Query 030313
Match_columns 179
No_of_seqs 125 out of 438
Neff 6.7
Searched_HMMs 46136
Date Fri Mar 29 11:50:31 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/030313.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/030313hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 TIGR01569 A_tha_TIGR01569 plan 100.0 1E-46 2.2E-51 295.0 17.3 152 8-164 1-154 (154)
2 PF04535 DUF588: Domain of unk 100.0 3.4E-41 7.3E-46 262.0 15.8 148 2-152 2-149 (149)
3 PF01284 MARVEL: Membrane-asso 98.6 1.3E-06 2.8E-11 65.8 12.3 142 3-158 2-143 (144)
4 PF12304 BCLP: Beta-casein lik 43.6 1.6E+02 0.0035 23.9 7.5 55 54-111 42-96 (188)
5 COG3647 Predicted membrane pro 37.7 2.2E+02 0.0047 23.0 7.5 34 111-150 164-197 (205)
6 PF06376 DUF1070: Protein of u 28.1 69 0.0015 18.8 2.3 14 93-106 13-26 (34)
7 PF05702 Herpes_UL49_5: Herpes 26.0 1.2E+02 0.0026 22.1 3.7 49 116-164 36-84 (98)
8 KOG4016 Synaptic vesicle prote 19.5 5.4E+02 0.012 21.5 12.3 143 4-160 22-166 (233)
9 PRK13183 psbN photosystem II r 17.5 1.3E+02 0.0028 18.9 2.2 23 151-173 13-35 (46)
10 PF02468 PsbN: Photosystem II 17.3 1.7E+02 0.0037 18.1 2.6 23 152-174 11-33 (43)
No 1
>TIGR01569 A_tha_TIGR01569 plant integral membrane protein TIGR01569. This model describes a region of ~160 residues found exclusively in plant proteins, generally as the near complete length of the protein. At least 24 different members are found in Arabidopsis thaliana. Members have four predicted transmembrane regions, the last of which is preceded by an invariant CXXXXX[FY]C motif. The family is not functionally characterized.
Probab=100.00 E-value=1e-46 Score=295.01 Aligned_cols=152 Identities=28% Similarity=0.417 Sum_probs=143.5
Q ss_pred HHHHHHHHHHHHHHHHHHHhccccceEEe--eeeeeeecchhhHHHHHHHHHHHHHHHHHHHHHhhhhhhccCCCCCCcc
Q 030313 8 AFVRVWAALLLLLTACLVGLDTQSKYIFY--VDRKITYKELHALGALVYVASAAAGYNLLQLGRSVFVSRYLGNSKGSYR 85 (179)
Q Consensus 8 l~LR~~a~~~sl~a~~vm~t~~q~~~~~~--~~~~~~f~~~~af~ylv~a~~i~~~Ysllql~~~~~~~l~~~~~~~~~~ 85 (179)
++||+++++++++|+++|+||+|+.+++. +++++||+|+++|+|+|++|+|+++|+++|+++++ +++.+++..
T Consensus 1 l~LR~~~~~~sl~A~vvm~t~~qt~~~~~~~~~~~a~f~d~~af~y~v~anai~~~Ysll~l~~~~-~~~~~~~~~---- 75 (154)
T TIGR01569 1 LILRVLAFSATLAAAIVMGTNRETKVVFVQLITFKAKFSDLPAFVYFVVANAIACGYSLLSLVVSI-FGLLKRRVF---- 75 (154)
T ss_pred CcHHHHHHHHHHHHHHHhhcccceeeeecccceeeeeeeccHHHHHHHHHHHHHHHHHHHHHHHHH-HHHhcccch----
Confidence 46999999999999999999999999987 89999999999999999999999999999999998 666555532
Q ss_pred hhHhHHHhHhHHHHHHHHHhhhhHHHHHHHHhhcccchhhhhhhhhhhhhhhhHHHHHHHHHHHHHHHHHHHHHHHHhh
Q 030313 86 YLAWVSYLLDQMVVYIAFGTNSAAVEHSVLALSGMKEFQWMKWCNKFTRFCFQIGGALVSGYAACALMVLATSISAFNL 164 (179)
Q Consensus 86 ~~~~~~f~~Dqv~ayLl~sa~sAA~~v~~l~~~G~~~~~W~~iC~~~~~FC~~~~~Si~~sf~A~~~~~~~s~iSa~~L 164 (179)
...|++|.+||+++|+++||++||+++++++|+||+|.+|+|+|+++|+||||+++|++++|+|++++++++++|++++
T Consensus 76 ~~~~~~f~~D~v~~~Ll~sa~sAA~av~~l~~~G~~~~~W~~iC~~~~~FC~~~~~sl~~s~~a~v~~~llsv~Sa~~~ 154 (154)
T TIGR01569 76 FKLIALFFLDLVMLALLSSGTSAAAAVAYVGKLGNKEAGWLKICGVFGKFCDRIAGSLALSLFAVILLVLLSILSAISL 154 (154)
T ss_pred hHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHccccccchhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcC
Confidence 3589999999999999999999999999999999999999999999999999999999999999999999999999985
No 2
>PF04535 DUF588: Domain of unknown function (DUF588); InterPro: IPR006702 This family of plant proteins contains a domain that may have a catalytic activity. It has a conserved arginine and aspartate that could form an active site. These proteins are predicted to contain 3 or 4 transmembrane helices.
Probab=100.00 E-value=3.4e-41 Score=261.98 Aligned_cols=148 Identities=27% Similarity=0.448 Sum_probs=139.7
Q ss_pred cchhHHHHHHHHHHHHHHHHHHHHHhccccceEEeeeeeeeecchhhHHHHHHHHHHHHHHHHHHHHHhhhhhhccCCCC
Q 030313 2 DVQKIEAFVRVWAALLLLLTACLVGLDTQSKYIFYVDRKITYKELHALGALVYVASAAAGYNLLQLGRSVFVSRYLGNSK 81 (179)
Q Consensus 2 ~~~~~~l~LR~~a~~~sl~a~~vm~t~~q~~~~~~~~~~~~f~~~~af~ylv~a~~i~~~Ysllql~~~~~~~l~~~~~~ 81 (179)
+.+.++++||+++++++++|+++|++|+||.++.+.+.+++|+|+++|+|+|++|+|+++|+++|++.++ +.+.+|+ .
T Consensus 2 ~~~~~~l~LR~~~~~~sl~a~~vm~t~~qt~~~~~~~~~~~f~~~~af~ylv~a~~i~~~Ysl~~~~~~~-~~~~~~~-~ 79 (149)
T PF04535_consen 2 SLRIASLVLRLLAFVLSLAALAVMATNKQTVSVFSIQFTAKFSDYPAFRYLVAANVIACVYSLLQLVLSI-YSLSRGK-L 79 (149)
T ss_pred CchhhhHHHHHHHHHHHHHHHHHHHhcCCcceeeccccceeecccHHHHHHHHHHHHHHHHHHHHHHHHH-HHHHccC-C
Confidence 5688999999999999999999999999999999999999999999999999999999999999999998 6776655 3
Q ss_pred CCcchhHhHHHhHhHHHHHHHHHhhhhHHHHHHHHhhcccchhhhhhhhhhhhhhhhHHHHHHHHHHHHHH
Q 030313 82 GSYRYLAWVSYLLDQMVVYIAFGTNSAAVEHSVLALSGMKEFQWMKWCNKFTRFCFQIGGALVSGYAACAL 152 (179)
Q Consensus 82 ~~~~~~~~~~f~~Dqv~ayLl~sa~sAA~~v~~l~~~G~~~~~W~~iC~~~~~FC~~~~~Si~~sf~A~~~ 152 (179)
++ +...|++|++||+++|+++||++||+++++++++|+++.+|+++|+.+++||+|+++|++++|+|+++
T Consensus 80 ~~-~~~~~~~f~~Dqv~~~ll~sa~~Aa~~~~~~~~~g~~~~~W~~vC~~~~~FC~~~~~sv~lsf~a~~~ 149 (149)
T PF04535_consen 80 RS-KLLAWFLFILDQVLAYLLFSAASAAAAVAYLGKKGNSHVQWSKVCSQFGKFCNRAAASVALSFLAFVA 149 (149)
T ss_pred cc-cchhhhhhhHHHHHHHHHHHHHHHHHHHHHHHHhccccccchhhccchhhHHHHHHHHHHHHHHHHHC
Confidence 33 77899999999999999999999999999999999999999999999999999999999999999874
No 3
>PF01284 MARVEL: Membrane-associating domain; InterPro: IPR021128 This entry represents the ~130-residue MARVEL (MAL and related proteins for vesicle trafficking and membrane link) domain. The MARVEL domain is a module with a four transmembrane-helix architecture that has been identified in proteins of the myelin and lymphocyte (MAL), physins, gyrins and occludin families. All described MARVEL domain-containing proteins are consistent with the M-shaped topology: four transmembrane-helix region architecture with cytoplasmic N- and C-terminal regions. Their function could be related to cholesterol-rich membrane apposition events in a variety of cellular processes, such as biogenesis of vesicular transport carriers or tight junction regulation [].
Probab=98.60 E-value=1.3e-06 Score=65.77 Aligned_cols=142 Identities=14% Similarity=0.083 Sum_probs=101.5
Q ss_pred chhHHHHHHHHHHHHHHHHHHHHHhccccceEEeeeeeeeecchhhHHHHHHHHHHHHHHHHHHHHHhhhhhhccCCCCC
Q 030313 3 VQKIEAFVRVWAALLLLLTACLVGLDTQSKYIFYVDRKITYKELHALGALVYVASAAAGYNLLQLGRSVFVSRYLGNSKG 82 (179)
Q Consensus 3 ~~~~~l~LR~~a~~~sl~a~~vm~t~~q~~~~~~~~~~~~f~~~~af~ylv~a~~i~~~Ysllql~~~~~~~l~~~~~~~ 82 (179)
++....+||+++++++++.+.+++....+... ......++..|.+.+.++...+++.-++... .. .+..+
T Consensus 2 l~s~~~ilR~lq~~~~~i~~~l~~~~~~~~~~------~~~~~~~~~~~~~~v~~~~~~~~~~~l~~~~-~~---~~~~~ 71 (144)
T PF01284_consen 2 LRSPSGILRILQLVFALIIFGLVASSIATGSQ------IYGGSPSACGFALFVAVLSFLYTLIFLLLYL-FS---LKYRP 71 (144)
T ss_pred CccHhHHHHHHHHHHHHHHHHHHHHHHhcccc------ccCCCCcchhHHHHHHHHHHHHHHHHHHHHH-HH---Hhccc
Confidence 35678899999999999999999987743221 2455667889999999999999998888765 22 11111
Q ss_pred CcchhHhHHHhHhHHHHHHHHHhhhhHHHHHHHHhhcccchhhhhhhhhhhhhhhhHHHHHHHHHHHHHHHHHHHH
Q 030313 83 SYRYLAWVSYLLDQMVVYIAFGTNSAAVEHSVLALSGMKEFQWMKWCNKFTRFCFQIGGALVSGYAACALMVLATS 158 (179)
Q Consensus 83 ~~~~~~~~~f~~Dqv~ayLl~sa~sAA~~v~~l~~~G~~~~~W~~iC~~~~~FC~~~~~Si~~sf~A~~~~~~~s~ 158 (179)
+ +...+.++..|.+++.+-+.+..+-+.-....+.+++ +++.+...++-|+...++.++++++++.+..+.+
T Consensus 72 ~-~~~~~~~~~~~~v~~il~l~a~~~~a~~~~~~~~~~~---~~~~~~~~~~~~~~~~Aa~~f~~~~~~l~~~s~~ 143 (144)
T PF01284_consen 72 R-IPWPLVEFIFDAVFAILWLAAFIALAAYLSDHSCSNT---GNDYSYSGCSRCGAWKAAAAFGFLNWLLFIVSAV 143 (144)
T ss_pred c-cccchhHHHHHHHHHHHHHHHHHHHHHHhcCcccccC---CCCcCCCCCCcchhHHHHHHHHHHHHHHHHHHHH
Confidence 2 4456889999999999999866655532211111111 2233445567899999999999999999887764
No 4
>PF12304 BCLP: Beta-casein like protein; InterPro: IPR020977 This entry represents eukaryotic proteins that are typically between 216 to 240 amino acids in length which have two conserved sequence motifs: VLR and TRIY. Beta-casein-like protein is associated with cell morphology and a regulation of growth pattern of tumours. It is found in adenocarcinomas of uterine cervical tissues[].
Probab=43.63 E-value=1.6e+02 Score=23.89 Aligned_cols=55 Identities=13% Similarity=0.138 Sum_probs=33.9
Q ss_pred HHHHHHHHHHHHHHHHhhhhhhccCCCCCCcchhHhHHHhHhHHHHHHHHHhhhhHHH
Q 030313 54 YVASAAAGYNLLQLGRSVFVSRYLGNSKGSYRYLAWVSYLLDQMVVYIAFGTNSAAVE 111 (179)
Q Consensus 54 ~a~~i~~~Ysllql~~~~~~~l~~~~~~~~~~~~~~~~f~~Dqv~ayLl~sa~sAA~~ 111 (179)
++|+|...=.++.+.-.+ .++.-.|-+.+ ++..|.++..-.. ..|+-.+++-+..
T Consensus 42 vsNiisv~Sgll~I~~GI-~AIvlSrnl~~-~~L~W~Ll~~S~l-n~LlSaAc~vGL~ 96 (188)
T PF12304_consen 42 VSNIISVTSGLLSIICGI-VAIVLSRNLRN-RPLHWTLLVVSLL-NALLSAACAVGLL 96 (188)
T ss_pred HHHHHHHHHHHHHHHHhH-HHHhhhccCCC-CcchHHHHHHHHH-HHHHHHHHHHHHH
Confidence 568888887888877777 66643333444 7788988876543 3344444444443
No 5
>COG3647 Predicted membrane protein [Function unknown]
Probab=37.71 E-value=2.2e+02 Score=22.99 Aligned_cols=34 Identities=21% Similarity=0.230 Sum_probs=23.1
Q ss_pred HHHHHHhhcccchhhhhhhhhhhhhhhhHHHHHHHHHHHH
Q 030313 111 EHSVLALSGMKEFQWMKWCNKFTRFCFQIGGALVSGYAAC 150 (179)
Q Consensus 111 ~v~~l~~~G~~~~~W~~iC~~~~~FC~~~~~Si~~sf~A~ 150 (179)
+++.++..|+ ||+. +-|-+|+..++=.++.+++.
T Consensus 164 giaFLGsQGD---qWDa---QkDmlcdtlGAltal~lla~ 197 (205)
T COG3647 164 GIAFLGSQGD---QWDA---QKDMLCDTLGALTALILLAR 197 (205)
T ss_pred hHHHhhcccc---hhhh---HHhHHHHHHHHHHHHHHHHH
Confidence 4556666665 7876 34678998887777766654
No 6
>PF06376 DUF1070: Protein of unknown function (DUF1070); InterPro: IPR009424 This entry represents the arabinogalactan peptide family found in plants [].
Probab=28.08 E-value=69 Score=18.85 Aligned_cols=14 Identities=21% Similarity=0.351 Sum_probs=11.4
Q ss_pred hHhHHHHHHHHHhh
Q 030313 93 LLDQMVVYIAFGTN 106 (179)
Q Consensus 93 ~~Dqv~ayLl~sa~ 106 (179)
..||.++|+|+-++
T Consensus 13 aiDqgiay~Lm~~A 26 (34)
T PF06376_consen 13 AIDQGIAYMLMLVA 26 (34)
T ss_pred hhhHHHHHHHHHHH
Confidence 57999999998643
No 7
>PF05702 Herpes_UL49_5: Herpesvirus UL49.5 envelope/tegument protein; InterPro: IPR008647 UL49.5 protein consists of 98 amino acids with a calculated molecular mass of 10,155 Da. It contains putative signal peptide and transmembrane domains but lacks a consensus sequence for N glycosylation. UL49.5 protein is an O-glycosylated structural component of the viral envelope [].
Probab=25.98 E-value=1.2e+02 Score=22.11 Aligned_cols=49 Identities=16% Similarity=0.022 Sum_probs=31.3
Q ss_pred HhhcccchhhhhhhhhhhhhhhhHHHHHHHHHHHHHHHHHHHHHHHHhh
Q 030313 116 ALSGMKEFQWMKWCNKFTRFCFQIGGALVSGYAACALMVLATSISAFNL 164 (179)
Q Consensus 116 ~~~G~~~~~W~~iC~~~~~FC~~~~~Si~~sf~A~~~~~~~s~iSa~~L 164 (179)
.++++.+.-|.+-|+.-|-.-+.-.++.++=+++.+.-.+..+.-+||.
T Consensus 36 ~~~e~~~~FW~a~CSArGv~i~~~s~asV~FY~sL~aV~vall~~aY~a 84 (98)
T PF05702_consen 36 AREESRRDFWSAACSARGVPIDFPSAASVLFYVSLLAVCVALLAYAYRA 84 (98)
T ss_pred hHhHHHhcccccccccCceecCCccHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 3445555689999998886666666666665665555555555555654
No 8
>KOG4016 consensus Synaptic vesicle protein Synaptogyrin involved in regulation of Ca2+-dependent exocytosis [Signal transduction mechanisms; Intracellular trafficking, secretion, and vesicular transport]
Probab=19.47 E-value=5.4e+02 Score=21.51 Aligned_cols=143 Identities=14% Similarity=-0.027 Sum_probs=80.7
Q ss_pred hhHHHHHHHHHHHHHHHHHHHHHhccccceEEeee-eeeeecchhhHHHHHHHHHHHHHHHHHHHHHhhhhhhccCCCCC
Q 030313 4 QKIEAFVRVWAALLLLLTACLVGLDTQSKYIFYVD-RKITYKELHALGALVYVASAAAGYNLLQLGRSVFVSRYLGNSKG 82 (179)
Q Consensus 4 ~~~~l~LR~~a~~~sl~a~~vm~t~~q~~~~~~~~-~~~~f~~~~af~ylv~a~~i~~~Ysllql~~~~~~~l~~~~~~~ 82 (179)
|+...++|+...+++++-.--+.+.--.+.--..+ .=+==+|..+.+|=+++.+.+..=+++-++++.|.. +-++.+
T Consensus 22 rkP~ti~R~~~~lFsliVf~si~~eGy~n~~~~~~~~Ciynrn~~ACsyg~avG~~Afla~~~flvlD~~f~--qISsv~ 99 (233)
T KOG4016|consen 22 RKPQTILRVVSWLFSLIVFGSIVNEGYLNSASSGEEFCIYNRNSNACSYGVAVGVLAFLACLAFLVLDVYFP--QISSVK 99 (233)
T ss_pred cCchhHHHHHHHHHHHhheeeeccccccCcccCCceEEEECCCCcchhHHHHHHHHHHHHHHHHHHHHhhhh--hhcccc
Confidence 56678999999999887665554432222111111 112235778999999999999999999898887322 111222
Q ss_pred CcchhHhHHHhHhHHHHHHHHHhhhhHHHHHHHHhhcccchhhhhhhh-hhhhhhhhHHHHHHHHHHHHHHHHHHHHHH
Q 030313 83 SYRYLAWVSYLLDQMVVYIAFGTNSAAVEHSVLALSGMKEFQWMKWCN-KFTRFCFQIGGALVSGYAACALMVLATSIS 160 (179)
Q Consensus 83 ~~~~~~~~~f~~Dqv~ayLl~sa~sAA~~v~~l~~~G~~~~~W~~iC~-~~~~FC~~~~~Si~~sf~A~~~~~~~s~iS 160 (179)
..|.....|+..-.+-+.+-+= +-.++.. ||..--. ..+-=-+.+.++|+.+|+..+.-...+.+.
T Consensus 100 ~RkraVl~Dl~~Salwtflwfv------GFc~l~n------qwqvs~p~~~~~~a~saraaIafsffSilsW~~~A~lA 166 (233)
T KOG4016|consen 100 DRKRAVLADLGVSALWAFLWFV------GFCFLAN------QWQVSKPKENPLGAGSARAAIAFSFFSILSWGGQAVLA 166 (233)
T ss_pred hhHHHHHHHHHHHHHHHHHHHH------HHHHHHH------HhhccCCCCCCcCcchHHHHHHHHHHHHHHHHHHHHHH
Confidence 2133333444444444444331 2223331 3421110 111112468889999998888887777765
No 9
>PRK13183 psbN photosystem II reaction center protein N; Provisional
Probab=17.54 E-value=1.3e+02 Score=18.89 Aligned_cols=23 Identities=4% Similarity=0.416 Sum_probs=16.6
Q ss_pred HHHHHHHHHHHHhhhhcccchhh
Q 030313 151 ALMVLATSISAFNLFRLYSSEKF 173 (179)
Q Consensus 151 ~~~~~~s~iSa~~L~r~~~~~~~ 173 (179)
....++.-+.+|.++.-+|||+-
T Consensus 13 ~i~~lL~~~TgyaiYtaFGppSk 35 (46)
T PRK13183 13 TILAILLALTGFGIYTAFGPPSK 35 (46)
T ss_pred HHHHHHHHHhhheeeeccCCccc
Confidence 34445566788999999999854
No 10
>PF02468 PsbN: Photosystem II reaction centre N protein (psbN); InterPro: IPR003398 Oxygenic photosynthesis uses two multi-subunit photosystems (I and II) located in the cell membranes of cyanobacteria and in the thylakoid membranes of chloroplasts in plants and algae. Photosystem II (PSII) has a P680 reaction centre containing chlorophyll 'a' that uses light energy to carry out the oxidation (splitting) of water molecules, and to produce ATP via a proton pump. Photosystem I (PSI) has a P700 reaction centre containing chlorophyll that takes the electron and associated hydrogen donated from PSII to reduce NADP+ to NADPH. Both ATP and NADPH are subsequently used in the light-independent reactions to convert carbon dioxide to glucose using the hydrogen atom extracted from water by PSII, releasing oxygen as a by-product. PSII is a multisubunit protein-pigment complex containing polypeptides both intrinsic and extrinsic to the photosynthetic membrane [, ]. Within the core of the complex, the chlorophyll and beta-carotene pigments are mainly bound to the antenna proteins CP43 (PsbC) and CP47 (PsbB), which pass the excitation energy on to the reaction centre proteins D1 (Qb, PsbA) and D2 (Qa, PsbD) that bind all the redox-active cofactors involved in the energy conversion process. The PSII oxygen-evolving complex (OEC) oxidises water to provide protons for use by PSI, and consists of OEE1 (PsbO), OEE2 (PsbP) and OEE3 (PsbQ). The remaining subunits in PSII are of low molecular weight (less than 10 kDa), and are involved in PSII assembly, stabilisation, dimerisation, and photo-protection []. This family represents the low molecular weight transmembrane protein PsbN found in PSII. PsbN may have a role in PSII stability, however its actual function unknown. PsbN does not appear to be essential for photoautotrophic growth or normal PSII function.; GO: 0015979 photosynthesis, 0009523 photosystem II, 0009539 photosystem II reaction center, 0016020 membrane
Probab=17.30 E-value=1.7e+02 Score=18.08 Aligned_cols=23 Identities=13% Similarity=0.336 Sum_probs=15.1
Q ss_pred HHHHHHHHHHHhhhhcccchhhh
Q 030313 152 LMVLATSISAFNLFRLYSSEKFL 174 (179)
Q Consensus 152 ~~~~~s~iSa~~L~r~~~~~~~~ 174 (179)
...++..+.+|.++.-+|||+-.
T Consensus 11 i~~~lv~~Tgy~iYtaFGppSk~ 33 (43)
T PF02468_consen 11 ISCLLVSITGYAIYTAFGPPSKE 33 (43)
T ss_pred HHHHHHHHHhhhhhheeCCCccc
Confidence 33444556678888888887643
Done!