Query 046052
Match_columns 318
No_of_seqs 129 out of 224
Neff 3.4
Searched_HMMs 46136
Date Fri Mar 29 08:15:57 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/046052.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/046052hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF01086 Clathrin_lg_ch: Clath 100.0 2.4E-34 5.3E-39 261.1 6.9 114 65-203 106-219 (225)
2 KOG4031 Vesicle coat protein c 100.0 6.1E-31 1.3E-35 238.8 17.3 115 67-207 102-216 (216)
3 KOG4031 Vesicle coat protein c 93.6 2.3 5E-05 40.2 13.4 64 62-125 100-164 (216)
4 PF08079 Ribosomal_L30_N: Ribo 78.9 21 0.00045 27.8 8.4 37 73-109 9-45 (71)
5 KOG1664 Vacuolar H+-ATPase V1 78.7 34 0.00075 32.6 11.2 52 72-123 16-68 (220)
6 CHL00019 atpF ATP synthase CF0 76.0 26 0.00057 31.1 9.4 55 72-126 84-138 (184)
7 PRK13454 F0F1 ATP synthase sub 75.4 40 0.00086 30.2 10.4 47 73-119 92-138 (181)
8 COG3461 Uncharacterized conser 74.1 20 0.00044 30.4 7.5 70 82-154 10-84 (103)
9 CHL00118 atpG ATP synthase CF0 72.2 40 0.00086 29.2 9.4 18 93-110 103-120 (156)
10 PF15466 DUF4635: Domain of un 71.8 19 0.00041 31.9 7.1 43 68-110 83-125 (135)
11 PRK07352 F0F1 ATP synthase sub 71.7 40 0.00086 29.6 9.4 48 73-120 80-127 (174)
12 TIGR03321 alt_F1F0_F0_B altern 69.3 41 0.0009 31.2 9.4 55 71-125 64-118 (246)
13 PRK06231 F0F1 ATP synthase sub 64.3 62 0.0014 29.6 9.4 53 72-124 108-160 (205)
14 PRK13453 F0F1 ATP synthase sub 64.1 70 0.0015 28.2 9.4 50 72-121 78-127 (173)
15 PF00430 ATP-synt_B: ATP synth 63.2 63 0.0014 26.2 8.3 38 72-109 59-96 (132)
16 PRK14474 F0F1 ATP synthase sub 63.1 63 0.0014 30.5 9.4 55 71-125 64-118 (250)
17 PRK13460 F0F1 ATP synthase sub 62.3 80 0.0017 27.7 9.4 19 91-109 95-113 (173)
18 PRK14471 F0F1 ATP synthase sub 60.9 91 0.002 27.0 9.4 45 73-117 69-113 (164)
19 PF04568 IATP: Mitochondrial A 58.7 39 0.00084 28.5 6.4 41 67-107 60-100 (100)
20 PRK14472 F0F1 ATP synthase sub 56.0 1.2E+02 0.0026 26.7 9.4 9 97-105 103-111 (175)
21 COG0488 Uup ATPase components 55.3 36 0.00077 35.8 6.9 43 73-116 235-277 (530)
22 TIGR01144 ATP_synt_b ATP synth 54.6 1.3E+02 0.0028 25.3 9.4 47 73-119 56-102 (147)
23 PRK13461 F0F1 ATP synthase sub 53.9 1.4E+02 0.0031 25.6 9.4 46 73-118 66-111 (159)
24 PF13019 Telomere_Sde2: Telome 53.7 18 0.00039 32.9 3.9 36 68-103 126-161 (162)
25 KOG1029 Endocytic adaptor prot 52.9 79 0.0017 35.8 9.1 24 79-102 342-365 (1118)
26 PRK13428 F0F1 ATP synthase sub 52.2 1E+02 0.0022 31.5 9.4 53 72-124 61-113 (445)
27 PF01346 FKBP_N: Domain amino 51.9 45 0.00098 27.2 5.7 34 102-135 70-107 (124)
28 PRK14473 F0F1 ATP synthase sub 50.6 1.7E+02 0.0036 25.4 9.4 37 73-109 69-105 (164)
29 PRK13455 F0F1 ATP synthase sub 47.9 1.9E+02 0.0041 25.6 9.4 11 74-84 53-63 (184)
30 PF07139 DUF1387: Protein of u 46.1 54 0.0012 32.6 6.1 36 70-105 181-219 (302)
31 KOG3838 Mannose lectin ERGIC-5 45.3 62 0.0013 33.9 6.6 34 80-114 284-317 (497)
32 TIGR01310 L7 60S ribosomal pro 44.9 1.1E+02 0.0024 29.3 7.9 43 74-116 11-53 (235)
33 PF11740 KfrA_N: Plasmid repli 44.1 1.7E+02 0.0037 23.6 8.9 60 69-128 37-104 (120)
34 PRK08476 F0F1 ATP synthase sub 43.1 2.2E+02 0.0047 24.5 9.4 12 74-85 58-69 (141)
35 PF12999 PRKCSH-like: Glucosid 41.3 1.8E+02 0.0038 26.9 8.3 34 71-105 121-154 (176)
36 PRK03963 V-type ATP synthase s 40.2 2.6E+02 0.0057 24.6 11.9 60 128-202 84-143 (198)
37 COG2811 NtpF Archaeal/vacuolar 40.0 2.5E+02 0.0053 24.3 9.6 52 71-122 21-72 (108)
38 PF01086 Clathrin_lg_ch: Clath 40.0 59 0.0013 30.3 5.2 59 68-126 112-171 (225)
39 PLN03086 PRLI-interacting fact 37.3 1.3E+02 0.0028 32.3 7.7 15 141-155 72-86 (567)
40 KOG1772 Vacuolar H+-ATPase V1 36.9 2E+02 0.0044 24.9 7.5 39 78-116 15-54 (108)
41 PF03179 V-ATPase_G: Vacuolar 36.5 2.3E+02 0.0049 22.9 8.9 47 79-125 14-61 (105)
42 PF06936 Selenoprotein_S: Sele 36.5 2.3E+02 0.0051 26.2 8.4 57 71-130 56-113 (190)
43 PF11875 DUF3395: Domain of un 36.0 1.8E+02 0.0039 25.6 7.3 36 81-116 8-43 (151)
44 KOG1029 Endocytic adaptor prot 36.0 2.5E+02 0.0054 32.0 9.7 6 144-149 410-415 (1118)
45 PRK05759 F0F1 ATP synthase sub 34.9 2.8E+02 0.0061 23.4 10.4 7 97-103 89-95 (156)
46 PRK00409 recombination and DNA 34.5 2.3E+02 0.005 31.2 9.2 15 188-202 607-621 (782)
47 PRK03963 V-type ATP synthase s 34.5 3.3E+02 0.007 24.1 10.9 32 74-105 13-44 (198)
48 PF05553 DUF761: Cotton fibre 33.7 1.3E+02 0.0028 21.4 4.9 27 96-122 3-29 (38)
49 PF10147 CR6_interact: Growth 33.7 3.2E+02 0.0069 26.1 8.9 56 70-129 134-199 (217)
50 PF07295 DUF1451: Protein of u 31.4 2.5E+02 0.0055 24.9 7.5 72 69-155 12-83 (146)
51 PF02898 NO_synthase: Nitric o 30.5 75 0.0016 32.5 4.5 33 94-126 5-41 (372)
52 TIGR01147 V_ATP_synt_G vacuola 29.9 3.3E+02 0.0071 23.4 7.7 39 78-116 15-54 (113)
53 PLN02413 choline-phosphate cyt 29.7 3.7E+02 0.008 26.9 8.9 32 94-125 227-258 (294)
54 PHA03065 Hypothetical protein; 29.5 2.1E+02 0.0045 30.1 7.5 41 95-137 99-145 (438)
55 TIGR00570 cdk7 CDK-activating 29.1 5.5E+02 0.012 25.8 10.1 23 70-92 119-141 (309)
56 PF00249 Myb_DNA-binding: Myb- 28.2 67 0.0015 22.3 2.8 25 126-155 7-32 (48)
57 COG5019 CDC3 Septin family pro 27.2 3.6E+02 0.0079 27.8 8.6 52 72-131 314-365 (373)
58 PF09731 Mitofilin: Mitochondr 26.8 5.3E+02 0.012 26.7 10.0 31 96-126 310-340 (582)
59 PF00836 Stathmin: Stathmin fa 24.0 5.2E+02 0.011 23.1 8.1 59 75-133 56-114 (140)
60 PF10453 NUFIP1: Nuclear fragi 23.5 1.4E+02 0.003 22.7 3.8 16 68-83 18-33 (56)
61 PF04358 DsrC: DsrC like prote 23.4 60 0.0013 27.5 2.1 39 74-115 21-59 (109)
62 cd00575 NOS_oxygenase Nitric o 21.9 1.1E+02 0.0023 31.3 3.8 28 98-125 2-33 (356)
63 cd00167 SANT 'SWI3, ADA2, N-Co 21.8 1.1E+02 0.0023 19.5 2.6 26 125-155 4-30 (45)
64 KOG0579 Ste20-like serine/thre 21.7 8.4E+02 0.018 28.0 10.6 47 70-116 785-831 (1187)
65 cd00795 NOS_oxygenase_euk Nitr 21.3 1.6E+02 0.0034 30.7 4.9 19 96-114 53-71 (412)
66 KOG4364 Chromatin assembly fac 21.0 1E+03 0.022 26.9 10.9 12 94-105 284-295 (811)
67 PRK07352 F0F1 ATP synthase sub 20.8 5.8E+02 0.012 22.4 9.2 36 94-129 79-114 (174)
68 COG2920 DsrC Dissimilatory sul 20.7 1.1E+02 0.0025 26.5 3.2 41 73-116 22-62 (111)
69 PF01765 RRF: Ribosome recycli 20.4 4.2E+02 0.0091 23.3 6.8 24 99-122 135-158 (165)
70 PRK08475 F0F1 ATP synthase sub 20.0 6.1E+02 0.013 22.4 9.2 57 78-134 66-122 (167)
No 1
>PF01086 Clathrin_lg_ch: Clathrin light chain; InterPro: IPR000996 Proteins synthesized on the ribosome and processed in the endoplasmic reticulum are transported from the Golgi apparatus to the trans-Golgi network (TGN), and from there via small carrier vesicles to their final destination compartment. These vesicles have specific coat proteins (such as clathrin or coatomer) that are important for cargo selection and direction of transport []. Clathrin coats contain both clathrin (acts as a scaffold) and adaptor complexes that link clathrin to receptors in coated vesicles. Clathrin-associated protein complexes are believed to interact with the cytoplasmic tails of membrane proteins, leading to their selection and concentration. The two major types of clathrin adaptor complexes are the heterotetrameric adaptor protein (AP) complexes, and the monomeric GGA (Golgi-localising, Gamma-adaptin ear domain homology, ARF-binding proteins) adaptors [, ]. Clathrin is a trimer composed of three heavy chains and three light chains, each monomer projecting outwards like a leg; this three-legged structure is known as a triskelion [, ]. The heavy chains form the legs, their N-terminal beta-propeller regions extending outwards, while their C-terminal alpha-alpha-superhelical regions form the central hub of the triskelion. Peptide motifs can bind between the beta-propeller blades. The light chains appear to have a regulatory role, and may help orient the assembly and disassembly of clathrin coats as they interact with hsc70 uncoating ATPase []. Clathrin triskelia self-polymerise into a curved lattice by twisting individual legs together. The clathrin lattice forms around a vesicle as it buds from the TGN, plasma membrane or endosomes, acting to stabilise the vesicle and facilitate the budding process []. The multiple blades created when the triskelia polymerise are involved in multiple protein interactions, enabling the recruitment of different cargo adaptors and membrane attachment proteins []. This entry represents clathrin light chains, which are more divergent in sequence than the heavy chains []. In higher eukaryotes, two genes encode distinct but related light chains, each of which can yield two separate forms via alternative splicing. In yeast there is a single light chain whose sequence is only distantly related to that of higher eukaryotes. Clathrin light chains have a conserved acidic N-terminal domain, a central coiled-coil domain and a conserved C-terminal domain. More information about these proteins can be found at Protein of the Month: Clathrin [].; GO: 0005198 structural molecule activity, 0006886 intracellular protein transport, 0016192 vesicle-mediated transport, 0030130 clathrin coat of trans-Golgi network vesicle, 0030132 clathrin coat of coated pit; PDB: 3LVG_E 3LVH_D.
Probab=100.00 E-value=2.4e-34 Score=261.12 Aligned_cols=114 Identities=38% Similarity=0.605 Sum_probs=56.4
Q ss_pred CCchhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHhhhhhcccccCC
Q 046052 65 MMPEEGFAFREWRRQNAVHLEEKEKREKEMRNQIIDEAEEYKRAFYEKRKLNVETNKAQNREREKLYMANKEKFHKEVDK 144 (318)
Q Consensus 65 m~~EEpEaIREWREeqa~rLeEKDk~EkEkKeeiikEAee~iD~FYe~rn~kkEknka~NRe~Ee~FLa~rE~f~~~a~g 144 (318)
+..|++++||+||++|+++|++||+++++++++|+++|+++|++||++|+.+|++++++||++|+.||++|+.| ..+|
T Consensus 106 ~~~E~~e~ireWre~~~~~i~ekD~~e~~kk~e~~~~A~k~lddfY~~~~~k~e~~k~~nr~~ee~fl~~~~~~--~~~~ 183 (225)
T PF01086_consen 106 VEEEEPEAIREWREERDKRIEEKDAEEEEKKEEIKEKAKKELDDFYENRNEKKEKNKKQNREEEEEFLAKREEF--LQPG 183 (225)
T ss_dssp TTTS-TTHHHHHHHHHTTTSTHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTT--------------------
T ss_pred ccchhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHccccc--CCCC
Confidence 33344999999999999999999999999999999999999999999999999999999999999999999998 7889
Q ss_pred ChHHHHHhhchhhhhhhhhhccCCCCCCCCcceeecCCCCCCCchhHHHHHHHHHhhCC
Q 046052 145 HYWKAIAELIPREVANIEKKKGRKDHDKKPSIVVIQGPKPGKPTDLSRMRQMYMKLKNN 203 (318)
Q Consensus 145 t~WERVaeLID~elp~sekK~~kkD~Dkkp~~tv~qGpKpGk~kDlSRMRqILLkLK~~ 203 (318)
|+|+|||+|||+ +++.+ +. .+|+||||+|||+||++
T Consensus 184 t~WerV~~Lid~----------------~~~~~-----~~--~kD~sRmR~iLl~LK~~ 219 (225)
T PF01086_consen 184 TEWERVAKLIDF----------------NPKSS-----KS--GKDVSRMREILLKLKGD 219 (225)
T ss_dssp -----------------------------------------------------------
T ss_pred CcHHHHHHHhCC----------------CCCCC-----CC--CCcHHHHHHHHHHhhhh
Confidence 999999999984 11111 22 39999999999999943
No 2
>KOG4031 consensus Vesicle coat protein clathrin, light chain [Intracellular trafficking, secretion, and vesicular transport]
Probab=99.97 E-value=6.1e-31 Score=238.78 Aligned_cols=115 Identities=24% Similarity=0.518 Sum_probs=102.0
Q ss_pred chhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHhhhhhcccccCCCh
Q 046052 67 PEEGFAFREWRRQNAVHLEEKEKREKEMRNQIIDEAEEYKRAFYEKRKLNVETNKAQNREREKLYMANKEKFHKEVDKHY 146 (318)
Q Consensus 67 ~EEpEaIREWREeqa~rLeEKDk~EkEkKeeiikEAee~iD~FYe~rn~kkEknka~NRe~Ee~FLa~rE~f~~~a~gt~ 146 (318)
.+|||.||+||++|+.||+|||..+++++++++++|.+.||+||.+|++++++++.+||.+++.|+..-+.| ..||.
T Consensus 102 ~~epE~IRkWkeeQ~~rl~ekD~~sek~k~ElrekAkKelddwy~~~~ek~~k~~~~nk~eee~~~~e~~~~---~~gTe 178 (216)
T KOG4031|consen 102 RDEPEKIRKWKEEQMKRLQEKDEASEKLKEELREKAKKELDDWYDQQNEKLEKTKANNKAEEEALVKENEEF---SPGTE 178 (216)
T ss_pred ccChHHHHHHHHHHHHHHHHhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHhhccc---CCCch
Confidence 489999999999999999999999999999999999999999999999999999999988777777655553 46799
Q ss_pred HHHHHhhchhhhhhhhhhccCCCCCCCCcceeecCCCCCCCchhHHHHHHHHHhhCCCCCC
Q 046052 147 WKAIAELIPREVANIEKKKGRKDHDKKPSIVVIQGPKPGKPTDLSRMRQMYMKLKNNPPSH 207 (318)
Q Consensus 147 WERVaeLID~elp~sekK~~kkD~Dkkp~~tv~qGpKpGk~kDlSRMRqILLkLK~~Pp~h 207 (318)
||||++||| +++++. |.| +|+||||+|||+|||.|.+|
T Consensus 179 WErv~kL~D----------------~n~k~s-----k~g--kD~SRlrslL~~LK~aP~a~ 216 (216)
T KOG4031|consen 179 WERVAKLCD----------------FNPKSS-----KQG--KDVSRLRSLLISLKQAPGAA 216 (216)
T ss_pred HHHHHHHHc----------------CCccch-----hcc--ccHHHHHHHHHHhhhCcCCC
Confidence 999999997 445444 457 99999999999999988764
No 3
>KOG4031 consensus Vesicle coat protein clathrin, light chain [Intracellular trafficking, secretion, and vesicular transport]
Probab=93.59 E-value=2.3 Score=40.16 Aligned_cols=64 Identities=20% Similarity=0.214 Sum_probs=54.3
Q ss_pred CCCCCchhhHHHHHHHHHHHHHHHHHH-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhH
Q 046052 62 PSEMMPEEGFAFREWRRQNAVHLEEKE-KREKEMRNQIIDEAEEYKRAFYEKRKLNVETNKAQNR 125 (318)
Q Consensus 62 P~em~~EEpEaIREWREeqa~rLeEKD-k~EkEkKeeiikEAee~iD~FYe~rn~kkEknka~NR 125 (318)
..+.++|--..-|+=++++-.++-+.+ +..+|++++.|+++++|.++|-+++...+..+++.-.
T Consensus 100 ~~~~epE~IRkWkeeQ~~rl~ekD~~sek~k~ElrekAkKelddwy~~~~ek~~k~~~~nk~eee 164 (216)
T KOG4031|consen 100 RLRDEPEKIRKWKEEQMKRLQEKDEASEKLKEELREKAKKELDDWYDQQNEKLEKTKANNKAEEE 164 (216)
T ss_pred CcccChHHHHHHHHHHHHHHHHhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhHHHHH
Confidence 356677888899999999888887776 5578999999999999999999999999999865443
No 4
>PF08079 Ribosomal_L30_N: Ribosomal L30 N-terminal domain; InterPro: IPR012988 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. This presumed domain is found at the N terminus of Ribosomal L30 proteins and has been termed RL30NT or NUC018 [].; PDB: 3IZR_e 3O5H_G 3O58_G 3IZS_e 4A1A_V 4A17_V 4A1E_V 4A1C_V.
Probab=78.92 E-value=21 Score=27.83 Aligned_cols=37 Identities=22% Similarity=0.444 Sum_probs=30.9
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 046052 73 FREWRRQNAVHLEEKEKREKEMRNQIIDEAEEYKRAF 109 (318)
Q Consensus 73 IREWREeqa~rLeEKDk~EkEkKeeiikEAee~iD~F 109 (318)
-.+|+..+.......-......+..|++.|+.|+.+|
T Consensus 9 ~~~~~~~~~~~~~~~k~~~~~~r~~~~kRAekY~kEY 45 (71)
T PF08079_consen 9 NEKLKAKRAKKAAARKKKRKKKRKEIFKRAEKYVKEY 45 (71)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 4579998888888877888889999999999995554
No 5
>KOG1664 consensus Vacuolar H+-ATPase V1 sector, subunit E [Energy production and conversion]
Probab=78.69 E-value=34 Score=32.60 Aligned_cols=52 Identities=21% Similarity=0.322 Sum_probs=37.7
Q ss_pred HHHHHHHHHHHHHHHHHHHH-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 046052 72 AFREWRRQNAVHLEEKEKRE-KEMRNQIIDEAEEYKRAFYEKRKLNVETNKAQ 123 (318)
Q Consensus 72 aIREWREeqa~rLeEKDk~E-kEkKeeiikEAee~iD~FYe~rn~kkEknka~ 123 (318)
.||+=-++.+++|.-+.++| .-.|.+|+++...-|++||+....+++.+++-
T Consensus 16 FI~qEA~EKA~EI~~kAeeEfnIEK~rlV~~q~~kI~~~yekKeKqve~~kkI 68 (220)
T KOG1664|consen 16 FIRQEAEEKAKEIDAKAEEEFNIEKGRLVQEQRLKIMQYYEKKEKQVELQKKI 68 (220)
T ss_pred HHHHHHHHHHHHhhhhhHHHhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 45555566666666554433 34678999999999999999998888876653
No 6
>CHL00019 atpF ATP synthase CF0 B subunit
Probab=76.02 E-value=26 Score=31.07 Aligned_cols=55 Identities=7% Similarity=0.059 Sum_probs=30.8
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhHH
Q 046052 72 AFREWRRQNAVHLEEKEKREKEMRNQIIDEAEEYKRAFYEKRKLNVETNKAQNRE 126 (318)
Q Consensus 72 aIREWREeqa~rLeEKDk~EkEkKeeiikEAee~iD~FYe~rn~kkEknka~NRe 126 (318)
.|.++|.+....|++-.+.....+++++.+|+..++...++-...++..+..-+.
T Consensus 84 ~L~~A~~ea~~ii~~A~~~ae~~~~~il~~A~~ea~~~~~~a~~~ie~Ek~~a~~ 138 (184)
T CHL00019 84 RLRQAELEADEIRVNGYSEIEREKENLINQAKEDLERLENYKNETIRFEQQRAIN 138 (184)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 4445555555555544455555666666666666666655555555555444443
No 7
>PRK13454 F0F1 ATP synthase subunit B'; Provisional
Probab=75.38 E-value=40 Score=30.17 Aligned_cols=47 Identities=11% Similarity=0.051 Sum_probs=19.9
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 046052 73 FREWRRQNAVHLEEKEKREKEMRNQIIDEAEEYKRAFYEKRKLNVET 119 (318)
Q Consensus 73 IREWREeqa~rLeEKDk~EkEkKeeiikEAee~iD~FYe~rn~kkEk 119 (318)
|+++|.+-...|++-.+..++.+++++.+|+..++...++-+.++++
T Consensus 92 L~~Ar~EA~~ii~~A~~ea~~~~~~~~~~A~~e~~~~~aea~~~I~~ 138 (181)
T PRK13454 92 LADARAEAQRIVAETRAEIQAELDVAIAKADAEIAAKAAESEKRIAE 138 (181)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 33344444333333333333444455555555544444443333333
No 8
>COG3461 Uncharacterized conserved protein [Function unknown]
Probab=74.06 E-value=20 Score=30.40 Aligned_cols=70 Identities=24% Similarity=0.318 Sum_probs=49.9
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH-----HHHHHHHHHhHHHHHHHHhhhhhcccccCCChHHHHHhhc
Q 046052 82 VHLEEKEKREKEMRNQIIDEAEEYKRAFYEKRK-----LNVETNKAQNREREKLYMANKEKFHKEVDKHYWKAIAELI 154 (318)
Q Consensus 82 ~rLeEKDk~EkEkKeeiikEAee~iD~FYe~rn-----~kkEknka~NRe~Ee~FLa~rE~f~~~a~gt~WERVaeLI 154 (318)
.+|.+|.+--..+++.+|++++.- -||.+|- .++-.-++.||.+|++..+-.-+|. ....-.|++-..-|
T Consensus 10 eeLs~kirdf~Ra~~SLiEEiEA~--~wY~qR~~~tKD~~~r~ImehnrdeE~eHa~mlLEwl-rR~~p~wd~eL~ei 84 (103)
T COG3461 10 EELSEKIRDFSRARQSLIEEIEAM--MWYDQRADATKDEDLRAIMEHNRDEEKEHAAMLLEWL-RRHDPAWDAELHEI 84 (103)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHH--HHHHHHhhccccHhHHHHHHHcccHHHHHHHHHHHHH-HHcCchHHHHHHHH
Confidence 356777777777888888888775 5799984 4677778899999987654433343 34467798877655
No 9
>CHL00118 atpG ATP synthase CF0 B' subunit; Validated
Probab=72.25 E-value=40 Score=29.21 Aligned_cols=18 Identities=17% Similarity=0.405 Sum_probs=7.1
Q ss_pred HHHHHHHHHHHHHHHHHH
Q 046052 93 EMRNQIIDEAEEYKRAFY 110 (318)
Q Consensus 93 EkKeeiikEAee~iD~FY 110 (318)
+.+++++.+|++..+...
T Consensus 103 ~~~~~~~~~A~~ea~~~~ 120 (156)
T CHL00118 103 EIVENELKQAQKYIDSLL 120 (156)
T ss_pred HHHHHHHHHHHHHHHHHH
Confidence 333444444444433333
No 10
>PF15466 DUF4635: Domain of unknown function (DUF4635)
Probab=71.78 E-value=19 Score=31.85 Aligned_cols=43 Identities=28% Similarity=0.377 Sum_probs=37.7
Q ss_pred hhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 046052 68 EEGFAFREWRRQNAVHLEEKEKREKEMRNQIIDEAEEYKRAFY 110 (318)
Q Consensus 68 EEpEaIREWREeqa~rLeEKDk~EkEkKeeiikEAee~iD~FY 110 (318)
|--..||.|-.++---+-||=++|-...+|+..+++.|+|.+.
T Consensus 83 EPik~~r~WLkenLhvflEkLE~EvreLEQlV~DLE~WLDalL 125 (135)
T PF15466_consen 83 EPIKAIRNWLKENLHVFLEKLEKEVRELEQLVRDLEEWLDALL 125 (135)
T ss_pred chHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence 3347899999999888888888888899999999999999874
No 11
>PRK07352 F0F1 ATP synthase subunit B; Validated
Probab=71.73 E-value=40 Score=29.59 Aligned_cols=48 Identities=10% Similarity=0.153 Sum_probs=21.8
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 046052 73 FREWRRQNAVHLEEKEKREKEMRNQIIDEAEEYKRAFYEKRKLNVETN 120 (318)
Q Consensus 73 IREWREeqa~rLeEKDk~EkEkKeeiikEAee~iD~FYe~rn~kkEkn 120 (318)
|.+||.+....|.+-.+.....+++++++|++.++.+.++-+..++..
T Consensus 80 L~~a~~ea~~ii~~a~~~a~~~~~~~~~~A~~e~~~~~~~a~~~i~~e 127 (174)
T PRK07352 80 LAQAQQEAERIRADAKARAEAIRAEIEKQAIEDMARLKQTAAADLSAE 127 (174)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 444444444444443334444455555555555444444444444333
No 12
>TIGR03321 alt_F1F0_F0_B alternate F1F0 ATPase, F0 subunit B. CC and in principle may run in either direction. This model represents the F0 subunit B of this apparent second ATP synthase.
Probab=69.26 E-value=41 Score=31.23 Aligned_cols=55 Identities=22% Similarity=0.236 Sum_probs=41.0
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhH
Q 046052 71 FAFREWRRQNAVHLEEKEKREKEMRNQIIDEAEEYKRAFYEKRKLNVETNKAQNR 125 (318)
Q Consensus 71 EaIREWREeqa~rLeEKDk~EkEkKeeiikEAee~iD~FYe~rn~kkEknka~NR 125 (318)
..+.+|+.+....+++-.......+++++++|++.++...++-...++..++.-+
T Consensus 64 ~~l~~a~~ea~~i~~~A~~eA~~~~~~i~~~A~~ea~~~~~~a~~~ie~E~~~a~ 118 (246)
T TIGR03321 64 EKNEELDQQREVLLTKAKEEAQAERQRLLDEAREEADEIREKWQEALRREQAALS 118 (246)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 3567777777777776666667788888999988888887777777776666555
No 13
>PRK06231 F0F1 ATP synthase subunit B; Validated
Probab=64.34 E-value=62 Score=29.65 Aligned_cols=53 Identities=8% Similarity=0.119 Sum_probs=27.0
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Q 046052 72 AFREWRRQNAVHLEEKEKREKEMRNQIIDEAEEYKRAFYEKRKLNVETNKAQN 124 (318)
Q Consensus 72 aIREWREeqa~rLeEKDk~EkEkKeeiikEAee~iD~FYe~rn~kkEknka~N 124 (318)
.+.+||.+-...+.+-.+.....+++++++|++.++..-.+-+..++..+++-
T Consensus 108 ~L~~A~~eA~~Ii~~A~~eAe~~~e~i~~~A~~eae~ii~~A~~~Ie~Ek~~a 160 (205)
T PRK06231 108 RHENALAQAKEIIDQANYEALQLKSELEKEANRQANLIIFQARQEIEKERREL 160 (205)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 34455554444444444444445566666666665555555454444444443
No 14
>PRK13453 F0F1 ATP synthase subunit B; Provisional
Probab=64.07 E-value=70 Score=28.22 Aligned_cols=50 Identities=20% Similarity=0.314 Sum_probs=24.2
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 046052 72 AFREWRRQNAVHLEEKEKREKEMRNQIIDEAEEYKRAFYEKRKLNVETNK 121 (318)
Q Consensus 72 aIREWREeqa~rLeEKDk~EkEkKeeiikEAee~iD~FYe~rn~kkEknk 121 (318)
.|.++|.+....+.+-.+..++.+++++.+|++..+.+.++-...++..+
T Consensus 78 ~l~~a~~ea~~ii~~a~~~a~~~~~~~~~~A~~ea~~~~~~A~~~I~~ek 127 (173)
T PRK13453 78 KLKETQEEVQKILEDAKVQARQQQEQIIHEANVRANGMIETAQSEINSQK 127 (173)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 34444444444444444444455556666666555555444444444333
No 15
>PF00430 ATP-synt_B: ATP synthase B/B' CF(0); InterPro: IPR002146 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 subunits B and B' from the F0 complex in F-ATPases found in chloroplasts and in bacterial plasma membranes. The B subunits are part of the peripheral stalk that links the F1 and F0 complexes together, and which acts as a stator to prevent certain subunits from rotating with the central rotary element. The peripheral stalk differs in subunit composition between mitochondrial, chloroplast and bacterial F-ATPases. In bacterial and chloroplast F-ATPases, the peripheral stalk is composed of one copy of the delta subunit (homologous to OSCP in mitochondria), and two copies of subunit B in bacteria, or one copy each of subunits B and B' in chloroplasts and photosynthetic bacteria []. 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, 0045263 proton-transporting ATP synthase complex, coupling factor F(o); PDB: 1L2P_A 2KHK_A 1B9U_A.
Probab=63.21 E-value=63 Score=26.19 Aligned_cols=38 Identities=21% Similarity=0.320 Sum_probs=16.2
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 046052 72 AFREWRRQNAVHLEEKEKREKEMRNQIIDEAEEYKRAF 109 (318)
Q Consensus 72 aIREWREeqa~rLeEKDk~EkEkKeeiikEAee~iD~F 109 (318)
.|.++|.+-...+.+-.....+.+++++.+|++.++..
T Consensus 59 ~l~~a~~ea~~i~~~a~~~a~~~~~~~~~ea~~~~~~~ 96 (132)
T PF00430_consen 59 KLAEAREEAQEIIEEAKEEAEKEKEEILAEAEKEAERI 96 (132)
T ss_dssp HHHHHHHHHCHHHHHHCHHHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 34444444444443333333444444444444443333
No 16
>PRK14474 F0F1 ATP synthase subunit B; Provisional
Probab=63.09 E-value=63 Score=30.52 Aligned_cols=55 Identities=16% Similarity=0.181 Sum_probs=38.7
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhH
Q 046052 71 FAFREWRRQNAVHLEEKEKREKEMRNQIIDEAEEYKRAFYEKRKLNVETNKAQNR 125 (318)
Q Consensus 71 EaIREWREeqa~rLeEKDk~EkEkKeeiikEAee~iD~FYe~rn~kkEknka~NR 125 (318)
..+.+++.+....|++-.....+.+++++++|++.++...++-...++..++.-.
T Consensus 64 ~~l~~a~~ea~~ii~~A~~eA~~~~~~il~~A~~ea~~~~~~a~~~ie~Ek~~a~ 118 (250)
T PRK14474 64 QKQQSLEQQRASFMAQAQEAADEQRQHLLNEAREDVATARDEWLEQLEREKQEFF 118 (250)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 3466777777777766666667778888888888888777766666665554444
No 17
>PRK13460 F0F1 ATP synthase subunit B; Provisional
Probab=62.26 E-value=80 Score=27.74 Aligned_cols=19 Identities=16% Similarity=0.393 Sum_probs=8.2
Q ss_pred HHHHHHHHHHHHHHHHHHH
Q 046052 91 EKEMRNQIIDEAEEYKRAF 109 (318)
Q Consensus 91 EkEkKeeiikEAee~iD~F 109 (318)
....+++++.+|++.++..
T Consensus 95 a~~~~~~~~~~A~~ea~~~ 113 (173)
T PRK13460 95 ALKLKNKLLEETNNEVKAQ 113 (173)
T ss_pred HHHHHHHHHHHHHHHHHHH
Confidence 3334444444444443333
No 18
>PRK14471 F0F1 ATP synthase subunit B; Provisional
Probab=60.95 E-value=91 Score=26.98 Aligned_cols=45 Identities=20% Similarity=0.258 Sum_probs=19.0
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 046052 73 FREWRRQNAVHLEEKEKREKEMRNQIIDEAEEYKRAFYEKRKLNV 117 (318)
Q Consensus 73 IREWREeqa~rLeEKDk~EkEkKeeiikEAee~iD~FYe~rn~kk 117 (318)
|.++|.+....|.+-.+...+.+++++++|++..+...++-...+
T Consensus 69 l~~A~~ea~~ii~~A~~~a~~~~~~~~~~A~~ea~~~~~~a~~~i 113 (164)
T PRK14471 69 LKEARAERDAILKEAREIKEKMIADAKEEAQVEGDKMIEQAKASI 113 (164)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 344444444444333333334444455555554444433333333
No 19
>PF04568 IATP: Mitochondrial ATPase inhibitor, IATP; InterPro: IPR007648 ATP synthase inhibitor prevents the enzyme from switching to ATP hydrolysis during collapse of the electrochemical gradient, for example during oxygen deprivation [] ATP synthase inhibitor forms a one to one complex with the F1 ATPase, possibly by binding at the alpha-beta interface. It is thought to inhibit ATP synthesis by preventing the release of ATP []. The minimum inhibitory region for bovine inhibitor (P01096 from SWISSPROT) is from residues 39 to 72 []. The inhibitor has two oligomeric states, dimer (the active state) and tetramer. At low pH , the inhibitor forms a dimer via antiparallel coiled coil interactions between the C-terminal regions of two monomers. At high pH, the inhibitor forms tetramers and higher oligomers by coiled coil interactions involving the N terminus and inhibitory region, thus preventing the inhibitory activity []. ; GO: 0004857 enzyme inhibitor activity, 0045980 negative regulation of nucleotide metabolic process, 0005739 mitochondrion; PDB: 1GMJ_B 1OHH_H 1HF9_B 2V7Q_J.
Probab=58.66 E-value=39 Score=28.48 Aligned_cols=41 Identities=32% Similarity=0.334 Sum_probs=32.5
Q ss_pred chhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 046052 67 PEEGFAFREWRRQNAVHLEEKEKREKEMRNQIIDEAEEYKR 107 (318)
Q Consensus 67 ~EEpEaIREWREeqa~rLeEKDk~EkEkKeeiikEAee~iD 107 (318)
..|-..||++..+|-+.|.++-..+.+..++-|++.++.|+
T Consensus 60 A~E~~Y~r~~EkEqL~~Lk~kl~~e~~~~~k~i~~le~~I~ 100 (100)
T PF04568_consen 60 AQEEQYFRKKEKEQLKKLKEKLKEEIEHHRKEIDELEKHIE 100 (100)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred hhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcC
Confidence 46778899998888888888777777777777888887764
No 20
>PRK14472 F0F1 ATP synthase subunit B; Provisional
Probab=55.98 E-value=1.2e+02 Score=26.66 Aligned_cols=9 Identities=22% Similarity=0.335 Sum_probs=3.2
Q ss_pred HHHHHHHHH
Q 046052 97 QIIDEAEEY 105 (318)
Q Consensus 97 eiikEAee~ 105 (318)
+++++|++.
T Consensus 103 ~~~~~A~~e 111 (175)
T PRK14472 103 EITEKAHTE 111 (175)
T ss_pred HHHHHHHHH
Confidence 333333333
No 21
>COG0488 Uup ATPase components of ABC transporters with duplicated ATPase domains [General function prediction only]
Probab=55.32 E-value=36 Score=35.75 Aligned_cols=43 Identities=16% Similarity=0.204 Sum_probs=33.0
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 046052 73 FREWRRQNAVHLEEKEKREKEMRNQIIDEAEEYKRAFYEKRKLN 116 (318)
Q Consensus 73 IREWREeqa~rLeEKDk~EkEkKeeiikEAee~iD~FYe~rn~k 116 (318)
.-.|.+++++++ ++++++.+++++.+++.++||+.|...+...
T Consensus 235 y~~~~~~r~~~~-~~~~~~~~~~~~~~~~~~~~i~r~~~~~~~~ 277 (530)
T COG0488 235 YSSYLEQKAERL-RQEAAAYEKQQKELAKEQEWIRRGKAAASKA 277 (530)
T ss_pred HHHHHHHHHHHH-HHHHHHHHHHHHHHHHHHHHHHHHHhccchH
Confidence 356666666665 5566666778899999999999999888774
No 22
>TIGR01144 ATP_synt_b ATP synthase, F0 subunit b. This model describes the F1/F0 ATP synthase b subunit in bacteria only. Scoring just below the trusted cutoff are the N-terminal domains of Mycobacterial b/delta fusion proteins and a subunit from an archaeon, Methanosarcina barkeri, in which the ATP synthase homolog differs in architecture and is not experimentally confirmed. This model helps resolve b from the related b' subunit. Within the family is an example from a sodium-translocating rather than proton-translocating ATP synthase.
Probab=54.64 E-value=1.3e+02 Score=25.29 Aligned_cols=47 Identities=19% Similarity=0.299 Sum_probs=21.2
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 046052 73 FREWRRQNAVHLEEKEKREKEMRNQIIDEAEEYKRAFYEKRKLNVET 119 (318)
Q Consensus 73 IREWREeqa~rLeEKDk~EkEkKeeiikEAee~iD~FYe~rn~kkEk 119 (318)
+.+|+.+-...|++-.......+++++.+|++.++...++-+..++.
T Consensus 56 l~~A~~ea~~i~~~a~~~a~~~~~~~~~~a~~e~~~~~~~a~~~i~~ 102 (147)
T TIGR01144 56 LKEAKDEAQEIIENANKRGSEILEEAKAEAREEREKIKAQARAEIEA 102 (147)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 33444444444433334444445555555555544444444444333
No 23
>PRK13461 F0F1 ATP synthase subunit B; Provisional
Probab=53.95 E-value=1.4e+02 Score=25.64 Aligned_cols=46 Identities=20% Similarity=0.343 Sum_probs=20.2
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 046052 73 FREWRRQNAVHLEEKEKREKEMRNQIIDEAEEYKRAFYEKRKLNVE 118 (318)
Q Consensus 73 IREWREeqa~rLeEKDk~EkEkKeeiikEAee~iD~FYe~rn~kkE 118 (318)
|.+++.+...-|++-.+.....+++++.+|+...+...++=...++
T Consensus 66 l~~a~~ea~~ii~~a~~~a~~~~~~i~~~A~~ea~~~~~~a~~~i~ 111 (159)
T PRK13461 66 LKNAKEEGKKIVEEYKSKAENVYEEIVKEAHEEADLIIERAKLEAQ 111 (159)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 3334433333333333333444555555555555544444444443
No 24
>PF13019 Telomere_Sde2: Telomere stability and silencing
Probab=53.69 E-value=18 Score=32.93 Aligned_cols=36 Identities=11% Similarity=0.341 Sum_probs=24.2
Q ss_pred hhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 046052 68 EEGFAFREWRRQNAVHLEEKEKREKEMRNQIIDEAE 103 (318)
Q Consensus 68 EEpEaIREWREeqa~rLeEKDk~EkEkKeeiikEAe 103 (318)
.+-..|.+|.+.+.++-+++.++.+++.++|.+.++
T Consensus 126 ~~~k~l~~~~~~~~er~k~~~e~~~~k~~~l~~~~e 161 (162)
T PF13019_consen 126 NEEKKLAEWLEKKPEREKKEKEKRRKKLEKLVEMLE 161 (162)
T ss_pred HHHHHHHHHHhcChhHHHHHHHHHHHHHHHHHHHhc
Confidence 345689999998887765555555555666666554
No 25
>KOG1029 consensus Endocytic adaptor protein intersectin [Signal transduction mechanisms; Intracellular trafficking, secretion, and vesicular transport]
Probab=52.88 E-value=79 Score=35.75 Aligned_cols=24 Identities=25% Similarity=0.398 Sum_probs=11.8
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHH
Q 046052 79 QNAVHLEEKEKREKEMRNQIIDEA 102 (318)
Q Consensus 79 eqa~rLeEKDk~EkEkKeeiikEA 102 (318)
+.+++++.|+++|.++|+.-..|.
T Consensus 342 reree~eqkEreE~ekkererqEq 365 (1118)
T KOG1029|consen 342 REREEVEQKEREEEEKKERERQEQ 365 (1118)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHH
Confidence 334445555555555555444443
No 26
>PRK13428 F0F1 ATP synthase subunit delta; Provisional
Probab=52.18 E-value=1e+02 Score=31.53 Aligned_cols=53 Identities=17% Similarity=0.164 Sum_probs=31.4
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Q 046052 72 AFREWRRQNAVHLEEKEKREKEMRNQIIDEAEEYKRAFYEKRKLNVETNKAQN 124 (318)
Q Consensus 72 aIREWREeqa~rLeEKDk~EkEkKeeiikEAee~iD~FYe~rn~kkEknka~N 124 (318)
.|.+++.+...-|++-.+..++.+++++++|++.++...++=+.+++..+.+-
T Consensus 61 ~L~~Ak~ea~~Ii~~A~~~A~~~~~~~~~~A~~ea~~i~~~a~~~Ie~ek~~a 113 (445)
T PRK13428 61 AVEDAKAEAARVVEEAREDAERIAEQLRAQADAEAERIKVQGARQVQLLRAQL 113 (445)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 35666666666555555556666777777777776666555555554444433
No 27
>PF01346 FKBP_N: Domain amino terminal to FKBP-type peptidyl-prolyl isomerase; InterPro: IPR000774 Peptidyl-prolyl cis-trans isomerase (PPIase) catalyses the cis-trans isomerisation of proline imidic peptide bonds in oligopeptides [, ]. This alpha helical domain is found at the N terminus of proteins belonging to the FKBP-type peptidyl-prolyl cis-trans isomerase(IPR001179 from INTERPRO) family. Peptidyl-prolyl cis-trans isomerase has been shown to accelerate the refolding of several proteins in vitro [, , ]; the FKPB-type enzymes probably act in the folding of extracytoplasmic proteins.; GO: 0006457 protein folding; PDB: 1FD9_A 2VCD_A 3OE2_A 2UZ5_A 3B09_A 1Q6H_B 1Q6I_B 1Q6U_A.
Probab=51.87 E-value=45 Score=27.18 Aligned_cols=34 Identities=21% Similarity=0.339 Sum_probs=19.0
Q ss_pred HHHHHHHHHHHHHHHH----HHHHHHhHHHHHHHHhhh
Q 046052 102 AEEYKRAFYEKRKLNV----ETNKAQNREREKLYMANK 135 (318)
Q Consensus 102 Aee~iD~FYe~rn~kk----Eknka~NRe~Ee~FLa~r 135 (318)
+++.|..|..++..+. .+..+.|++..+.||++.
T Consensus 70 ~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~fla~n 107 (124)
T PF01346_consen 70 AQEALQAFQQKMQAKQQEKMAKAAEKNKAEGEAFLAEN 107 (124)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHhhcchhhhhhhhHHHHHHHHHHH
Confidence 3334444444444433 333777888888888754
No 28
>PRK14473 F0F1 ATP synthase subunit B; Provisional
Probab=50.57 E-value=1.7e+02 Score=25.35 Aligned_cols=37 Identities=16% Similarity=0.270 Sum_probs=15.2
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 046052 73 FREWRRQNAVHLEEKEKREKEMRNQIIDEAEEYKRAF 109 (318)
Q Consensus 73 IREWREeqa~rLeEKDk~EkEkKeeiikEAee~iD~F 109 (318)
|.++|.+....|++--+...+.+++++++|++..+..
T Consensus 69 l~~A~~ea~~ii~~A~~~a~~~~~~~l~~A~~ea~~~ 105 (164)
T PRK14473 69 LAKARQEAAKIVAQAQERARAQEAEIIAQARREAEKI 105 (164)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 3344443333333333333344444555555443333
No 29
>PRK13455 F0F1 ATP synthase subunit B; Provisional
Probab=47.87 E-value=1.9e+02 Score=25.64 Aligned_cols=11 Identities=9% Similarity=-0.046 Sum_probs=4.6
Q ss_pred HHHHHHHHHHH
Q 046052 74 REWRRQNAVHL 84 (318)
Q Consensus 74 REWREeqa~rL 84 (318)
+.+-++|...|
T Consensus 53 ~~~L~~R~~~I 63 (184)
T PRK13455 53 GGMLDKRAEGI 63 (184)
T ss_pred HHHHHHHHHHH
Confidence 44444444444
No 30
>PF07139 DUF1387: Protein of unknown function (DUF1387); InterPro: IPR009816 This family represents a conserved region approximately 300 residues long within a number of hypothetical proteins of unknown function that seem to be restricted to mammals.
Probab=46.07 E-value=54 Score=32.64 Aligned_cols=36 Identities=14% Similarity=0.067 Sum_probs=16.1
Q ss_pred hHHHHHHHHHHHHHH---HHHHHHHHHHHHHHHHHHHHH
Q 046052 70 GFAFREWRRQNAVHL---EEKEKREKEMRNQIIDEAEEY 105 (318)
Q Consensus 70 pEaIREWREeqa~rL---eEKDk~EkEkKeeiikEAee~ 105 (318)
-.+|+.-+.-|++.. .+|+-.=-....+.++||-+-
T Consensus 181 d~S~k~ik~~F~~l~~cL~dREvaLl~EmdkVK~EAmei 219 (302)
T PF07139_consen 181 DSSIKKIKQTFAELQSCLMDREVALLAEMDKVKAEAMEI 219 (302)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 345666665555443 333322222233445555544
No 31
>KOG3838 consensus Mannose lectin ERGIC-53, involved in glycoprotein traffic [Intracellular trafficking, secretion, and vesicular transport]
Probab=45.29 E-value=62 Score=33.86 Aligned_cols=34 Identities=24% Similarity=0.300 Sum_probs=17.8
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 046052 80 NAVHLEEKEKREKEMRNQIIDEAEEYKRAFYEKRK 114 (318)
Q Consensus 80 qa~rLeEKDk~EkEkKeeiikEAee~iD~FYe~rn 114 (318)
++.+|+.+..+=++-.-...++.++| ++||+.-.
T Consensus 284 ~q~elek~k~efkk~hpd~~~e~ee~-~~~yEs~~ 317 (497)
T KOG3838|consen 284 AQLELEKRKDEFKKSHPDAQGEGEEL-FDLYESLG 317 (497)
T ss_pred HHHHHhhhHhhhccCCchhhcchhhh-hhhhhccc
Confidence 33444444333334444566776666 44887544
No 32
>TIGR01310 L7 60S ribosomal protein L7, eukaryotic. Members of this family average ~ 250 residues in length, somewhat longer than the archaeal L30P/L7E homolog (~ 155 residues) and much longer than the related bacterial/organellar form (~ 60 residues).
Probab=44.89 E-value=1.1e+02 Score=29.27 Aligned_cols=43 Identities=19% Similarity=0.308 Sum_probs=28.3
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 046052 74 REWRRQNAVHLEEKEKREKEMRNQIIDEAEEYKRAFYEKRKLN 116 (318)
Q Consensus 74 REWREeqa~rLeEKDk~EkEkKeeiikEAee~iD~FYe~rn~k 116 (318)
..|+.+++++..++-+.....+..+++.|+.|+.+|.....+.
T Consensus 11 ~~~~~~~~~~~~~~k~~~~~~k~~~fkr~e~~~~~y~~~e~d~ 53 (235)
T TIGR01310 11 QELAVVRAKQAKAKKKRNKKKKKHYFKRAESFVHEYRKAERER 53 (235)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHH
Confidence 4566666666555555566677888999999977775544433
No 33
>PF11740 KfrA_N: Plasmid replication region DNA-binding N-term; InterPro: IPR021104 The KfrA family of protiens are encoded on plasmids, generally in or near gene clusters invloved in stable inheritance functions. These proteins are thought to form an all-helical structure, consisting of an N-terminal helix-turn-helix DNA binding domain and an extended coiled-coil tail. The best-characterised KfrA protein, encoded on the broad host-range Plasmid RK2, is a site-specific DNA-binding protein whose operator overlaps its own promoter. The DNA-binding domain is essential for function, while the coiled-coil domain is probably responsible for formation of multimers, and may provide an example of a bridge to host structures required for plasmid partitioning []. This entry represents the N-terminal DNA-binding domain.
Probab=44.10 E-value=1.7e+02 Score=23.59 Aligned_cols=60 Identities=17% Similarity=0.284 Sum_probs=32.8
Q ss_pred hhHHHHHHHHHHHHHH--------HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhHHHH
Q 046052 69 EGFAFREWRRQNAVHL--------EEKEKREKEMRNQIIDEAEEYKRAFYEKRKLNVETNKAQNRERE 128 (318)
Q Consensus 69 EpEaIREWREeqa~rL--------eEKDk~EkEkKeeiikEAee~iD~FYe~rn~kkEknka~NRe~E 128 (318)
-...|++|++++..+. ..--..-...-..+...|......-|......++..........
T Consensus 37 i~~~l~~w~~~~~~~~~~~~~~lP~~l~~~~~~~~~~~~~~a~~~a~~~~~~~~~~~~~~~~~~~~~~ 104 (120)
T PF11740_consen 37 ISKHLKEWREEREAQVSEAAPDLPEALQDALAELMARLWEAAQEEAEEELEAARAELEQERAAAEAEL 104 (120)
T ss_pred HHHHHHHHHHhhhccccccccCCChhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 4568999999998888 22222223333444444444444445555555555555444433
No 34
>PRK08476 F0F1 ATP synthase subunit B'; Validated
Probab=43.14 E-value=2.2e+02 Score=24.50 Aligned_cols=12 Identities=17% Similarity=0.127 Sum_probs=5.0
Q ss_pred HHHHHHHHHHHH
Q 046052 74 REWRRQNAVHLE 85 (318)
Q Consensus 74 REWREeqa~rLe 85 (318)
.+++++.+..|.
T Consensus 58 ~~~~~e~e~~l~ 69 (141)
T PRK08476 58 SEIEHEIETILK 69 (141)
T ss_pred HHHHHHHHHHHH
Confidence 334444444443
No 35
>PF12999 PRKCSH-like: Glucosidase II beta subunit-like
Probab=41.25 E-value=1.8e+02 Score=26.91 Aligned_cols=34 Identities=21% Similarity=0.234 Sum_probs=21.6
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 046052 71 FAFREWRRQNAVHLEEKEKREKEMRNQIIDEAEEY 105 (318)
Q Consensus 71 EaIREWREeqa~rLeEKDk~EkEkKeeiikEAee~ 105 (318)
+.-++||+..+.+++... .--+.|++++.++++.
T Consensus 121 e~~~~~~~~~~~~~~~~~-~G~~~r~~~i~~a~~~ 154 (176)
T PF12999_consen 121 ELGKEYREELEEEEEIYK-EGLKIRQELIEEAKKK 154 (176)
T ss_pred HHHHHHHHHHHHHHHHHH-HHHHHHHHHHHHHHHH
Confidence 456777776666655433 3445677788777766
No 36
>PRK03963 V-type ATP synthase subunit E; Provisional
Probab=40.18 E-value=2.6e+02 Score=24.65 Aligned_cols=60 Identities=13% Similarity=0.307 Sum_probs=32.1
Q ss_pred HHHHHhhhhhcccccCCChHHHHHhhchhhhhhhhhhccCCCCCCCCcceeecCCCCCCCchhHHHHHHHHHhhC
Q 046052 128 EKLYMANKEKFHKEVDKHYWKAIAELIPREVANIEKKKGRKDHDKKPSIVVIQGPKPGKPTDLSRMRQMYMKLKN 202 (318)
Q Consensus 128 Ee~FLa~rE~f~~~a~gt~WERVaeLID~elp~sekK~~kkD~Dkkp~~tv~qGpKpGk~kDlSRMRqILLkLK~ 202 (318)
++.|-.-++.........||+=+..||..-+-.+. ...++|. +.+.|+...+.+|-.|+.
T Consensus 84 ~~v~~~a~~~l~~~~~~~Y~~~l~~li~~a~~~l~----------~~~i~i~-----~~~~D~~~~~~~~~~~~~ 143 (198)
T PRK03963 84 SEVLEAVRERLAELPEDEYFETLKALTKEAVEELG----------EDKVVVR-----SNERTLKLIDSRLEEIRD 143 (198)
T ss_pred HHHHHHHHHHHHhhhhhhHHHHHHHHHHHHHHHhC----------CCcEEEE-----EccccHHHHHHHHHHHHH
Confidence 33444434333223345888888888852111111 1233443 235888888887777764
No 37
>COG2811 NtpF Archaeal/vacuolar-type H+-ATPase subunit H [Energy production and conversion]
Probab=40.05 E-value=2.5e+02 Score=24.27 Aligned_cols=52 Identities=15% Similarity=0.243 Sum_probs=32.9
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 046052 71 FAFREWRRQNAVHLEEKEKREKEMRNQIIDEAEEYKRAFYEKRKLNVETNKA 122 (318)
Q Consensus 71 EaIREWREeqa~rLeEKDk~EkEkKeeiikEAee~iD~FYe~rn~kkEknka 122 (318)
+.|.+-++++...|.+--....+..+++-.+|++-.++|......+.+.-..
T Consensus 21 ~~IeeAkEe~~~~i~eAr~eareiieeaE~eA~~~~~e~l~~~~ee~e~ea~ 72 (108)
T COG2811 21 EEIEEAKEEAEQIIKEAREEAREIIEEAEEEAEKLAQEILEEAREEAEEEAE 72 (108)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 4567777777777776666666666666666766666665555555444333
No 38
>PF01086 Clathrin_lg_ch: Clathrin light chain; InterPro: IPR000996 Proteins synthesized on the ribosome and processed in the endoplasmic reticulum are transported from the Golgi apparatus to the trans-Golgi network (TGN), and from there via small carrier vesicles to their final destination compartment. These vesicles have specific coat proteins (such as clathrin or coatomer) that are important for cargo selection and direction of transport []. Clathrin coats contain both clathrin (acts as a scaffold) and adaptor complexes that link clathrin to receptors in coated vesicles. Clathrin-associated protein complexes are believed to interact with the cytoplasmic tails of membrane proteins, leading to their selection and concentration. The two major types of clathrin adaptor complexes are the heterotetrameric adaptor protein (AP) complexes, and the monomeric GGA (Golgi-localising, Gamma-adaptin ear domain homology, ARF-binding proteins) adaptors [, ]. Clathrin is a trimer composed of three heavy chains and three light chains, each monomer projecting outwards like a leg; this three-legged structure is known as a triskelion [, ]. The heavy chains form the legs, their N-terminal beta-propeller regions extending outwards, while their C-terminal alpha-alpha-superhelical regions form the central hub of the triskelion. Peptide motifs can bind between the beta-propeller blades. The light chains appear to have a regulatory role, and may help orient the assembly and disassembly of clathrin coats as they interact with hsc70 uncoating ATPase []. Clathrin triskelia self-polymerise into a curved lattice by twisting individual legs together. The clathrin lattice forms around a vesicle as it buds from the TGN, plasma membrane or endosomes, acting to stabilise the vesicle and facilitate the budding process []. The multiple blades created when the triskelia polymerise are involved in multiple protein interactions, enabling the recruitment of different cargo adaptors and membrane attachment proteins []. This entry represents clathrin light chains, which are more divergent in sequence than the heavy chains []. In higher eukaryotes, two genes encode distinct but related light chains, each of which can yield two separate forms via alternative splicing. In yeast there is a single light chain whose sequence is only distantly related to that of higher eukaryotes. Clathrin light chains have a conserved acidic N-terminal domain, a central coiled-coil domain and a conserved C-terminal domain. More information about these proteins can be found at Protein of the Month: Clathrin [].; GO: 0005198 structural molecule activity, 0006886 intracellular protein transport, 0016192 vesicle-mediated transport, 0030130 clathrin coat of trans-Golgi network vesicle, 0030132 clathrin coat of coated pit; PDB: 3LVG_E 3LVH_D.
Probab=39.97 E-value=59 Score=30.26 Aligned_cols=59 Identities=19% Similarity=0.298 Sum_probs=39.2
Q ss_pred hhhHHH-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhHH
Q 046052 68 EEGFAF-REWRRQNAVHLEEKEKREKEMRNQIIDEAEEYKRAFYEKRKLNVETNKAQNRE 126 (318)
Q Consensus 68 EEpEaI-REWREeqa~rLeEKDk~EkEkKeeiikEAee~iD~FYe~rn~kkEknka~NRe 126 (318)
+--... ++|..+-+++=++-.++.+++++++++++++|..++-.+...++..|++...+
T Consensus 112 e~ireWre~~~~~i~ekD~~e~~kk~e~~~~A~k~lddfY~~~~~k~e~~k~~nr~~ee~ 171 (225)
T PF01086_consen 112 EAIREWREERDKRIEEKDAEEEEKKEEIKEKAKKELDDFYENRNEKKEKNKKQNREEEEE 171 (225)
T ss_dssp THHHHHHHHHTTTSTHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTT------
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 444344 44544444444444466788999999999999999999999999988887653
No 39
>PLN03086 PRLI-interacting factor K; Provisional
Probab=37.32 E-value=1.3e+02 Score=32.30 Aligned_cols=15 Identities=13% Similarity=0.062 Sum_probs=11.6
Q ss_pred ccCCChHHHHHhhch
Q 046052 141 EVDKHYWKAIAELIP 155 (318)
Q Consensus 141 ~a~gt~WERVaeLID 155 (318)
...|-+|.||.+-|.
T Consensus 72 ~~~g~~~~~~~~~~~ 86 (567)
T PLN03086 72 AGRGIVFSRIFEAVS 86 (567)
T ss_pred cCCCeEEEEEeeccc
Confidence 446899999888775
No 40
>KOG1772 consensus Vacuolar H+-ATPase V1 sector, subunit G [Energy production and conversion]
Probab=36.93 E-value=2e+02 Score=24.87 Aligned_cols=39 Identities=18% Similarity=0.227 Sum_probs=23.4
Q ss_pred HHHHHHHHHHHHH-HHHHHHHHHHHHHHHHHHHHHHHHHH
Q 046052 78 RQNAVHLEEKEKR-EKEMRNQIIDEAEEYKRAFYEKRKLN 116 (318)
Q Consensus 78 Eeqa~rLeEKDk~-EkEkKeeiikEAee~iD~FYe~rn~k 116 (318)
|+++.+|-+..+. ...++.++++||+..|+.|-.+|+..
T Consensus 15 EK~A~e~V~~ARk~K~~RLKQAKeEA~~Eie~yr~qrE~e 54 (108)
T KOG1772|consen 15 EKRAAEKVEEARKRKLRRLKQAKEEAEKEIEEYRSQREKE 54 (108)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 3444444333322 33456788999999988885555443
No 41
>PF03179 V-ATPase_G: Vacuolar (H+)-ATPase G subunit; InterPro: IPR005124 This family represents the eukaryotic vacuolar (H+)-ATPase (V-ATPase) G subunit. V-ATPases generate an acidic environment in several intracellular compartments. Correspondingly, they are found as membrane-attached proteins in several organelles. They are also found in the plasma membranes of some specialised cells. V-ATPases consist of peripheral (V1) and membrane integral (V0) heteromultimeric complexes. The G subunit is part of the V1 subunit, but is also thought to be strongly attached to the V0 complex. It may be involved in the coupling of ATP degradation to H+ translocation.; GO: 0016820 hydrolase activity, acting on acid anhydrides, catalyzing transmembrane movement of substances, 0015992 proton transport, 0016471 vacuolar proton-transporting V-type ATPase complex; PDB: 2KWY_A 2K88_A.
Probab=36.48 E-value=2.3e+02 Score=22.86 Aligned_cols=47 Identities=17% Similarity=0.260 Sum_probs=26.0
Q ss_pred HHHHHHHHHHHH-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhH
Q 046052 79 QNAVHLEEKEKR-EKEMRNQIIDEAEEYKRAFYEKRKLNVETNKAQNR 125 (318)
Q Consensus 79 eqa~rLeEKDk~-EkEkKeeiikEAee~iD~FYe~rn~kkEknka~NR 125 (318)
+.+..|-++-+. ...+..+++.+|+..|+.|..+++...........
T Consensus 14 ~eA~~iV~~Ar~~r~~~lk~Ak~eA~~ei~~~r~~~e~~~~~~~~~~~ 61 (105)
T PF03179_consen 14 KEAQEIVEEARKEREQRLKQAKEEAEKEIEEFRAEAEEEFKEKEAEAE 61 (105)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH-S-----
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhh
Confidence 344444443333 33456678888888888888777776665554444
No 42
>PF06936 Selenoprotein_S: Selenoprotein S (SelS); InterPro: IPR009703 This family consists of several mammalian selenoprotein S (SelS) sequences. SelS is a plasma membrane protein and is present in a variety of tissues and cell types. These proteins are involved in the degradation process of misfolded endoplasmic reticulum (ER) luminal proteins which participate in the transfer of misfolded proteins from the ER to the cytosol, where they are destroyed by the proteasome in a ubiquitin-dependent manner []. They probably serve as a linker between DER1, which mediates the retro-translocation of misfolded proteins into the cytosol, and the ATPase complex VCP, which mediates the translocation and ubiquitination.; GO: 0008430 selenium binding, 0006886 intracellular protein transport, 0030176 integral to endoplasmic reticulum membrane; PDB: 2Q2F_A.
Probab=36.47 E-value=2.3e+02 Score=26.24 Aligned_cols=57 Identities=18% Similarity=0.265 Sum_probs=29.7
Q ss_pred HHHHHHHHHHHH-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhHHHHHH
Q 046052 71 FAFREWRRQNAV-HLEEKEKREKEMRNQIIDEAEEYKRAFYEKRKLNVETNKAQNREREKL 130 (318)
Q Consensus 71 EaIREWREeqa~-rLeEKDk~EkEkKeeiikEAee~iD~FYe~rn~kkEknka~NRe~Ee~ 130 (318)
..+|.|++++.. ....+|......+++.+..|.. .+.++|+.+.+..++.-++.|++
T Consensus 56 ~~~r~~r~~~~~~~~~~~dpd~v~~rqEa~eaAR~---RmQEE~dakA~~~kEKq~q~EEE 113 (190)
T PF06936_consen 56 PSFRSLRERRQLDAAAKKDPDVVVRRQEAMEAARR---RMQEELDAKAEEYKEKQKQEEEE 113 (190)
T ss_dssp HHHHHHHHHHHHHHHHTTSHHHHHHHHHHHHHHHH---HHHHHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHhhhhhhhhhcChhHHHHHHHHHHHHHH---HHHHHHHHHHHHHHHHHHHHHHH
Confidence 356888765431 1222233333445555555444 35667777777665555555443
No 43
>PF11875 DUF3395: Domain of unknown function (DUF3395); InterPro: IPR024586 Chaperone DnaJ was originally characterised from Escherichia coli as a 41 kDa heat shock protein. DnaJ has a modular structure consisting of a J-domain, a proximal G/F-domain, and a distal zinc finger domain, followed by less conserved C-terminal sequences. Since then, a large number of DnaJ-related proteins containing a J-domain have been characterised from a variety of different organisms. In the genome of Arabidopsis thaliana a total of 89 J-domain proteins have been identified []. This entry represents a C-terminal domain found in some eukaryotic DnaJ-like proteins, including member 11 from the subfamily C1 and protein DnaJ 13 from Arabidopsis. This domain is typically between 147 to 176 amino acids in length.
Probab=36.05 E-value=1.8e+02 Score=25.62 Aligned_cols=36 Identities=22% Similarity=0.195 Sum_probs=19.2
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 046052 81 AVHLEEKEKREKEMRNQIIDEAEEYKRAFYEKRKLN 116 (318)
Q Consensus 81 a~rLeEKDk~EkEkKeeiikEAee~iD~FYe~rn~k 116 (318)
+.+++++-++-++...+.+.+|.+.+......++.+
T Consensus 8 ~~~~~~~r~~~~~~~~~~r~eA~~~~~lm~~~a~r~ 43 (151)
T PF11875_consen 8 KREIEEQREKNKEEIAEKRAEAESAIELMKETAERK 43 (151)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 334444444445555566677777765554444433
No 44
>KOG1029 consensus Endocytic adaptor protein intersectin [Signal transduction mechanisms; Intracellular trafficking, secretion, and vesicular transport]
Probab=35.97 E-value=2.5e+02 Score=32.04 Aligned_cols=6 Identities=17% Similarity=0.650 Sum_probs=3.5
Q ss_pred CChHHH
Q 046052 144 KHYWKA 149 (318)
Q Consensus 144 gt~WER 149 (318)
...|||
T Consensus 410 qlewEr 415 (1118)
T KOG1029|consen 410 QLEWER 415 (1118)
T ss_pred HHHHHH
Confidence 456764
No 45
>PRK05759 F0F1 ATP synthase subunit B; Validated
Probab=34.86 E-value=2.8e+02 Score=23.44 Aligned_cols=7 Identities=43% Similarity=0.387 Sum_probs=2.5
Q ss_pred HHHHHHH
Q 046052 97 QIIDEAE 103 (318)
Q Consensus 97 eiikEAe 103 (318)
+++++|+
T Consensus 89 ~~~~~a~ 95 (156)
T PRK05759 89 EAKAEAE 95 (156)
T ss_pred HHHHHHH
Confidence 3333333
No 46
>PRK00409 recombination and DNA strand exchange inhibitor protein; Reviewed
Probab=34.52 E-value=2.3e+02 Score=31.21 Aligned_cols=15 Identities=20% Similarity=0.231 Sum_probs=7.7
Q ss_pred chhHHHHHHHHHhhC
Q 046052 188 TDLSRMRQMYMKLKN 202 (318)
Q Consensus 188 kDlSRMRqILLkLK~ 202 (318)
..+...++.|-++++
T Consensus 607 ~~~~~~~~~l~~~~~ 621 (782)
T PRK00409 607 HELIEARKRLNKANE 621 (782)
T ss_pred HHHHHHHHHHHHhhh
Confidence 444555555555544
No 47
>PRK03963 V-type ATP synthase subunit E; Provisional
Probab=34.50 E-value=3.3e+02 Score=24.06 Aligned_cols=32 Identities=25% Similarity=0.315 Sum_probs=14.4
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 046052 74 REWRRQNAVHLEEKEKREKEMRNQIIDEAEEY 105 (318)
Q Consensus 74 REWREeqa~rLeEKDk~EkEkKeeiikEAee~ 105 (318)
.+=+.+-+..|++-.+...+.++++.++|+.-
T Consensus 13 ~~A~~ea~~il~~A~~~a~~i~~~a~~~a~~~ 44 (198)
T PRK03963 13 REAEQKIEYILEEAQKEAEKIKEEARKRAESK 44 (198)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 33344444444443344444445555555543
No 48
>PF05553 DUF761: Cotton fibre expressed protein; InterPro: IPR008480 This family consists of several plant proteins of unknown function. Three of the sequences from Gossypium hirsutum (Upland cotton) in this family are described as G. hirsutum fibre expressed proteins []. The remaining sequences, found in Arabidopsis thaliana, are uncharacterised.
Probab=33.73 E-value=1.3e+02 Score=21.40 Aligned_cols=27 Identities=22% Similarity=0.354 Sum_probs=20.5
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 046052 96 NQIIDEAEEYKRAFYEKRKLNVETNKA 122 (318)
Q Consensus 96 eeiikEAee~iD~FYe~rn~kkEknka 122 (318)
.++=..|+++|..||++-..+......
T Consensus 3 ~evd~rAe~FI~~f~~qlrlqr~~S~~ 29 (38)
T PF05553_consen 3 DEVDRRAEEFIAKFREQLRLQRQESLQ 29 (38)
T ss_pred hHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 356678999999999988777665444
No 49
>PF10147 CR6_interact: Growth arrest and DNA-damage-inducible proteins-interacting protein 1; InterPro: IPR018472 Members of this family of proteins act as negative regulators of G1 to S cell cycle phase progression by inhibiting cyclin-dependent kinases. Inhibitory effects are additive with GADD45 proteins but occur also in the absence of GADD45 proteins. Furthermore, they act as a repressor of the orphan nuclear receptor NR4A1 by inhibiting AB domain-mediated transcriptional activity []. They may be involved in the hormone-mediated regulation of NR4A1 transcriptional activity.; GO: 0007049 cell cycle, 0005634 nucleus
Probab=33.71 E-value=3.2e+02 Score=26.08 Aligned_cols=56 Identities=20% Similarity=0.359 Sum_probs=0.0
Q ss_pred hHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH----------HHHHHHHHHHHHHHhHHHHH
Q 046052 70 GFAFREWRRQNAVHLEEKEKREKEMRNQIIDEAEEYKRAF----------YEKRKLNVETNKAQNREREK 129 (318)
Q Consensus 70 pEaIREWREeqa~rLeEKDk~EkEkKeeiikEAee~iD~F----------Ye~rn~kkEknka~NRe~Ee 129 (318)
+..|.+|+.++++.-++.. .+++.++.++++++++ | |.++=.++|+.-+.-++..+
T Consensus 134 pk~i~e~~~~~~kk~~~~~-~~k~rkerl~eEvre~---fGy~vDprdprF~eml~~kEkeeKKk~K~aK 199 (217)
T PF10147_consen 134 PKWIAEWKAKIAKKEAKAQ-AAKERKERLIEEVREH---FGYKVDPRDPRFQEMLQEKEKEEKKKKKEAK 199 (217)
T ss_pred HHHHHHHHHHHHHHHHHHH-HHHHHHHHHHHHHHHH---hCCcCCCCChHHHHHHHHHHHHHHHHHHHHH
No 50
>PF07295 DUF1451: Protein of unknown function (DUF1451); InterPro: IPR009912 This family consists of several hypothetical bacterial proteins of around 160 residues in length. Members of this family contain four highly conserved cysteine resides toward the C-terminal region of the protein. The function of this family is unknown.
Probab=31.44 E-value=2.5e+02 Score=24.92 Aligned_cols=72 Identities=10% Similarity=0.027 Sum_probs=51.8
Q ss_pred hhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHhhhhhcccccCCChHH
Q 046052 69 EGFAFREWRRQNAVHLEEKEKREKEMRNQIIDEAEEYKRAFYEKRKLNVETNKAQNREREKLYMANKEKFHKEVDKHYWK 148 (318)
Q Consensus 69 EpEaIREWREeqa~rLeEKDk~EkEkKeeiikEAee~iD~FYe~rn~kkEknka~NRe~Ee~FLa~rE~f~~~a~gt~WE 148 (318)
....|.+|-+.-.+.+.+...-.++..+.+..-.+..|.+|...++. -+.....|+.-. ..+.|+
T Consensus 12 ~~~~L~~~le~a~e~~~~~~elT~eEl~lv~~ylkRDl~~~a~~~~~--------~~~~~~~~~~li-------e~slw~ 76 (146)
T PF07295_consen 12 SEEELQEALEKAKEYLVAAGELTREELALVSAYLKRDLEEFARYYEE--------LREWLSPDLQLI-------EESLWD 76 (146)
T ss_pred CHHHHHHHHHHHHHHHHHHhhcCHHHHHHHHHHHHHHHHHHHHHHHH--------hhhhccccHHHH-------HHHHHH
Confidence 35678888888888888888888888889999999999999888877 233333333322 245677
Q ss_pred HHHhhch
Q 046052 149 AIAELIP 155 (318)
Q Consensus 149 RVaeLID 155 (318)
..+.+-|
T Consensus 77 ~L~~ItD 83 (146)
T PF07295_consen 77 ELSSITD 83 (146)
T ss_pred HHHhhhc
Confidence 7766665
No 51
>PF02898 NO_synthase: Nitric oxide synthase, oxygenase domain; InterPro: IPR004030 Nitric oxide synthase (1.14.13.39 from EC) (NOS) enzymes produce nitric oxide (NO) by catalysing a five-electron oxidation of a guanidino nitrogen of L-arginine (L-Arg). Oxidation of L-Arg to L-citrulline occurs via two successive monooxygenation reactions producing N(omega)-hydroxy-L-arginine as an intermediate. 2 mol of O(2) and 1.5 mol of NADPH are consumed per mole of NO formed []. Arginine-derived NO synthesis has been identified in mammals, fish, birds, invertebrates, plants, and bacteria []. Best studied are mammals, where three distinct genes encode NOS isozymes: neuronal (nNOS or NOS-1), cytokine-inducible (iNOS or NOS-2) and endothelial (eNOS or NOS-3) []. iNOS and nNOS are soluble and found predominantly in the cytosol, while eNOS is membrane associated. The enzymes exist as homodimers, each monomer consisting of two major domains: an N-terminal oxygenase domain, which belongs to the class of haem-thiolate proteins, and a C-terminal reductase domain, which is homologous to NADPH:P450 reductase (1.6.2.4 from EC). The interdomain linker between the oxygenase and reductase domains contains a calmodulin (CaM)-binding sequence. NOSs are the only enzymes known to simultaneously require five bound cofactors animal NOS isozymes are catalytically self-sufficient. The electron flow in the NO synthase reaction is: NADPH --> FAD --> FMN --> haem --> O(2). eNOS localisation to endothelial membranes is mediated by cotranslational N-terminal myristoylation and post-translational palmitoylation []. The subcellular localisation of nNOS in skeletal muscle is mediated by anchoring of nNOS to dystrophin. nNOS contains an additional N-terminal domain, the PDZ domain []. Some bacteria, like Bacillus halodurans, Bacillus subtilis or Deinococcus radiodurans, contain homologs of NOS oxygenase domain. The pattern is directed against the N-terminal haem binding site. This entry represents the oxygenase domain of NOS.; GO: 0004517 nitric-oxide synthase activity, 0006809 nitric oxide biosynthetic process, 0055114 oxidation-reduction process; PDB: 2FBZ_X 2AMO_A 2AN0_A 1M7V_A 2FC1_A 2FC2_B 1M7Z_A 2AN2_A 2ORS_A 1QW5_B ....
Probab=30.46 E-value=75 Score=32.51 Aligned_cols=33 Identities=21% Similarity=0.424 Sum_probs=23.8
Q ss_pred HHHHHHHHHHHHHHHHHHHHH----HHHHHHHHHhHH
Q 046052 94 MRNQIIDEAEEYKRAFYEKRK----LNVETNKAQNRE 126 (318)
Q Consensus 94 kKeeiikEAee~iD~FYe~rn----~kkEknka~NRe 126 (318)
.+++++.+|+++|++||.+.+ ...+.++++.+.
T Consensus 5 ~~e~l~~~A~~Fi~~~y~e~~~~~~~~~~~Rl~ev~~ 41 (372)
T PF02898_consen 5 SKEELLEEAKEFIDQYYSELKRSGSEAHERRLEEVRR 41 (372)
T ss_dssp THHHHHHHHHHHHHHHHHHTTSTTCHHHHHHHHHHHH
T ss_pred CHHHHHHHHHHHHHHHHHhcCCccchHHHHHHHHHHh
Confidence 467999999999999998743 234555555443
No 52
>TIGR01147 V_ATP_synt_G vacuolar ATP synthase, subunit G. This model describes the vacuolar ATP synthase G subunit in eukaryotes and includes members from diverse groups e.g., fungi, plants, parasites etc. V-ATPases are multi-subunit enzymes composed of two functional domains: A transmembrane Vo domain and a peripheral catalytic domain V1. The G subunit is one of the subunits of the catalytic domain. V-ATPases are responsible for the acidification of endosomes and lysosomes, which are part of the central vacuolar system.
Probab=29.93 E-value=3.3e+02 Score=23.40 Aligned_cols=39 Identities=13% Similarity=0.210 Sum_probs=23.1
Q ss_pred HHHHHHHHHHHHHH-HHHHHHHHHHHHHHHHHHHHHHHHH
Q 046052 78 RQNAVHLEEKEKRE-KEMRNQIIDEAEEYKRAFYEKRKLN 116 (318)
Q Consensus 78 Eeqa~rLeEKDk~E-kEkKeeiikEAee~iD~FYe~rn~k 116 (318)
|+.+.+|-.+.+.. ..+..+++.+|+..|+.|-.+++..
T Consensus 15 E~eA~~IV~~AR~~r~~RLKqAK~EA~~EI~~yr~~kE~e 54 (113)
T TIGR01147 15 EKRAAEKVSEARKRKTKRLKQAKEEAQKEVEKYKQQREKE 54 (113)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 34444454444322 3455688899999988885544433
No 53
>PLN02413 choline-phosphate cytidylyltransferase
Probab=29.70 E-value=3.7e+02 Score=26.88 Aligned_cols=32 Identities=19% Similarity=0.298 Sum_probs=18.5
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhH
Q 046052 94 MRNQIIDEAEEYKRAFYEKRKLNVETNKAQNR 125 (318)
Q Consensus 94 kKeeiikEAee~iD~FYe~rn~kkEknka~NR 125 (318)
.++++.+.|.+||..|.+-+.+-|-.--..-|
T Consensus 227 ~~~~w~~~~~~~~~~f~~~f~~~~~~~~~~~~ 258 (294)
T PLN02413 227 HRNEWVENADRWVAGFLEKFEEGCHKMGTAIK 258 (294)
T ss_pred hHHHHHHhhHHHHHHHHHHHHHHHHHHHHHHH
Confidence 34566777777777776666555544333333
No 54
>PHA03065 Hypothetical protein; Provisional
Probab=29.47 E-value=2.1e+02 Score=30.06 Aligned_cols=41 Identities=22% Similarity=0.359 Sum_probs=27.5
Q ss_pred HHHHHHHHHHHH------HHHHHHHHHHHHHHHHHhHHHHHHHHhhhhh
Q 046052 95 RNQIIDEAEEYK------RAFYEKRKLNVETNKAQNREREKLYMANKEK 137 (318)
Q Consensus 95 KeeiikEAee~i------D~FYe~rn~kkEknka~NRe~Ee~FLa~rE~ 137 (318)
|.+.++.++..| |.||++-+..++.++..++=+ .||++...
T Consensus 99 K~~ei~~l~~~i~~ld~~d~~yEEikt~~~lrI~Kl~F~--~fLa~~~n 145 (438)
T PHA03065 99 KREEIEKLEDDIKNLDVDDEMYEEIKTDLELKIDKLSFQ--LFLANSNN 145 (438)
T ss_pred HHHHHHHHHHHHhcCCcchHHHHHHHHHHHHHHHHHHHH--HHHcchhh
Confidence 334444455443 689999999999888877654 46766554
No 55
>TIGR00570 cdk7 CDK-activating kinase assembly factor MAT1. All proteins in this family for which functions are known are cyclin dependent protein kinases that are components of TFIIH, a complex that is involved in nucleotide excision repair and transcription initiation. Also known as MAT1 (menage a trois 1). This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=29.08 E-value=5.5e+02 Score=25.76 Aligned_cols=23 Identities=4% Similarity=0.247 Sum_probs=18.1
Q ss_pred hHHHHHHHHHHHHHHHHHHHHHH
Q 046052 70 GFAFREWRRQNAVHLEEKEKREK 92 (318)
Q Consensus 70 pEaIREWREeqa~rLeEKDk~Ek 92 (318)
-..|++|+++++..|.+...+..
T Consensus 119 e~~l~~y~~~n~~~I~~n~~~~~ 141 (309)
T TIGR00570 119 KKKIETYQKENKDVIQKNKEKST 141 (309)
T ss_pred HHHHHHHHHHhHHHHHHHHHHHH
Confidence 46899999999999987654443
No 56
>PF00249 Myb_DNA-binding: Myb-like DNA-binding domain; InterPro: IPR014778 The retroviral oncogene v-myb, and its cellular counterpart c-myb, encode nuclear DNA-binding proteins. These belong to the SANT domain family that specifically recognise the sequence YAAC(G/T)G [, ]. In myb, one of the most conserved regions consisting of three tandem repeats has been shown to be involved in DNA-binding [].; PDB: 1X41_A 2XAF_B 2XAG_B 2XAH_B 2UXN_B 2Y48_B 2XAQ_B 2X0L_B 2IW5_B 2XAJ_B ....
Probab=28.23 E-value=67 Score=22.30 Aligned_cols=25 Identities=28% Similarity=0.605 Sum_probs=17.8
Q ss_pred HHHHHHHhhhhhcccccCCCh-HHHHHhhch
Q 046052 126 EREKLYMANKEKFHKEVDKHY-WKAIAELIP 155 (318)
Q Consensus 126 e~Ee~FLa~rE~f~~~a~gt~-WERVaeLID 155 (318)
++++.|+.--..+ |.. |..|+++|.
T Consensus 7 eE~~~l~~~v~~~-----g~~~W~~Ia~~~~ 32 (48)
T PF00249_consen 7 EEDEKLLEAVKKY-----GKDNWKKIAKRMP 32 (48)
T ss_dssp HHHHHHHHHHHHS-----TTTHHHHHHHHHS
T ss_pred HHHHHHHHHHHHh-----CCcHHHHHHHHcC
Confidence 5566676665554 555 999999995
No 57
>COG5019 CDC3 Septin family protein [Cell division and chromosome partitioning / Cytoskeleton]
Probab=27.25 E-value=3.6e+02 Score=27.75 Aligned_cols=52 Identities=27% Similarity=0.381 Sum_probs=33.6
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHH
Q 046052 72 AFREWRRQNAVHLEEKEKREKEMRNQIIDEAEEYKRAFYEKRKLNVETNKAQNREREKLY 131 (318)
Q Consensus 72 aIREWREeqa~rLeEKDk~EkEkKeeiikEAee~iD~FYe~rn~kkEknka~NRe~Ee~F 131 (318)
-.|+-+..+..++.++++.-+++.++++++-++. +.++++...+-++.|+..
T Consensus 314 ~~~~~k~~~~~ki~~~e~~l~~~E~~l~~e~~~~--------n~~Le~~~~~l~~~e~~l 365 (373)
T COG5019 314 EERELKKKFTEKIREKEKRLEELEQNLIEERKEL--------NSKLEEIQKKLEDLEKRL 365 (373)
T ss_pred HHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHH--------HHHHHHHHHHHHHHHHHH
Confidence 3455555566666666666666777776666555 777777777776666543
No 58
>PF09731 Mitofilin: Mitochondrial inner membrane protein; InterPro: IPR019133 Mitofilin controls mitochondrial cristae morphology. Mitofilin is enriched in the narrow space between the inner boundary and the outer membranes, where it forms a homotypic interaction and assembles into a large multimeric protein complex []. The first 78 amino acids contain a typical amino-terminal-cleavable mitochondrial presequence (residues 1-43) rich in positive-charged and hydroxylated residues and a membrane anchor domain (residues 47-66). In addition, it has three centrally located coiled coil domains (residues 200-240,280-310 and 400-420) []. ; GO: 0031305 integral to mitochondrial inner membrane
Probab=26.82 E-value=5.3e+02 Score=26.65 Aligned_cols=31 Identities=16% Similarity=0.236 Sum_probs=16.9
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHhHH
Q 046052 96 NQIIDEAEEYKRAFYEKRKLNVETNKAQNRE 126 (318)
Q Consensus 96 eeiikEAee~iD~FYe~rn~kkEknka~NRe 126 (318)
+++..+.+..+..+-+.|+.++...++...+
T Consensus 310 ~~~~~e~~~~~~~l~~~~~~~L~~eL~~~~~ 340 (582)
T PF09731_consen 310 EELREEFEREREELEEKYEEELRQELKRQEE 340 (582)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 3444555555555556666666655555443
No 59
>PF00836 Stathmin: Stathmin family; InterPro: IPR000956 Stathmin is a ubiquitous phosphorylated protein thought to act as an intracellular relay for diverse regulatory pathways [], functioning through a variety of secondary messengers. Its phosphorylation and gene expression are regulated throughout development [] and in response to extracellular signals regulating cell proliferation, differentiation and function []. Stathmin, and the related proteins SCG10 and XB3, contain a N-terminal domain (XB3 contains an additional N-terminal hydrophobic region), a 78 amino acid coiled-coil region, and a short C-terminal domain.; GO: 0035556 intracellular signal transduction; PDB: 3RYC_E 3RYH_E 3N2K_E 1Z2B_E 1SA1_E 3HKD_E 3DU7_E 3HKC_E 3HKB_E 3HKE_E ....
Probab=23.98 E-value=5.2e+02 Score=23.07 Aligned_cols=59 Identities=17% Similarity=0.267 Sum_probs=36.6
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHh
Q 046052 75 EWRRQNAVHLEEKEKREKEMRNQIIDEAEEYKRAFYEKRKLNVETNKAQNREREKLYMA 133 (318)
Q Consensus 75 EWREeqa~rLeEKDk~EkEkKeeiikEAee~iD~FYe~rn~kkEknka~NRe~Ee~FLa 133 (318)
+=|..+..++-.+-....+...++...|.+.-.+||.--.+++...+.++++.-+..|+
T Consensus 56 ERRKs~Ea~~l~~laekreh~~ev~~Ka~E~n~~f~k~aeEkl~~KmE~~~EnRea~l~ 114 (140)
T PF00836_consen 56 ERRKSQEAQVLKKLAEKREHEREVLQKALEENNNFSKMAEEKLNQKMEQYKENREAHLA 114 (140)
T ss_dssp HHHHHHHHHHHHTTHHHHHHHHHHHHHHHHHHHHHHHHHTHHHHTTSHHHHHHHHHHHH
T ss_pred HHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 33333333333333334444456667777777889999888888888777765555554
No 60
>PF10453 NUFIP1: Nuclear fragile X mental retardation-interacting protein 1 (NUFIP1); InterPro: IPR019496 Nuclear fragile X mental retardation-interacting protein 1 (Nufip1) has been implicated in the assembly of the large subunit of the ribosome [] and in telomere maintenance []. It is known to bind RNA [] and is phosphorylated upon DNA damage []. This entry represents a conserved domain found within Nufip1. Some proteins containing this region also contain a CCCH zinc finger.
Probab=23.47 E-value=1.4e+02 Score=22.73 Aligned_cols=16 Identities=6% Similarity=0.227 Sum_probs=12.8
Q ss_pred hhhHHHHHHHHHHHHH
Q 046052 68 EEGFAFREWRRQNAVH 83 (318)
Q Consensus 68 EEpEaIREWREeqa~r 83 (318)
.-++-|.+|+++|.+.
T Consensus 18 ~t~eeI~~W~eERrk~ 33 (56)
T PF10453_consen 18 QTPEEIAKWIEERRKN 33 (56)
T ss_pred CCHHHHHHHHHHHHHc
Confidence 3467899999999765
No 61
>PF04358 DsrC: DsrC like protein; InterPro: IPR007453 DsrC (P45573 from SWISSPROT) has been observed to co-purify with Desulphovibrio vulgaris dissimilatory sulphite reductase []. However, DsrC appears to be only loosely associated to the sulphite reductase, which suggests that it may not be an integral part of the dissimilatory sulphite reductase. Many proteins in this entry are found in organisms such as Escherichia coli and Haemophilus influenzae which do not contain dissimilatory sulphite reductases but can synthesise assimilatory sirohaem sulphite and nitrite reductases. It is speculated that DsrC may be involved in the assembly, folding or stabilisation of sirohaem proteins []. The strictly conserved cysteine in the C terminus suggests that DsrC may have a catalytic function in the metabolism of sulphur compounds []. Also included in this entry is TusE, a partner to TusBCD in a sulphur relay system for 2-thiouridine biosynthesis, a tRNA base modification process. Many proteins in this entry are annotated as the third (gamma) subunit of dissimilatory sulphite reductase ; PDB: 2V4J_F 2A5W_C 1SAU_A 1JI8_A 1YX3_A.
Probab=23.40 E-value=60 Score=27.49 Aligned_cols=39 Identities=21% Similarity=0.343 Sum_probs=23.8
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 046052 74 REWRRQNAVHLEEKEKREKEMRNQIIDEAEEYKRAFYEKRKL 115 (318)
Q Consensus 74 REWREeqa~rLeEKDk~EkEkKeeiikEAee~iD~FYe~rn~ 115 (318)
..|-++-+..|++.+-.+ .-+.-=+...++.+||.+|+.
T Consensus 21 ~dW~eevA~~lA~~egI~---Ltd~HW~vI~flR~~y~~~~~ 59 (109)
T PF04358_consen 21 EDWNEEVAEALAKEEGIE---LTDEHWEVIRFLRDYYQEYGV 59 (109)
T ss_dssp GG--HHHHHHHHHCTT-S-----HHHHHHHHHHHHHHHHHSS
T ss_pred HhCCHHHHHHHHHHcCCC---CCHHHHHHHHHHHHHHHHHCC
Confidence 479999999999877554 223333444566667999884
No 62
>cd00575 NOS_oxygenase Nitric oxide synthase (NOS) produces nitric oxide (NO) by catalyzing a five-electron heme-based oxidation of a guanidine nitrogen of L-arginine to L-citrulline via two successive monooxygenation reactions producing N(omega)-hydroxy-L-arginine (NHA) as an intermediate. In mammals, there are three distinct NOS isozymes: neuronal (nNOS or NOS-1), cytokine-inducible (iNOS or NOS-2) and endothelial (eNOS or NOS-3) . Nitric oxide synthases are homodimers. In eukaryotes, each monomer has an N-terminal oxygenase domain which binds to the substrate L-Arg, zinc, and to the cofactors heme and 5.6.7.8-(6R)-tetrahydrobiopterin (BH4) . Eukaryotic NOSs also have a C-terminal electron supplying reductase region, which is homologous to cytochrome P450 reductase and binds NADH, FAD and FMN. While prokaryotes can produce NO as a byproduct of denitrification, using a completely different set of enzymes than NOS, a few prokaryotes also have a NOS which consists solely of the NOS oxy
Probab=21.92 E-value=1.1e+02 Score=31.29 Aligned_cols=28 Identities=14% Similarity=0.325 Sum_probs=20.1
Q ss_pred HHHHHHHHHHHHHHHHH----HHHHHHHHHhH
Q 046052 98 IIDEAEEYKRAFYEKRK----LNVETNKAQNR 125 (318)
Q Consensus 98 iikEAee~iD~FYe~rn----~kkEknka~NR 125 (318)
++.+|+++|++||.+.+ ..++.++++.+
T Consensus 2 l~~eA~~Fi~~~y~e~~~~~~~~~~~Rl~ev~ 33 (356)
T cd00575 2 LLPQAKDFINQYYSSIKRSGSEAHEARLEEVE 33 (356)
T ss_pred hHHHHHHHHHHHHHhhCcCCcHHHHHHHHHHH
Confidence 57899999999999886 34444444444
No 63
>cd00167 SANT 'SWI3, ADA2, N-CoR and TFIIIB' DNA-binding domains. Tandem copies of the domain bind telomeric DNA tandem repeatsas part of the capping complex. Binding is sequence dependent for repeats which contain the G/C rich motif [C2-3 A (CA)1-6]. The domain is also found in regulatory transcriptional repressor complexes where it also binds DNA.
Probab=21.83 E-value=1.1e+02 Score=19.52 Aligned_cols=26 Identities=27% Similarity=0.661 Sum_probs=17.2
Q ss_pred HHHHHHHHhhhhhcccccCC-ChHHHHHhhch
Q 046052 125 REREKLYMANKEKFHKEVDK-HYWKAIAELIP 155 (318)
Q Consensus 125 Re~Ee~FLa~rE~f~~~a~g-t~WERVaeLID 155 (318)
.++++.|+.-...+ | ..|..|++.+.
T Consensus 4 ~eE~~~l~~~~~~~-----g~~~w~~Ia~~~~ 30 (45)
T cd00167 4 EEEDELLLEAVKKY-----GKNNWEKIAKELP 30 (45)
T ss_pred HHHHHHHHHHHHHH-----CcCCHHHHHhHcC
Confidence 34555555544443 4 78999999995
No 64
>KOG0579 consensus Ste20-like serine/threonine protein kinase [Signal transduction mechanisms]
Probab=21.74 E-value=8.4e+02 Score=27.97 Aligned_cols=47 Identities=17% Similarity=0.121 Sum_probs=32.6
Q ss_pred hHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 046052 70 GFAFREWRRQNAVHLEEKEKREKEMRNQIIDEAEEYKRAFYEKRKLN 116 (318)
Q Consensus 70 pEaIREWREeqa~rLeEKDk~EkEkKeeiikEAee~iD~FYe~rn~k 116 (318)
-|-||-.|++.--+|....+.+...++++..+.+..+++.+.++...
T Consensus 785 ~eemrflRrQeLreLR~LQkeE~R~qqqL~~k~~~q~Eq~~rrFeqE 831 (1187)
T KOG0579|consen 785 DEEMRFLRRQELRELRRLQKEEARQQQQLQAKGIKQVEQQARRFEQE 831 (1187)
T ss_pred hHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 45677777777777777777777777888777777766665554433
No 65
>cd00795 NOS_oxygenase_euk Nitric oxide synthase (NOS) eukaryotic oxygenase domain. NOS produces nitric oxide (NO) by catalyzing a five-electron heme-based oxidation of a guanidine nitrogen of L-arginine to L-citrulline via two successive monooxygenation reactions producing N(omega)-hydroxy-L-arginine (NHA) as an intermediate. In mammals, there are three distinct NOS isozymes: neuronal (nNOS or NOS-1), cytokine-inducible (iNOS or NOS-2) and endothelial (eNOS or NOS-3) . Nitric oxide synthases are homodimers. In eukaryotes, each monomer has an N-terminal oxygenase domain, which binds to the substrate L-Arg, zinc, and to the cofactors heme and 5.6.7.8-(6R)-tetrahydrobiopterin (BH4) . Eukaryotic NOS's also have a C-terminal electron supplying reductase region, which is homologous to cytochrome P450 reductase and binds NADH, FAD and FMN.
Probab=21.28 E-value=1.6e+02 Score=30.67 Aligned_cols=19 Identities=16% Similarity=0.573 Sum_probs=15.4
Q ss_pred HHHHHHHHHHHHHHHHHHH
Q 046052 96 NQIIDEAEEYKRAFYEKRK 114 (318)
Q Consensus 96 eeiikEAee~iD~FYe~rn 114 (318)
++++.+|+++|++||.+..
T Consensus 53 e~l~~eA~~Fi~~~y~e~~ 71 (412)
T cd00795 53 EELLPQAKDFINQYYSSIK 71 (412)
T ss_pred HHHHHHHHHHHHHHHHhhc
Confidence 4568999999999997543
No 66
>KOG4364 consensus Chromatin assembly factor-I [Chromatin structure and dynamics]
Probab=21.00 E-value=1e+03 Score=26.91 Aligned_cols=12 Identities=17% Similarity=0.241 Sum_probs=5.7
Q ss_pred HHHHHHHHHHHH
Q 046052 94 MRNQIIDEAEEY 105 (318)
Q Consensus 94 kKeeiikEAee~ 105 (318)
.+++|++++.+.
T Consensus 284 ek~~~keE~~ke 295 (811)
T KOG4364|consen 284 EKKAIKEENNKE 295 (811)
T ss_pred HHHHHHHHHHHH
Confidence 344455555444
No 67
>PRK07352 F0F1 ATP synthase subunit B; Validated
Probab=20.75 E-value=5.8e+02 Score=22.35 Aligned_cols=36 Identities=17% Similarity=0.001 Sum_probs=18.2
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhHHHHH
Q 046052 94 MRNQIIDEAEEYKRAFYEKRKLNVETNKAQNREREK 129 (318)
Q Consensus 94 kKeeiikEAee~iD~FYe~rn~kkEknka~NRe~Ee 129 (318)
+.+++..+|.+.+++-..+-...++.-+.+-+++-+
T Consensus 79 ~L~~a~~ea~~ii~~a~~~a~~~~~~~~~~A~~e~~ 114 (174)
T PRK07352 79 KLAQAQQEAERIRADAKARAEAIRAEIEKQAIEDMA 114 (174)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 344555555555555555555555555544444333
No 68
>COG2920 DsrC Dissimilatory sulfite reductase (desulfoviridin), gamma subunit [Inorganic ion transport and metabolism]
Probab=20.74 E-value=1.1e+02 Score=26.45 Aligned_cols=41 Identities=27% Similarity=0.365 Sum_probs=27.7
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 046052 73 FREWRRQNAVHLEEKEKREKEMRNQIIDEAEEYKRAFYEKRKLN 116 (318)
Q Consensus 73 IREWREeqa~rLeEKDk~EkEkKeeiikEAee~iD~FYe~rn~k 116 (318)
..+|-|.-++.|++++..+ .-+--=+...++.+||.+|+..
T Consensus 22 ~~dW~E~vAe~lA~~e~i~---LT~eHWevv~fvR~fy~ef~ts 62 (111)
T COG2920 22 SEDWSEKVAEALAEREGIE---LTEEHWEVVRFVREFYEEFNTS 62 (111)
T ss_pred hhhhCHHHHHHHHHHhccC---ccHHHHHHHHHHHHHHHHHCCC
Confidence 4689999999998877542 1122224456888889999854
No 69
>PF01765 RRF: Ribosome recycling factor; InterPro: IPR023584 The ribosome recycling factor or ribosome release factor (RRF) dissociates ribosomes from mRNA after termination of translation, and is essential for bacterial growth []. Thus ribosomes are 'recycled' and ready for another round of protein synthesis. This entry represents a domain found in ribosome recycling factors.; PDB: 3R8N_Y 1Y69_8 1ISE_A 1EK8_A 1DD5_A 1WIH_A 2Z4L_6 2QBE_6 2V46_Y 1EH1_A ....
Probab=20.39 E-value=4.2e+02 Score=23.27 Aligned_cols=24 Identities=13% Similarity=0.094 Sum_probs=14.2
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHH
Q 046052 99 IDEAEEYKRAFYEKRKLNVETNKA 122 (318)
Q Consensus 99 ikEAee~iD~FYe~rn~kkEknka 122 (318)
+..+++.|+..+++|..+++.-.+
T Consensus 135 ~~~~~~~iq~l~~~~~~~id~~~~ 158 (165)
T PF01765_consen 135 IKKLEKEIQKLTDKYIKKIDELLK 158 (165)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred hHHHHHHHHHHHHHHHHHHHHHHH
Confidence 445556666666666666665544
No 70
>PRK08475 F0F1 ATP synthase subunit B; Validated
Probab=20.04 E-value=6.1e+02 Score=22.36 Aligned_cols=57 Identities=9% Similarity=0.073 Sum_probs=0.0
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHhh
Q 046052 78 RQNAVHLEEKEKREKEMRNQIIDEAEEYKRAFYEKRKLNVETNKAQNREREKLYMAN 134 (318)
Q Consensus 78 Eeqa~rLeEKDk~EkEkKeeiikEAee~iD~FYe~rn~kkEknka~NRe~Ee~FLa~ 134 (318)
++...+.++...+.++...++..+|.+-+++-..+.+..++..+.+-+.+-+..++.
T Consensus 66 e~~~~ea~~~~~e~e~~L~~Ar~eA~~Ii~~A~~eAe~~~~~ii~~A~~ea~~~~~~ 122 (167)
T PRK08475 66 QEKLKESKEKKEDALKKLEEAKEKAELIVETAKKEAYILTQKIEKQTKDDIENLIKS 122 (167)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Done!