Query 012766
Match_columns 457
No_of_seqs 124 out of 828
Neff 2.6
Searched_HMMs 46136
Date Fri Mar 29 06:05:18 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/012766.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/012766hhsearch_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 1.3E-29 2.9E-34 210.7 10.4 87 317-406 3-89 (90)
2 cd00435 ACBP Acyl CoA binding 100.0 2.2E-29 4.8E-34 205.7 9.5 84 315-403 1-84 (85)
3 PF00887 ACBP: Acyl CoA bindin 100.0 3.1E-29 6.7E-34 202.2 8.2 87 315-404 1-87 (87)
4 KOG0817 Acyl-CoA-binding prote 99.9 2.7E-27 5.9E-32 211.0 11.2 114 313-431 3-117 (142)
5 COG4281 ACB Acyl-CoA-binding p 99.9 1.2E-22 2.5E-27 168.4 8.2 84 315-403 2-85 (87)
6 KOG3878 Protein involved in ma 99.0 8.4E-10 1.8E-14 111.8 7.9 90 314-405 31-123 (469)
7 smart00295 B41 Band 4.1 homolo 96.7 0.0065 1.4E-07 53.2 7.5 84 315-404 99-203 (207)
8 PF00373 FERM_M: FERM central 95.8 0.073 1.6E-06 43.6 8.6 84 314-403 10-121 (126)
9 KOG3530 FERM domain protein EH 80.2 4.1 9E-05 45.1 6.5 66 332-398 117-194 (616)
10 PF06716 DUF1201: Protein of u 34.1 46 0.00099 26.7 2.9 24 1-24 1-24 (54)
11 PF04434 SWIM: SWIM zinc finge 26.4 38 0.00082 23.8 1.2 23 29-51 11-34 (40)
12 PTZ00474 tryptophan/threonine- 20.4 1.1E+02 0.0023 31.7 3.6 35 5-39 32-66 (316)
No 1
>PTZ00458 acyl CoA binding protein; Provisional
Probab=99.96 E-value=1.3e-29 Score=210.67 Aligned_cols=87 Identities=29% Similarity=0.547 Sum_probs=81.7
Q ss_pred HHHHHHHHHHhhccCCCCCCCCChHHHHHHHHhhhhhccCCCCCCCCCccChhhHHHHHHHHHcCCCChHHHHHHHHHHH
Q 012766 317 RLFGAAVAFVGNKCNAGRISSIGSDVKMQLYGLHKIATVGPCREPQPMALKVSARANWNAWKQLGNMTPEIAMEQYVTIL 396 (457)
Q Consensus 317 ErFeaAVefVksLPk~G~vsqLS~DdKLeLYGLYKQATeGDCn~pKPG~fD~VGRAKWnAWKaLKGMSKEEAMkKYIELV 396 (457)
+.|++|+.+|++++.++ .++++++|+|||||||||+|||+.++|++|++++|+||+||++++|||+++||++||++|
T Consensus 3 ~~F~~A~~~v~~~~~~~---~~s~d~~L~lYalyKQAt~G~c~~~~P~~~d~~~raKw~AW~~l~~ms~~eA~~~YI~l~ 79 (90)
T PTZ00458 3 DLFEECVSFINSLPKTV---NLSVEIKLDLYKYYKQSTVGNCNIKEPSMFKYQDRKKYEAWKSIENLNREDAKKRYVEIV 79 (90)
T ss_pred HHHHHHHHHHHhCCCCC---CCCHHHHHHHHHHHhhhccCCCCCCCCCcccHHHHHHHHHHHHcCCCCHHHHHHHHHHHH
Confidence 46999999999987653 579999999999999999999999999999999999999999999999999999999999
Q ss_pred HhhCcccccC
Q 012766 397 SRSIPGCIQD 406 (457)
Q Consensus 397 eeLiP~W~e~ 406 (457)
.++.|+|...
T Consensus 80 ~~l~~~w~~~ 89 (90)
T PTZ00458 80 TELFPNWEKG 89 (90)
T ss_pred HHHhhccccC
Confidence 9999999753
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=99.96 E-value=2.2e-29 Score=205.73 Aligned_cols=84 Identities=35% Similarity=0.556 Sum_probs=80.5
Q ss_pred HHHHHHHHHHHHhhccCCCCCCCCChHHHHHHHHhhhhhccCCCCCCCCCccChhhHHHHHHHHHcCCCChHHHHHHHHH
Q 012766 315 LERLFGAAVAFVGNKCNAGRISSIGSDVKMQLYGLHKIATVGPCREPQPMALKVSARANWNAWKQLGNMTPEIAMEQYVT 394 (457)
Q Consensus 315 LEErFeaAVefVksLPk~G~vsqLS~DdKLeLYGLYKQATeGDCn~pKPG~fD~VGRAKWnAWKaLKGMSKEEAMkKYIE 394 (457)
|++.|++|+.+|++++ .+++++++|+|||||||||+|||+.++|++||+++|+||+||++++|||+++||++||+
T Consensus 1 ~~~~F~~A~~~v~~~~-----~~~~~~~~L~lYalyKQAt~G~~~~~~P~~~d~~~~~K~~AW~~l~~ms~~eA~~~YV~ 75 (85)
T cd00435 1 LQEEFEAAAEKVKKLK-----TKPSNEEKLQLYSLYKQATVGDCNTERPGMFDLKGRAKWDAWNSLKGMSKEDAMKAYIA 75 (85)
T ss_pred ChHHHHHHHHHHHhCC-----CCcCHHHHHHHHHHHHHhccCCCCCCCCCcccHhhHHHHHHHHHcCCCCHHHHHHHHHH
Confidence 4679999999999986 36899999999999999999999999999999999999999999999999999999999
Q ss_pred HHHhhCccc
Q 012766 395 ILSRSIPGC 403 (457)
Q Consensus 395 LVeeLiP~W 403 (457)
++++++|.|
T Consensus 76 ~~~~l~~~~ 84 (85)
T cd00435 76 KVEELIAKY 84 (85)
T ss_pred HHHHHhhcc
Confidence 999999998
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=3.1e-29 Score=202.15 Aligned_cols=87 Identities=41% Similarity=0.694 Sum_probs=78.5
Q ss_pred HHHHHHHHHHHHhhccCCCCCCCCChHHHHHHHHhhhhhccCCCCCCCCCccChhhHHHHHHHHHcCCCChHHHHHHHHH
Q 012766 315 LERLFGAAVAFVGNKCNAGRISSIGSDVKMQLYGLHKIATVGPCREPQPMALKVSARANWNAWKQLGNMTPEIAMEQYVT 394 (457)
Q Consensus 315 LEErFeaAVefVksLPk~G~vsqLS~DdKLeLYGLYKQATeGDCn~pKPG~fD~VGRAKWnAWKaLKGMSKEEAMkKYIE 394 (457)
|+++|..|+.+|+.++.. .+++++++|+|||||||||+|||+.++|+++|+++|+||+||++++|||+++||++||+
T Consensus 1 Le~~F~~A~~~v~~~~~~---~~~~~~~~L~LYalyKQAt~Gd~~~~~P~~~d~~~~~K~~AW~~l~gms~~eA~~~Yi~ 77 (87)
T PF00887_consen 1 LEEEFEAAVEFVSNLPKK---SQLSNDDKLELYALYKQATHGDCDTPRPGFFDIEGRAKWDAWKALKGMSKEEAMREYIE 77 (87)
T ss_dssp HHHHHHHHHHHHHHSSSC---STS-HHHHHHHHHHHHHHHTSS--S-CTTTTCHHHHHHHHHHHTTTTTHHHHHHHHHHH
T ss_pred CHHHHHHHHHHHHhcccc---CCCCHHHHHHHHHHHHHHHhCCCcCCCCcchhHHHHHHHHHHHHccCCCHHHHHHHHHH
Confidence 789999999999999853 37899999999999999999999999999999999999999999999999999999999
Q ss_pred HHHhhCcccc
Q 012766 395 ILSRSIPGCI 404 (457)
Q Consensus 395 LVeeLiP~W~ 404 (457)
+|++++|.|.
T Consensus 78 ~v~~~~~~~~ 87 (87)
T PF00887_consen 78 LVEELIPKYE 87 (87)
T ss_dssp HHHHHHHHH-
T ss_pred HHHHHHHhcC
Confidence 9999999883
No 4
>KOG0817 consensus Acyl-CoA-binding protein [Lipid transport and metabolism]
Probab=99.94 E-value=2.7e-27 Score=211.00 Aligned_cols=114 Identities=30% Similarity=0.453 Sum_probs=99.4
Q ss_pred chHHHHHHHHHHHHhhccCCCCCCCCChHHHHHHHHhhhhhccCCCCCCCCCccChhhHHHHHHHHHcCCCChHHHHHHH
Q 012766 313 TELERLFGAAVAFVGNKCNAGRISSIGSDVKMQLYGLHKIATVGPCREPQPMALKVSARANWNAWKQLGNMTPEIAMEQY 392 (457)
Q Consensus 313 sELEErFeaAVefVksLPk~G~vsqLS~DdKLeLYGLYKQATeGDCn~pKPG~fD~VGRAKWnAWKaLKGMSKEEAMkKY 392 (457)
..+...|..|+..++++++ .++++++|.|||||||||+|||++++||+||+++|+||+||++++|||+++||+.|
T Consensus 3 ~~~~~~Fe~a~~~~~~l~~-----~p~~ee~L~lYglyKQAt~G~~~~~kPg~~d~~~k~Kw~AW~~l~~~s~~eA~~~Y 77 (142)
T KOG0817|consen 3 ATLEAKFEAAAEAVKNLKK-----KPSNEELLKLYGLYKQATVGDCNTPKPGFFDEEGKAKWQAWNSLGGMSKEEAMEAY 77 (142)
T ss_pred chHHHHHHHHHHHHHhccc-----CCCHHHHHHHHHHHHhhccCCCCCCCCchhhHHHHHHHHHHHhcCCCCHHHHHHHH
Confidence 4578899999999999974 58999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHhhCcccccCCCCCCCCCCCc-cccccccccchhhH
Q 012766 393 VTILSRSIPGCIQDGIGGDIKPVSA-DAEACGELVCDLKA 431 (457)
Q Consensus 393 IELVeeLiP~W~e~s~~~~~kPssS-E~~t~ggl~~DlSt 431 (457)
|+++.+++|.|....+......... .......+.++.++
T Consensus 78 v~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 117 (142)
T KOG0817|consen 78 VEKVEELIPKYGAEAETEEKTELTISEDDDWEGIEPSELE 117 (142)
T ss_pred HHHHHHHHHHhhcccccccCcccccccccccccccccchh
Confidence 9999999999999877765444432 33355556666666
No 5
>COG4281 ACB Acyl-CoA-binding protein [Lipid metabolism]
Probab=99.88 E-value=1.2e-22 Score=168.41 Aligned_cols=84 Identities=23% Similarity=0.341 Sum_probs=79.3
Q ss_pred HHHHHHHHHHHHhhccCCCCCCCCChHHHHHHHHhhhhhccCCCCCCCCCccChhhHHHHHHHHHcCCCChHHHHHHHHH
Q 012766 315 LERLFGAAVAFVGNKCNAGRISSIGSDVKMQLYGLHKIATVGPCREPQPMALKVSARANWNAWKQLGNMTPEIAMEQYVT 394 (457)
Q Consensus 315 LEErFeaAVefVksLPk~G~vsqLS~DdKLeLYGLYKQATeGDCn~pKPG~fD~VGRAKWnAWKaLKGMSKEEAMkKYIE 394 (457)
+..+|+.|..-|+.|+ ..|++++.|+|||||||+++||.+..+||+||++||+||+||..|+|.|+++|.++||.
T Consensus 2 ~s~~Feqa~~dV~~L~-----~kP~~d~LLkLYAL~KQ~s~GD~~~ekPG~~d~~gr~K~eAW~~LKGksqedA~qeYia 76 (87)
T COG4281 2 LSTRFEQAQTDVKELS-----EKPSNDELLKLYALFKQGSVGDNDGEKPGFFDIVGRYKYEAWAGLKGKSQEDARQEYIA 76 (87)
T ss_pred hhhHHHHHHHHHHHhc-----cCCCcHHHHHHHHHHHhccccccCCCCCCccccccchhHHHHhhccCccHHHHHHHHHH
Confidence 5678999999999997 46899999999999999999999999999999999999999999999999999999999
Q ss_pred HHHhhCccc
Q 012766 395 ILSRSIPGC 403 (457)
Q Consensus 395 LVeeLiP~W 403 (457)
+|+++..++
T Consensus 77 lVeeLkak~ 85 (87)
T COG4281 77 LVEELKAKY 85 (87)
T ss_pred HHHHHHhhc
Confidence 999997654
No 6
>KOG3878 consensus Protein involved in maintenance of Golgi structure and ER-Golgi transport [Intracellular trafficking, secretion, and vesicular transport]
Probab=98.99 E-value=8.4e-10 Score=111.78 Aligned_cols=90 Identities=26% Similarity=0.432 Sum_probs=82.0
Q ss_pred hHHHHHHHHHHHHhhccCCCCCCCCChHHHHHHHHhhhhhccCCCCCC---CCCccChhhHHHHHHHHHcCCCChHHHHH
Q 012766 314 ELERLFGAAVAFVGNKCNAGRISSIGSDVKMQLYGLHKIATVGPCREP---QPMALKVSARANWNAWKQLGNMTPEIAME 390 (457)
Q Consensus 314 ELEErFeaAVefVksLPk~G~vsqLS~DdKLeLYGLYKQATeGDCn~p---KPG~fD~VGRAKWnAWKaLKGMSKEEAMk 390 (457)
.|++.+..|+.|.+.. .|+..+++.+++|+|-+|.||+..||+++. .-|++|++|+....+|..|+.||+++||.
T Consensus 31 ~LeElY~LA~~fyKe~--~GKa~h~~YEd~lKLial~kQv~~Gp~n~d~~p~~G~lDv~GnDr~~~W~~LG~~sre~AM~ 108 (469)
T KOG3878|consen 31 PLEELYRLAFTFYKEN--SGKAIHLSYEDNLKLIALKKQVALGPFNTDRAPALGVLDVIGNDRQQHWQLLGEISREQAME 108 (469)
T ss_pred CHHHHHHHHHHHHHhc--cCCccCCChhhhhhhhhhHhhhhcCCCCcccCcccceeecccChHHHHHHHHhcccHHHHHH
Confidence 5899999999999955 577678999999999999999999999963 34899999999999999999999999999
Q ss_pred HHHHHHHhhCccccc
Q 012766 391 QYVTILSRSIPGCIQ 405 (457)
Q Consensus 391 KYIELVeeLiP~W~e 405 (457)
.||.||++++|.|..
T Consensus 109 ~FV~Lldr~C~~F~~ 123 (469)
T KOG3878|consen 109 GFVDLLDRMCSAFRP 123 (469)
T ss_pred HHHHHHHhcchhhhh
Confidence 999999999998854
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=96.71 E-value=0.0065 Score=53.23 Aligned_cols=84 Identities=21% Similarity=0.211 Sum_probs=61.1
Q ss_pred HHHHHHHHHHHHhhccCCCCCCCCChHHHHHHHHhhhhhccCCCCCCC-------------CC-ccCh-------hhHHH
Q 012766 315 LERLFGAAVAFVGNKCNAGRISSIGSDVKMQLYGLHKIATVGPCREPQ-------------PM-ALKV-------SARAN 373 (457)
Q Consensus 315 LEErFeaAVefVksLPk~G~vsqLS~DdKLeLYGLYKQATeGDCn~pK-------------PG-~fD~-------VGRAK 373 (457)
+.--|..+..-+.. |.+ +.+.++-+.|-||.-|+..|+++.+. |. ..+- ....=
T Consensus 99 ~~~ly~Q~~~di~~----g~~-~~~~~~~~~Laal~~q~~~gd~~~~~~~~~~~~~~~~~lP~~~~~~~~~~~~~~~~~i 173 (207)
T smart00295 99 LNLLYLQVRNDILE----GRL-PCPEEEALLLAALALQAEFGDYDEELHVLLKELSLKRFLPKQLLDSEKRTLKEWRERI 173 (207)
T ss_pred HHHHHHHHHHHHHc----Ccc-CCCHHHHHHHHHHHHHHHhcCCChHhcCCccccccceeCChhhhhhccccHHHHHHHH
Confidence 45567777776653 333 56889999999999999999988532 11 1111 12223
Q ss_pred HHHHHHcCCCChHHHHHHHHHHHHhhCcccc
Q 012766 374 WNAWKQLGNMTPEIAMEQYVTILSRSIPGCI 404 (457)
Q Consensus 374 WnAWKaLKGMSKEEAMkKYIELVeeLiP~W~ 404 (457)
.++|+++.|||+.+||.+||+++.++ |.|.
T Consensus 174 ~~~~~~~~~~s~~~a~~~yl~~~~~l-p~fG 203 (207)
T smart00295 174 VSLHKELIGLSPEEAKLKYLELAEKL-PTYG 203 (207)
T ss_pred HHHHHHcCCCCHHHHHHHHHHHhccc-cccC
Confidence 48899999999999999999999976 7663
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=95.80 E-value=0.073 Score=43.55 Aligned_cols=84 Identities=24% Similarity=0.286 Sum_probs=57.3
Q ss_pred hHHHHHHHHHHHHhhccCCCCCCCCChHHHHHHHHhhhhhccCCCCCCC---CCc-------------cC-------hhh
Q 012766 314 ELERLFGAAVAFVGNKCNAGRISSIGSDVKMQLYGLHKIATVGPCREPQ---PMA-------------LK-------VSA 370 (457)
Q Consensus 314 ELEErFeaAVefVksLPk~G~vsqLS~DdKLeLYGLYKQATeGDCn~pK---PG~-------------fD-------~VG 370 (457)
.+.--|..+...|-. |.+ ..+.++-++|-||.-|+..|+++... .+. +. ...
T Consensus 10 ~~~lly~Q~~~~vl~----g~~-~~~~e~a~~LAAl~~q~~~gd~~~~~~~~~~~~~~~~~~~~~~~~iP~~~~~~~~~~ 84 (126)
T PF00373_consen 10 TRHLLYLQARRDVLQ----GRL-PCSEEDAIKLAALQLQAEYGDYNSEQEHSSGYIDPEIKEFQLENFIPKAPKLIKKMK 84 (126)
T ss_dssp HHHHHHHHHHHHHHT----TSS-TS-HHHHHHHHHHHHHHHHTSSTTTTTSSTTTTTGSHHCTCGHGTSSHHHHHHCCST
T ss_pred HHHHHHHHHHHHHHc----CcC-CCCHHHHHHHHHHHHHHHhcCCCcccccCcccccccccchhhhhhhhhhHHHHhhhh
Confidence 455567777776643 333 68999999999999999999998321 111 11 112
Q ss_pred HHHH-----HHHHHcCCCChHHHHHHHHHHHHhhCccc
Q 012766 371 RANW-----NAWKQLGNMTPEIAMEQYVTILSRSIPGC 403 (457)
Q Consensus 371 RAKW-----nAWKaLKGMSKEEAMkKYIELVeeLiP~W 403 (457)
...| ..|++++|||+.+||..||+++.++ |.|
T Consensus 85 ~~~~~~~I~~~~~~l~~~s~~~a~~~fl~~~~~~-p~y 121 (126)
T PF00373_consen 85 QKEWEKRILEQHKKLRGMSPEEAKLQFLQICQSL-PTY 121 (126)
T ss_dssp HHHHHHHHHHHHHHTTT--HHHHHHHHHHHHCTS-TTT
T ss_pred HHHHHHHHHHHHHHhhCCCHHHHHHHHHHHHhcC-CCC
Confidence 2333 7899999999999999999999863 555
No 9
>KOG3530 consensus FERM domain protein EHM2 [General function prediction only]
Probab=80.20 E-value=4.1 Score=45.08 Aligned_cols=66 Identities=17% Similarity=0.202 Sum_probs=51.5
Q ss_pred CCCCCCCChHHHHHHHHhhhhhccCCCCCCC--CC---ccChh-------hHHHHHHHHHcCCCChHHHHHHHHHHHHh
Q 012766 332 AGRISSIGSDVKMQLYGLHKIATVGPCREPQ--PM---ALKVS-------ARANWNAWKQLGNMTPEIAMEQYVTILSR 398 (457)
Q Consensus 332 ~G~vsqLS~DdKLeLYGLYKQATeGDCn~pK--PG---~fD~V-------GRAKWnAWKaLKGMSKEEAMkKYIELVee 398 (457)
.|++ +.|-+.-.+|=||==|+-.|||+.+. |+ .|.++ .-+=.+-||.++|+++..|+-.|+..+.-
T Consensus 117 ~GRL-~Cp~~~AaeLaAl~lQsELGDYn~~~Ht~~yVSefRf~p~Qte~LE~~I~e~hK~~rGqspaqAElnyLnkAkw 194 (616)
T KOG3530|consen 117 SGRL-YCPFETAAELAALILQSELGDYNEEEHTGGYVSEFRFLPNQTEELEERIFELHKELRGQSPAQAELNYLNKAKW 194 (616)
T ss_pred cCCC-CCchhhHHHHHHHHHHHHhcCCChhhccccceeeeEecccccHHHHHHHHHHHHHhcCCCHHHHHHHHHhhhhh
Confidence 3554 67889999999999999999999853 32 23322 33446889999999999999999998863
No 10
>PF06716 DUF1201: Protein of unknown function (DUF1201); InterPro: IPR009591 This entry consists of several Beet yellows virus (BYV) putative membrane-binding proteins of around 54 residues in length. The function of this currently unknown.
Probab=34.05 E-value=46 Score=26.67 Aligned_cols=24 Identities=33% Similarity=0.552 Sum_probs=18.4
Q ss_pred CcchhhhhhhHHHHHHHHHHHHHH
Q 012766 1 MEVFLEFVLPIAFSLIFSFFLAKL 24 (457)
Q Consensus 1 ~~~~~~~~~~~~~~~~~~~~~~~~ 24 (457)
|.-.|.-.||.+|.+++.|||+-+
T Consensus 1 MDCvLRs~L~~~F~~lIC~Fl~~~ 24 (54)
T PF06716_consen 1 MDCVLRSYLLLAFGFLICLFLFCL 24 (54)
T ss_pred CchHHHHHHHHHHHHHHHHHHHHH
Confidence 555677789999999888887643
No 11
>PF04434 SWIM: SWIM zinc finger; InterPro: IPR007527 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents the SWIM (SWI2/SNF2 and MuDR) zinc-binding domain, which is found in a variety of prokaryotic and eukaryotic proteins, such as mitogen-activated protein kinase kinase kinase 1 (or MEKK1). It is also found in the related protein MEX (MEKK1-related protein X), a testis-expressed protein that acts as an E3 ubiquitin ligase through the action of E2 ubiquitin-conjugating enzymes in the proteasome degradation pathway; the SWIM domain is critical for MEX ubiquitination []. SWIM domains are also found in the homologous recombination protein Sws1 [], as well as in several hypothetical proteins. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding
Probab=26.37 E-value=38 Score=23.79 Aligned_cols=23 Identities=30% Similarity=0.730 Sum_probs=17.8
Q ss_pred CCCCCCccccccc-CCcchhhhhh
Q 012766 29 SSPSTNCDCDLVS-GLKPCKHFIQ 51 (457)
Q Consensus 29 ~~~~~~~~~~~~~-~~~~~~~~~~ 51 (457)
+.....|+|.--. .-.||+|-+-
T Consensus 11 ~~~~~~CsC~~~~~~~~~CkHi~a 34 (40)
T PF04434_consen 11 SIEQASCSCPYFQFRGGPCKHIVA 34 (40)
T ss_pred cccccEeeCCCccccCCcchhHHH
Confidence 4457789998765 7789999874
No 12
>PTZ00474 tryptophan/threonine-rich antigen superfamily; Provisional
Probab=20.42 E-value=1.1e+02 Score=31.68 Aligned_cols=35 Identities=26% Similarity=0.114 Sum_probs=24.3
Q ss_pred hhhhhhHHHHHHHHHHHHHHhcccCCCCCCccccc
Q 012766 5 LEFVLPIAFSLIFSFFLAKLFSLSSSPSTNCDCDL 39 (457)
Q Consensus 5 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 39 (457)
..|.++..+++||++..|-+++.|++++.+=.++.
T Consensus 32 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 66 (316)
T PTZ00474 32 STSTLSRLTILIFALSCAFFVNTASGASTNRPNKN 66 (316)
T ss_pred hhHHHHHHHHHHHHHHHHHHhcccccccccccccC
Confidence 45555667777788877888888877776654443
Done!