~~K~~fg 208 (222)
T PF01036_consen 195 FYGILDLLAKVGFG 208 (222)
T ss_dssp HHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHH
Confidence 55555655 34443
No 23
>PF10601 zf-LITAF-like: LITAF-like zinc ribbon domain; InterPro: IPR006629 Members of this family display a conserved zinc ribbon structure [] with the motif C-XX-C- separated from the more C-terminal HX-C(P)X-C-X4-G-R motif by a variable region of usually 25-30 (hydrophobic) residues. Although it belongs to one of the zinc finger's fold groups (zinc ribbon), this particular domain was first identified in LPS-induced tumour necrosis alpha factor (LITAF) which is produced in mammalian cells after being challenged with lipopolysaccharide (LPS). The hydrophobic region probably inserts into the membrane rather than traversing it. Such an insertion brings together the N- and C-terminal C-XX-C motifs to form a compact Zn2+-binding structure [].
Probab=24.10 E-value=89 Score=23.04 Aligned_cols=15 Identities=47% Similarity=1.287 Sum_probs=9.2
Q ss_pred HHHHHHHHhhHHHHH
Q 025004 230 CLIGIALCCCLPCII 244 (259)
Q Consensus 230 cli~ialCCCLPcII 244 (259)
|+++...|||+|+.+
T Consensus 37 ~~~~~~~~~~iP~~~ 51 (73)
T PF10601_consen 37 CLFGCWPCCCIPFCC 51 (73)
T ss_pred HHHHHHHHhhHhhcc
Confidence 444445568888765
No 24
>PF06814 Lung_7-TM_R: Lung seven transmembrane receptor; InterPro: IPR009637 This family represents a conserved region with eukaryotic lung seven transmembrane receptors and related proteins.; GO: 0016021 integral to membrane
Probab=22.87 E-value=5.9e+02 Score=23.30 Aligned_cols=122 Identities=11% Similarity=0.208 Sum_probs=78.9
Q ss_pred CchhhHHHHHHHHHHHHHHHHHHhc-cCCCCCchHHHHHHHhhhhHHHHHHHHHHHHHHhhcccCCCccCCCCCCCCCCC
Q 025004 72 KPVVALDIMWNSAFVIVSAAMLIIT-INERPSTRIRLWICGYALQCLVHVVLVWMEYRRRNTRRVRDDEMGGEDFRDVNN 150 (259)
Q Consensus 72 k~~v~LelvwnLaqIvaAivVL~lS-~~E~P~~PLr~WIvGYa~gCv~hl~lV~~rYr~Rn~~~~~~~~~~~~~~~~~~~ 150 (259)
.|-..+-.+..++..+.++.-+... |+-+--.|+.-||.+..+=..+.+.+.+..|...|....+.
T Consensus 45 ~pl~~~y~~~~i~y~~~~~~W~~~~~~~~~~~~~ih~~i~~vl~l~~~~~~~~~~~y~~~n~~G~~~------------- 111 (295)
T PF06814_consen 45 YPLPPFYGVMSIVYAVLLIIWLFLCFKNRKSVLPIHYLILAVLILKMLELAFWFIYYHYINKTGTPS------------- 111 (295)
T ss_pred cccHHHHHHHHHHHHHHHHHHHHHHHHHhcchhhHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCCC-------------
Confidence 4556677778888888877777766 45566789999999999999999999999998888753210
Q ss_pred CCCccccccccccccchhhHHHHhHHHHHHHHHHHHhhheeeeeecCccccccCchhHHHHHHHHhhhhH
Q 025004 151 DSEDEEEDGIVYRTSTRTSFTKRCESINTMASFLWWIVGFYWVVSGGDLLLQAAPRLYWLAVVFLAFDVF 220 (259)
Q Consensus 151 ~~~~~~~e~~~~~~~~~~~i~k~lesalt~Ff~VWfVVGf~WV~~gg~ss~~daP~LYwLcivFLAFd~i 220 (259)
+.. .--..+.+.+|. ++++++=.++|--|-+. ...+.+.--+...+-+.+..++.+
T Consensus 112 -------~~~----~~~~~i~~~~k~--~~~~~llllis~Gygiv-kp~L~~~~~~v~~l~i~~~v~~~i 167 (295)
T PF06814_consen 112 -------EGW----MIFAYIFSALKR--TLSFFLLLLISLGYGIV-KPSLGRREKKVLMLVILYFVFSNI 167 (295)
T ss_pred -------chH----HHHHHHHHHHHH--HHHHHHHHHHhcchhee-ccccCcceeehhHHHHHHHHHHHH
Confidence 000 012455666664 44555566777778773 444433333444555555555554
No 25
>PF02932 Neur_chan_memb: Neurotransmitter-gated ion-channel transmembrane region ion channel family signature gamma-aminobutyric acid (GABA) receptor signature nicotinic acetylcholine receptor signature; InterPro: IPR006029 Neurotransmitter ligand-gated ion channels are transmembrane receptor-ion channel complexes that open transiently upon binding of specific ligands, allowing rapid transmission of signals at chemical synapses [, ]. Five of these ion channel receptor families have been shown to form a sequence-related superfamily: Nicotinic acetylcholine receptor (AchR), an excitatory cation channel in vertebrates and invertebrates; in vertebrate motor endplates it is composed of alpha, beta, gamma and delta/epsilon subunits; in neurons it is composed of alpha and non-alpha (or beta) subunits []. Glycine receptor, an inhibitory chloride ion channel composed of alpha and beta subunits []. Gamma-aminobutyric acid (GABA) receptor, an inhibitory chloride ion channel; at least four types of subunits (alpha, beta, gamma and delta) are known []. Serotonin 5HT3 receptor, of which there are seven major types (5HT3-5HT7) []. Glutamate receptor, an excitatory cation channel of which at least three types have been described (kainate, N-methyl-D-aspartate (NMDA) and quisqualate) []. These receptors possess a pentameric structure (made up of varying subunits), surrounding a central pore. All known sequences of subunits from neurotransmitter-gated ion-channels are structurally related. They are composed of a large extracellular glycosylated N-terminal ligand-binding domain, followed by three hydrophobic transmembrane regions which form the ionic channel, followed by an intracellular region of variable length. A fourth hydrophobic region is found at the C-terminal of the sequence [, ]. This domain represents four transmembrane helices of a variety of neurotransmitter-gated ion-channels.; GO: 0006811 ion transport, 0016020 membrane; PDB: 1DXZ_A 3MRA_A 1EQ8_C 1OED_C 2PR9_P 1A11_A 1CEK_A 2BG9_E 2KSR_A 2K59_B ....
Probab=22.50 E-value=2.4e+02 Score=22.12 Aligned_cols=12 Identities=33% Similarity=0.661 Sum_probs=7.7
Q ss_pred HHHhhhhHHHHH
Q 025004 213 VFLAFDVFFAIF 224 (259)
Q Consensus 213 vFLAFd~ifvvf 224 (259)
++||+.+++-+.
T Consensus 33 ~lL~~~~~~~~~ 44 (237)
T PF02932_consen 33 TLLAMTVFLLMV 44 (237)
T ss_dssp HHHHHHHHHHHH
T ss_pred HHHHHHHHHhhh
Confidence 477777775444
No 26
>PF02411 MerT: MerT mercuric transport protein; InterPro: IPR003457 MerT is an mercuric transport integral membrane protein and is responsible for transport of the Hg2+ iron from periplasmic MerP (also part of the transport system) to mercuric reductase (MerA).; GO: 0015097 mercury ion transmembrane transporter activity, 0015694 mercury ion transport, 0016020 membrane
Probab=22.32 E-value=80 Score=26.18 Aligned_cols=18 Identities=28% Similarity=0.519 Sum_probs=14.1
Q ss_pred HHHHHHHhhHHHHHHHHH
Q 025004 231 LIGIALCCCLPCIIAILY 248 (259)
Q Consensus 231 li~ialCCCLPcIIaiLy 248 (259)
-++++.||-+|.+...++
T Consensus 18 Av~aS~CCi~Pllll~lG 35 (116)
T PF02411_consen 18 AVLASLCCIGPLLLLSLG 35 (116)
T ss_pred HHHHHHHHHHHHHHHHHh
Confidence 457889999997776664
No 27
>PF09125 COX2-transmemb: Cytochrome C oxidase subunit II, transmembrane; InterPro: IPR015209 This N-terminal domain forms the transmembrane region in subunit II of cytochrome c oxidase from Thermus thermophilus. This domain adopts a tertiary structure consisting of two antiparallel transmembrane helices, in a transmembrane helix hairpin fold []. ; PDB: 1EHK_B 2QPE_B 3S8F_B 4EV3_B 3BVD_B 3S8G_B 3EH3_B 3S3C_B 3S39_B 3QJQ_B ....
Probab=22.11 E-value=51 Score=22.65 Aligned_cols=22 Identities=14% Similarity=0.309 Sum_probs=17.3
Q ss_pred CCCCchhhHHHHHHHHHHHHHH
Q 025004 69 GYSKPVVALDIMWNSAFVIVSA 90 (259)
Q Consensus 69 aySk~~v~LelvwnLaqIvaAi 90 (259)
+|.|-|+..-++.-++||+...
T Consensus 11 aYEr~Wi~F~l~mi~vFi~li~ 32 (38)
T PF09125_consen 11 AYERGWIAFALAMILVFIALIG 32 (38)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHhHHHHHHHHHHHHHHHHH
Confidence 4889999988888888876443
No 28
>PF08370 PDR_assoc: Plant PDR ABC transporter associated; InterPro: IPR013581 ABC transporters belong to the ATP-Binding Cassette (ABC) superfamily, which uses the hydrolysis of ATP to energise diverse biological systems. ABC transporters minimally consist of two conserved regions: a highly conserved ATP binding cassette (ABC) and a less conserved transmembrane domain (TMD). These can be found on the same protein or on two different ones. Most ABC transporters function as a dimer and therefore are constituted of four domains, two ABC modules and two TMDs. ABC transporters are involved in the export or import of a wide variety of substrates ranging from small ions to macromolecules. The major function of ABC import systems is to provide essential nutrients to bacteria. They are found only in prokaryotes and their four constitutive domains are usually encoded by independent polypeptides (two ABC proteins and two TMD proteins). Prokaryotic importers require additional extracytoplasmic binding proteins (one or more per systems) for function. In contrast, export systems are involved in the extrusion of noxious substances, the export of extracellular toxins and the targeting of membrane components. They are found in all living organisms and in general the TMD is fused to the ABC module in a variety of combinations. Some eukaryotic exporters encode the four domains on the same polypeptide chain []. The ABC module (approximately two hundred amino acid residues) is known to bind and hydrolyse ATP, thereby coupling transport to ATP hydrolysis in a large number of biological processes. The cassette is duplicated in several subfamilies. Its primary sequence is highly conserved, displaying a typical phosphate-binding loop: Walker A, and a magnesium binding site: Walker B. Besides these two regions, three other conserved motifs are present in the ABC cassette: the switch region which contains a histidine loop, postulated to polarise the attaching water molecule for hydrolysis, the signature conserved motif (LSGGQ) specific to the ABC transporter, and the Q-motif (between Walker A and the signature), which interacts with the gamma phosphate through a water bond. The Walker A, Walker B, Q-loop and switch region form the nucleotide binding site [, , ]. The 3D structure of a monomeric ABC module adopts a stubby L-shape with two distinct arms. ArmI (mainly beta-strand) contains Walker A and Walker B. The important residues for ATP hydrolysis and/or binding are located in the P-loop. The ATP-binding pocket is located at the extremity of armI. The perpendicular armII contains mostly the alpha helical subdomain with the signature motif. It only seems to be required for structural integrity of the ABC module. ArmII is in direct contact with the TMD. The hinge between armI and armII contains both the histidine loop and the Q-loop, making contact with the gamma phosphate of the ATP molecule. ATP hydrolysis leads to a conformational change that could facilitate ADP release. In the dimer the two ABC cassettes contact each other through hydrophobic interactions at the antiparallel beta-sheet of armI by a two-fold axis [, , , , , ]. The ATP-Binding Cassette (ABC) superfamily forms one of the largest of all protein families with a diversity of physiological functions []. Several studies have shown that there is a correlation between the functional characterisation and the phylogenetic classification of the ABC cassette [, ]. More than 50 subfamilies have been described based on a phylogenetic and functional classification [, , ]; (for further information see http://www.tcdb.org/tcdb/index.php?tc=3.A.1). This domain is found on the C terminus of ABC-2 type transporter domains (IPR013525 from INTERPRO). It seems to be associated with the plant pleiotropic drug resistance (PDR) protein family of ABC transporters. Like in yeast, plant PDR ABC transporters may also play a role in the transport of antifungal agents [] (see also IPR010929 from INTERPRO). The PDR family is characterised by a configuration in which the ABC domain is nearer the N terminus of the protein than the transmembrane domain [].
Probab=21.69 E-value=66 Score=24.24 Aligned_cols=16 Identities=44% Similarity=0.937 Sum_probs=9.5
Q ss_pred hhHHHHHH-HHhhhhHH
Q 025004 206 RLYWLAVV-FLAFDVFF 221 (259)
Q Consensus 206 ~LYwLciv-FLAFd~if 221 (259)
.-||.++. .++|.++|
T Consensus 27 ~WyWIgvgaL~G~~vlF 43 (65)
T PF08370_consen 27 YWYWIGVGALLGFIVLF 43 (65)
T ss_pred cEEeehHHHHHHHHHHH
Confidence 45677765 44555555
No 29
>PRK14010 potassium-transporting ATPase subunit B; Provisional
Probab=21.46 E-value=2e+02 Score=30.45 Aligned_cols=41 Identities=27% Similarity=0.425 Sum_probs=22.2
Q ss_pred HHHHHHHHhhhhHHHHH------HHHHHHHHHHHHHhhHHHHHHHHHH
Q 025004 208 YWLAVVFLAFDVFFAIF------CVVLACLIGIALCCCLPCIIAILYA 249 (259)
Q Consensus 208 YwLcivFLAFd~ifvvf------cyal~cli~ialCCCLPcIIaiLya 249 (259)
+.++++||++-+++..+ ...+.+++.+++|.| ||-+..+..
T Consensus 223 ~~l~ii~l~~~~~~~~~~~~~~~~~~~~~~val~V~~I-P~aL~~~~~ 269 (673)
T PRK14010 223 MTLTIIFLVVILTMYPLAKFLNFNLSIAMLIALAVCLI-PTTIGGLLS 269 (673)
T ss_pred HHHhHHHHHHHHHHHHHHhhccHHHHHHHHHHHHHHhh-hhhHHHHHH
Confidence 45666666654432111 123456666667765 997655443
No 30
>PRK14749 hypothetical protein; Provisional
Probab=20.54 E-value=1.7e+02 Score=19.19 Aligned_cols=23 Identities=43% Similarity=0.982 Sum_probs=16.7
Q ss_pred HHHHHHhhhhHHHHH-HHHHHHHH
Q 025004 106 RLWICGYALQCLVHV-VLVWMEYR 128 (259)
Q Consensus 106 r~WIvGYa~gCv~hl-~lV~~rYr 128 (259)
+.||.|-.+.|...+ -.++.|.+
T Consensus 4 faWiLG~~lAc~f~ilna~w~E~~ 27 (30)
T PRK14749 4 LLWFVGILLMCSLSTLVLVWLDPR 27 (30)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHH
Confidence 789999999998544 45555533
Done!