Query 029231
Match_columns 197
No_of_seqs 38 out of 40
Neff 2.0
Searched_HMMs 46136
Date Fri Mar 29 09:36:37 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/029231.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/029231hhsearch_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 99.5 4.3E-14 9.4E-19 117.6 6.8 73 69-141 101-173 (225)
2 KOG4031 Vesicle coat protein c 98.4 3.2E-06 7E-11 73.1 11.2 82 55-138 81-164 (216)
3 PF08079 Ribosomal_L30_N: Ribo 79.8 12 0.00027 26.8 6.8 48 82-129 9-56 (71)
4 COG5346 Predicted membrane pro 77.3 12 0.00026 31.2 6.9 15 67-81 37-51 (136)
5 KOG4031 Vesicle coat protein c 77.2 16 0.00035 32.4 8.0 83 45-133 79-163 (216)
6 PF10883 DUF2681: Protein of u 72.3 18 0.0004 27.7 6.4 49 82-136 25-73 (87)
7 PF13019 Telomere_Sde2: Telome 66.3 10 0.00022 31.9 4.2 36 77-112 126-161 (162)
8 KOG4364 Chromatin assembly fac 66.1 50 0.0011 34.0 9.6 66 62-129 231-310 (811)
9 PRK13454 F0F1 ATP synthase sub 65.2 38 0.00083 27.5 7.3 54 80-133 90-143 (181)
10 PRK07352 F0F1 ATP synthase sub 65.0 41 0.00089 26.7 7.3 54 81-134 79-132 (174)
11 TIGR03321 alt_F1F0_F0_B altern 64.6 37 0.0008 28.6 7.3 53 81-133 65-117 (246)
12 KOG1029 Endocytic adaptor prot 62.3 26 0.00057 36.8 7.0 15 91-105 345-359 (1118)
13 TIGR00570 cdk7 CDK-activating 61.9 36 0.00078 31.2 7.2 25 78-102 118-142 (309)
14 KOG3088 Secretory carrier memb 61.2 54 0.0012 30.6 8.2 7 16-22 6-12 (313)
15 PRK07353 F0F1 ATP synthase sub 56.7 76 0.0017 23.9 7.2 51 81-131 65-115 (140)
16 KOG4672 Uncharacterized conser 56.6 17 0.00038 35.3 4.5 48 83-132 69-121 (487)
17 CHL00019 atpF ATP synthase CF0 56.5 66 0.0014 25.9 7.2 51 81-131 84-134 (184)
18 PF01086 Clathrin_lg_ch: Clath 56.3 29 0.00062 29.4 5.3 59 76-134 111-170 (225)
19 CHL00118 atpG ATP synthase CF0 54.5 83 0.0018 24.7 7.3 48 81-128 82-129 (156)
20 TIGR01310 L7 60S ribosomal pro 54.3 51 0.0011 29.0 6.7 42 83-124 11-52 (235)
21 KOG1318 Helix loop helix trans 51.5 2E+02 0.0044 27.5 10.5 119 8-128 149-295 (411)
22 TIGR01144 ATP_synt_b ATP synth 50.1 1.1E+02 0.0023 23.3 7.1 51 81-131 55-105 (147)
23 COG0488 Uup ATPase components 49.5 40 0.00087 32.3 5.7 50 82-135 235-284 (530)
24 PRK14474 F0F1 ATP synthase sub 48.7 89 0.0019 26.9 7.2 50 82-131 66-115 (250)
25 PF08404 Baculo_p74_N: Baculov 48.6 13 0.00029 34.1 2.2 22 65-88 242-263 (301)
26 PRK06231 F0F1 ATP synthase sub 48.2 99 0.0021 25.8 7.2 51 81-131 108-158 (205)
27 PF09753 Use1: Membrane fusion 47.6 1.2E+02 0.0026 25.6 7.7 7 161-167 226-232 (251)
28 PRK14472 F0F1 ATP synthase sub 47.4 1.2E+02 0.0025 24.2 7.2 50 81-130 78-127 (175)
29 PRK13453 F0F1 ATP synthase sub 46.1 1.3E+02 0.0028 24.1 7.3 48 81-128 78-125 (173)
30 PRK14471 F0F1 ATP synthase sub 45.3 1.4E+02 0.0031 23.3 7.3 50 81-130 68-117 (164)
31 PF04521 Viral_P18: ssRNA posi 45.1 47 0.001 27.1 4.7 34 84-117 68-105 (120)
32 PF15466 DUF4635: Domain of un 43.5 80 0.0017 26.4 5.8 41 79-119 85-125 (135)
33 PRK13461 F0F1 ATP synthase sub 43.3 1.6E+02 0.0034 23.0 7.2 50 81-130 65-114 (159)
34 PRK13428 F0F1 ATP synthase sub 43.0 1.1E+02 0.0024 28.4 7.3 49 81-129 61-109 (445)
35 PF15086 UPF0542: Uncharacteri 41.5 47 0.001 25.3 3.9 31 82-112 39-69 (74)
36 PF10147 CR6_interact: Growth 40.3 63 0.0014 28.3 5.0 53 55-108 69-127 (217)
37 PRK13460 F0F1 ATP synthase sub 40.2 1.7E+02 0.0036 23.3 7.1 47 82-128 77-123 (173)
38 PF04568 IATP: Mitochondrial A 38.0 1.2E+02 0.0025 23.7 5.7 39 76-114 60-98 (100)
39 PF04652 DUF605: Vta1 like; I 37.3 1.1E+02 0.0023 26.7 6.0 42 79-120 21-62 (380)
40 PRK14473 F0F1 ATP synthase sub 36.2 2.1E+02 0.0046 22.4 7.3 48 81-128 68-115 (164)
41 cd02988 Phd_like_VIAF Phosduci 35.2 90 0.002 25.7 5.0 41 86-128 33-74 (192)
42 PF05499 DMAP1: DNA methyltran 35.1 38 0.00082 29.0 2.8 36 77-115 1-37 (176)
43 KOG1144 Translation initiation 33.2 1.4E+02 0.003 31.8 6.8 36 82-117 216-251 (1064)
44 PF10675 DUF2489: Protein of u 31.5 1E+02 0.0022 24.5 4.6 32 79-110 9-40 (131)
45 COG3461 Uncharacterized conser 31.4 1.5E+02 0.0032 23.9 5.4 50 91-142 10-64 (103)
46 KOG2357 Uncharacterized conser 31.3 97 0.0021 30.1 5.1 38 80-117 369-416 (440)
47 PRK05759 F0F1 ATP synthase sub 31.3 2.4E+02 0.0052 21.5 7.2 46 82-127 65-110 (156)
48 PF09753 Use1: Membrane fusion 30.6 3.3E+02 0.0072 23.0 10.0 27 87-113 180-206 (251)
49 PF00430 ATP-synt_B: ATP synth 30.5 2.1E+02 0.0046 20.7 6.9 48 80-127 58-105 (132)
50 PF11875 DUF3395: Domain of un 30.4 1.9E+02 0.0041 23.3 5.9 29 86-114 4-32 (151)
51 PF10186 Atg14: UV radiation r 30.1 2.4E+02 0.0052 22.9 6.6 16 105-120 73-88 (302)
52 PF07768 PVL_ORF50: PVL ORF-50 29.8 1.4E+02 0.0029 24.0 5.0 34 66-106 41-75 (118)
53 cd02987 Phd_like_Phd Phosducin 29.6 95 0.0021 25.0 4.2 43 81-129 12-54 (175)
54 PF14244 UBN2_3: gag-polypepti 29.5 44 0.00094 25.6 2.1 26 63-93 38-63 (152)
55 PF07765 KIP1: KIP1-like prote 29.5 79 0.0017 23.9 3.4 41 84-127 14-57 (74)
56 COG2914 Uncharacterized protei 29.3 29 0.00062 27.7 1.1 21 65-96 75-95 (99)
57 PRK13455 F0F1 ATP synthase sub 29.3 3E+02 0.0065 22.1 7.2 12 133-144 133-144 (184)
58 PF15046 DUF4532: Protein of u 29.2 46 0.001 30.6 2.5 41 63-104 111-159 (279)
59 COG0359 RplI Ribosomal protein 28.9 1.2E+02 0.0027 25.1 4.8 35 86-120 40-74 (148)
60 PRK14145 heat shock protein Gr 28.9 1.2E+02 0.0026 26.0 4.9 14 181-194 130-143 (196)
61 PF13256 DUF4047: Domain of un 26.2 1.4E+02 0.003 24.7 4.6 31 80-115 64-94 (125)
62 PRK00137 rplI 50S ribosomal pr 26.1 1.6E+02 0.0035 23.6 4.8 34 86-119 40-73 (147)
63 PLN02316 synthase/transferase 25.6 1.8E+02 0.004 30.6 6.3 79 47-126 394-479 (1036)
64 PF00664 ABC_membrane: ABC tra 25.5 2.7E+02 0.0059 20.4 8.2 18 102-119 174-191 (275)
65 COG3935 DnaD Putative primosom 25.3 66 0.0014 28.6 2.8 25 81-105 185-209 (246)
66 PF05680 ATP-synt_E: ATP synth 24.9 1.6E+02 0.0035 22.2 4.4 29 85-113 26-57 (86)
67 PRK14139 heat shock protein Gr 24.7 1.5E+02 0.0033 25.1 4.7 12 182-193 119-130 (185)
68 PF11166 DUF2951: Protein of u 24.7 2.8E+02 0.006 22.2 5.8 60 84-147 10-76 (98)
69 COG2825 HlpA Outer membrane pr 24.6 2.5E+02 0.0054 23.2 5.8 42 81-122 98-139 (170)
70 KOG4800 Neuronal membrane glyc 24.5 32 0.00069 31.1 0.6 12 158-169 44-55 (248)
71 PF05313 Pox_P21: Poxvirus P21 24.1 36 0.00079 29.7 0.9 41 28-69 2-47 (189)
72 PF13904 DUF4207: Domain of un 24.1 3E+02 0.0065 23.9 6.5 29 69-97 173-201 (264)
73 PF10037 MRP-S27: Mitochondria 24.0 3.5E+02 0.0077 25.7 7.4 61 77-138 340-412 (429)
74 PF01346 FKBP_N: Domain amino 23.7 1.1E+02 0.0024 22.5 3.3 27 98-124 87-113 (124)
75 PF02209 VHP: Villin headpiece 23.7 48 0.001 21.7 1.2 18 73-90 12-29 (36)
76 PHA00452 T3/T7-like RNA polyme 23.5 1.6E+02 0.0035 30.0 5.3 37 80-116 337-375 (807)
77 PF07261 DnaB_2: Replication i 23.3 20 0.00043 24.0 -0.7 21 81-101 56-76 (77)
78 PF07946 DUF1682: Protein of u 23.3 3.2E+02 0.007 24.1 6.6 23 91-113 263-285 (321)
79 PF12752 SUZ: SUZ domain; Int 23.1 26 0.00056 24.2 -0.1 27 85-111 32-58 (59)
80 PF08367 M16C_assoc: Peptidase 23.0 1.4E+02 0.003 24.9 4.1 18 99-116 26-43 (248)
81 PF10549 ORF11CD3: ORF11CD3 do 22.9 1E+02 0.0022 22.0 2.8 26 79-104 26-51 (57)
82 KOG1029 Endocytic adaptor prot 22.8 2.8E+02 0.0061 29.7 6.9 26 78-106 324-349 (1118)
83 KOG2678 Predicted membrane pro 22.3 96 0.0021 28.1 3.2 22 169-190 222-243 (244)
84 PF08592 DUF1772: Domain of un 21.7 80 0.0017 23.0 2.2 23 70-92 101-124 (139)
85 PF00855 PWWP: PWWP domain; I 21.7 1.5E+02 0.0033 20.1 3.5 24 91-114 63-86 (86)
86 PF09403 FadA: Adhesion protei 21.6 3E+02 0.0065 22.2 5.6 35 88-122 34-68 (126)
87 PRK00026 trmD tRNA (guanine-N( 21.4 1.4E+02 0.003 26.9 3.9 25 70-94 192-216 (244)
88 KOG3312 Predicted membrane pro 21.4 1.5E+02 0.0033 25.8 4.1 61 96-158 45-107 (186)
89 PF03248 Rer1: Rer1 family; I 21.2 58 0.0013 27.7 1.6 33 25-71 59-91 (176)
90 PF10661 EssA: WXG100 protein 20.2 4.8E+02 0.01 21.2 7.3 12 110-121 83-94 (145)
91 PRK08475 F0F1 ATP synthase sub 20.1 4.6E+02 0.01 21.0 6.9 30 93-122 94-123 (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=99.49 E-value=4.3e-14 Score=117.60 Aligned_cols=73 Identities=37% Similarity=0.507 Sum_probs=58.1
Q ss_pred CCCCCCCcchhhHhHHHHHHhhHhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhHhhhhhchhhhhhhhc
Q 029231 69 PPPSDMVPEEGFALREWRRENAIRLEEKEKKEKEMLNQIIEEAEEYKLEFYRKSIVTRENNKASNREREKVSG 141 (197)
Q Consensus 69 PpP~eM~~EEG~~LREWRRQNAi~LEEKEk~EKE~r~QII~EAeeyK~eFYeKR~~n~EtnKa~NREKEKly~ 141 (197)
|++..+..|+..++|+||+++..+|++|+++|++++.+|+++|.+|+..||+.|+..+|++|++||+.|+.+.
T Consensus 101 ~~~~~~~~E~~e~ireWre~~~~~i~ekD~~e~~kk~e~~~~A~k~lddfY~~~~~k~e~~k~~nr~~ee~fl 173 (225)
T PF01086_consen 101 SPAPPVEEEEPEAIREWREERDKRIEEKDAEEEEKKEEIKEKAKKELDDFYENRNEKKEKNKKQNREEEEEFL 173 (225)
T ss_dssp ---STTTTS-TTHHHHHHHHHTTTSTHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTT--------
T ss_pred CccccccchhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 3444555555999999999999999999999999999999999999999999999999999999999998654
No 2
>KOG4031 consensus Vesicle coat protein clathrin, light chain [Intracellular trafficking, secretion, and vesicular transport]
Probab=98.42 E-value=3.2e-06 Score=73.11 Aligned_cols=82 Identities=26% Similarity=0.427 Sum_probs=68.9
Q ss_pred CCCCCCCCCCCC--CCCCCCCCCcchhhHhHHHHHHhhHhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhHhhhhhc
Q 029231 55 YGEYADGGSDGP--ILPPPSDMVPEEGFALREWRRENAIRLEEKEKKEKEMLNQIIEEAEEYKLEFYRKSIVTRENNKAS 132 (197)
Q Consensus 55 f~p~~ng~sdGP--iLPpP~eM~~EEG~~LREWRRQNAi~LEEKEk~EKE~r~QII~EAeeyK~eFYeKR~~n~EtnKa~ 132 (197)
+.+..||..+|+ |.++|. ..+|-...|.||-+-+.+|+||...++.++...++.|......||+.+.-+++.+|++
T Consensus 81 ~f~~~nG~~d~~a~is~~~~--~~~epE~IRkWkeeQ~~rl~ekD~~sek~k~ElrekAkKelddwy~~~~ek~~k~~~~ 158 (216)
T KOG4031|consen 81 VFQEDNGPADGYAGISQGPR--LRDEPEKIRKWKEEQMKRLQEKDEASEKLKEELREKAKKELDDWYDQQNEKLEKTKAN 158 (216)
T ss_pred ccccCCCCcccccccCCCCC--cccChHHHHHHHHHHHHHHHHhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 446667755555 445555 4478889999999999999999999999999999999999999999999999999999
Q ss_pred hhhhhh
Q 029231 133 NREREK 138 (197)
Q Consensus 133 NREKEK 138 (197)
||.-|.
T Consensus 159 nk~eee 164 (216)
T KOG4031|consen 159 NKAEEE 164 (216)
T ss_pred hHHHHH
Confidence 975544
No 3
>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=79.80 E-value=12 Score=26.78 Aligned_cols=48 Identities=21% Similarity=0.261 Sum_probs=40.0
Q ss_pred hHHHHHHhhHhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhHhhh
Q 029231 82 LREWRRENAIRLEEKEKKEKEMLNQIIEEAEEYKLEFYRKSIVTRENN 129 (197)
Q Consensus 82 LREWRRQNAi~LEEKEk~EKE~r~QII~EAeeyK~eFYeKR~~n~Etn 129 (197)
..+|+-..+....+..+.-+..+..|+..|+.|-.+|-.+-...|+.+
T Consensus 9 ~~~~~~~~~~~~~~~k~~~~~~r~~~~kRAekY~kEYr~~erd~Irl~ 56 (71)
T PF08079_consen 9 NEKLKAKRAKKAAARKKKRKKKRKEIFKRAEKYVKEYRQKERDEIRLK 56 (71)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 457888888888888888999999999999999999977766655543
No 4
>COG5346 Predicted membrane protein [Function unknown]
Probab=77.30 E-value=12 Score=31.23 Aligned_cols=15 Identities=33% Similarity=0.585 Sum_probs=11.0
Q ss_pred CCCCCCCCCcchhhH
Q 029231 67 ILPPPSDMVPEEGFA 81 (197)
Q Consensus 67 iLPpP~eM~~EEG~~ 81 (197)
+||||..+++=+.+.
T Consensus 37 ~LPpp~~l~qYnsI~ 51 (136)
T COG5346 37 ILPPPDLLSQYNSIY 51 (136)
T ss_pred cCCCHHHHHHHHhhc
Confidence 899999887555443
No 5
>KOG4031 consensus Vesicle coat protein clathrin, light chain [Intracellular trafficking, secretion, and vesicular transport]
Probab=77.17 E-value=16 Score=32.37 Aligned_cols=83 Identities=25% Similarity=0.295 Sum_probs=59.0
Q ss_pred CCccccCCccCCCCCCCCCCCCCC-CCCCCCCcchhhHhHHHHHHhhHhhHHHH-HHHHHHHHHHHHHHHHHHHHHHHHh
Q 029231 45 DDAFASQTSVYGEYADGGSDGPIL-PPPSDMVPEEGFALREWRRENAIRLEEKE-KKEKEMLNQIIEEAEEYKLEFYRKS 122 (197)
Q Consensus 45 dDvf~s~~~~f~p~~ng~sdGPiL-PpP~eM~~EEG~~LREWRRQNAi~LEEKE-k~EKE~r~QII~EAeeyK~eFYeKR 122 (197)
-|+|.-.--++..+ -|.+.||=+ =.| |--...||=++|-...+-+++ +.++|.|.+-|.+-+++-+.+=+++
T Consensus 79 ~~~f~~~nG~~d~~-a~is~~~~~~~ep-----E~IRkWkeeQ~~rl~ekD~~sek~k~ElrekAkKelddwy~~~~ek~ 152 (216)
T KOG4031|consen 79 GDVFQEDNGPADGY-AGISQGPRLRDEP-----EKIRKWKEEQMKRLQEKDEASEKLKEELREKAKKELDDWYDQQNEKL 152 (216)
T ss_pred ccccccCCCCcccc-cccCCCCCcccCh-----HHHHHHHHHHHHHHHHhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 44665443333222 244556654 223 445578888888888886664 5677899999999999999999999
Q ss_pred hhhHhhhhhch
Q 029231 123 IVTRENNKASN 133 (197)
Q Consensus 123 ~~n~EtnKa~N 133 (197)
+.+..+||+..
T Consensus 153 ~k~~~~nk~ee 163 (216)
T KOG4031|consen 153 EKTKANNKAEE 163 (216)
T ss_pred HHHHHHhHHHH
Confidence 99999998753
No 6
>PF10883 DUF2681: Protein of unknown function (DUF2681); InterPro: IPR020274 This entry contains membrane proteins with no known function.
Probab=72.29 E-value=18 Score=27.67 Aligned_cols=49 Identities=18% Similarity=0.243 Sum_probs=35.9
Q ss_pred hHHHHHHhhHhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhHhhhhhchhhh
Q 029231 82 LREWRRENAIRLEEKEKKEKEMLNQIIEEAEEYKLEFYRKSIVTRENNKASNRER 136 (197)
Q Consensus 82 LREWRRQNAi~LEEKEk~EKE~r~QII~EAeeyK~eFYeKR~~n~EtnKa~NREK 136 (197)
+..-+++|+..++|+|.-..|.. +.+=..+-|+.|+.|-|+....+|+.
T Consensus 25 ~~ka~~~~~kL~~en~qlk~Ek~------~~~~qvkn~~vrqknee~~~~~sr~~ 73 (87)
T PF10883_consen 25 VKKAKKQNAKLQKENEQLKTEKA------VAETQVKNAKVRQKNEENTRRLSRDS 73 (87)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHH------HHHHHHHHHHHHHHhHHhhccCCHHH
Confidence 44557888888888776655532 23345677899999999999999875
No 7
>PF13019 Telomere_Sde2: Telomere stability and silencing
Probab=66.28 E-value=10 Score=31.93 Aligned_cols=36 Identities=25% Similarity=0.458 Sum_probs=28.6
Q ss_pred chhhHhHHHHHHhhHhhHHHHHHHHHHHHHHHHHHH
Q 029231 77 EEGFALREWRRENAIRLEEKEKKEKEMLNQIIEEAE 112 (197)
Q Consensus 77 EEG~~LREWRRQNAi~LEEKEk~EKE~r~QII~EAe 112 (197)
.|--.|.||......+-+++..+++++.++|.+.+|
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 466788999988888877777777788888888776
No 8
>KOG4364 consensus Chromatin assembly factor-I [Chromatin structure and dynamics]
Probab=66.14 E-value=50 Score=34.02 Aligned_cols=66 Identities=26% Similarity=0.305 Sum_probs=33.4
Q ss_pred CCCCCCCCCCCCCCcchhhHhHHHHHHhh----------H-hhHH---HHHHHHHHHHHHHHHHHHHHHHHHHHhhhhHh
Q 029231 62 GSDGPILPPPSDMVPEEGFALREWRRENA----------I-RLEE---KEKKEKEMLNQIIEEAEEYKLEFYRKSIVTRE 127 (197)
Q Consensus 62 ~sdGPiLPpP~eM~~EEG~~LREWRRQNA----------i-~LEE---KEk~EKE~r~QII~EAeeyK~eFYeKR~~n~E 127 (197)
...-+++|-|+-- .++.++.+-|..=. . .|+| |++++++...+|.++++.-|.+=-.+|...-+
T Consensus 231 k~~s~~~pk~tk~--p~~l~~KQ~rk~meEreK~R~erEr~~leeKrlk~~~~~eek~~~keE~~kekee~Klekd~KKq 308 (811)
T KOG4364|consen 231 KNSSEMAPKDTKR--PEKLLLKQLRKNMEEREKERKERERQVLEEKRLKEKEQKEEKKAIKEENNKEKEETKLEKDIKKQ 308 (811)
T ss_pred cCCCcCCCCCCCc--chhHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 3446777777654 34555544441100 0 1222 34455566677777777666554444443333
Q ss_pred hh
Q 029231 128 NN 129 (197)
Q Consensus 128 tn 129 (197)
++
T Consensus 309 qk 310 (811)
T KOG4364|consen 309 QK 310 (811)
T ss_pred HH
Confidence 33
No 9
>PRK13454 F0F1 ATP synthase subunit B'; Provisional
Probab=65.22 E-value=38 Score=27.51 Aligned_cols=54 Identities=19% Similarity=0.060 Sum_probs=39.7
Q ss_pred hHhHHHHHHhhHhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhHhhhhhch
Q 029231 80 FALREWRRENAIRLEEKEKKEKEMLNQIIEEAEEYKLEFYRKSIVTRENNKASN 133 (197)
Q Consensus 80 ~~LREWRRQNAi~LEEKEk~EKE~r~QII~EAeeyK~eFYeKR~~n~EtnKa~N 133 (197)
..|.++|.+-...+++-.++-++.+++|+++|++-.....++-+..++.-|..-
T Consensus 90 ~~L~~Ar~EA~~ii~~A~~ea~~~~~~~~~~A~~e~~~~~aea~~~I~~~k~~a 143 (181)
T PRK13454 90 KALADARAEAQRIVAETRAEIQAELDVAIAKADAEIAAKAAESEKRIAEIRAGA 143 (181)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 356778888877787777777788888999998887777777666666555443
No 10
>PRK07352 F0F1 ATP synthase subunit B; Validated
Probab=64.97 E-value=41 Score=26.72 Aligned_cols=54 Identities=9% Similarity=0.057 Sum_probs=41.7
Q ss_pred HhHHHHHHhhHhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhHhhhhhchh
Q 029231 81 ALREWRRENAIRLEEKEKKEKEMLNQIIEEAEEYKLEFYRKSIVTRENNKASNR 134 (197)
Q Consensus 81 ~LREWRRQNAi~LEEKEk~EKE~r~QII~EAeeyK~eFYeKR~~n~EtnKa~NR 134 (197)
.|.+||.+-...+++-.++-...+++|+++|++-.+...++-+.+++..+..-+
T Consensus 79 ~L~~a~~ea~~ii~~a~~~a~~~~~~~~~~A~~e~~~~~~~a~~~i~~e~~~a~ 132 (174)
T PRK07352 79 KLAQAQQEAERIRADAKARAEAIRAEIEKQAIEDMARLKQTAAADLSAEQERVI 132 (174)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 467788887777777777777888899999999888888887777776554433
No 11
>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=64.64 E-value=37 Score=28.61 Aligned_cols=53 Identities=15% Similarity=0.155 Sum_probs=40.7
Q ss_pred HhHHHHHHhhHhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhHhhhhhch
Q 029231 81 ALREWRRENAIRLEEKEKKEKEMLNQIIEEAEEYKLEFYRKSIVTRENNKASN 133 (197)
Q Consensus 81 ~LREWRRQNAi~LEEKEk~EKE~r~QII~EAeeyK~eFYeKR~~n~EtnKa~N 133 (197)
.|.+|+.+-...+++-.++-+..+.+|+++|.+--+...++-+..+++.|+.-
T Consensus 65 ~l~~a~~ea~~i~~~A~~eA~~~~~~i~~~A~~ea~~~~~~a~~~ie~E~~~a 117 (246)
T TIGR03321 65 KNEELDQQREVLLTKAKEEAQAERQRLLDEAREEADEIREKWQEALRREQAAL 117 (246)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 57788888888888877888888889999998888877777666666655443
No 12
>KOG1029 consensus Endocytic adaptor protein intersectin [Signal transduction mechanisms; Intracellular trafficking, secretion, and vesicular transport]
Probab=62.26 E-value=26 Score=36.81 Aligned_cols=15 Identities=33% Similarity=0.474 Sum_probs=6.4
Q ss_pred HhhHHHHHHHHHHHH
Q 029231 91 IRLEEKEKKEKEMLN 105 (197)
Q Consensus 91 i~LEEKEk~EKE~r~ 105 (197)
.+++.|||+|.++++
T Consensus 345 ee~eqkEreE~ekke 359 (1118)
T KOG1029|consen 345 EEVEQKEREEEEKKE 359 (1118)
T ss_pred HHHHHHHHHHHHHHH
Confidence 344444444444333
No 13
>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=61.91 E-value=36 Score=31.21 Aligned_cols=25 Identities=12% Similarity=0.275 Sum_probs=17.8
Q ss_pred hhhHhHHHHHHhhHhhHHHHHHHHH
Q 029231 78 EGFALREWRRENAIRLEEKEKKEKE 102 (197)
Q Consensus 78 EG~~LREWRRQNAi~LEEKEk~EKE 102 (197)
-...|++|+++|+...++..+++++
T Consensus 118 te~~l~~y~~~n~~~I~~n~~~~~~ 142 (309)
T TIGR00570 118 TKKKIETYQKENKDVIQKNKEKSTR 142 (309)
T ss_pred HHHHHHHHHHHhHHHHHHHHHHHHh
Confidence 4467999999999887765444433
No 14
>KOG3088 consensus Secretory carrier membrane protein [Intracellular trafficking, secretion, and vesicular transport]
Probab=61.16 E-value=54 Score=30.56 Aligned_cols=7 Identities=14% Similarity=0.534 Sum_probs=4.0
Q ss_pred cccCCch
Q 029231 16 THSFDDT 22 (197)
Q Consensus 16 t~~fd~~ 22 (197)
+.+|+|.
T Consensus 6 ~NPFadp 12 (313)
T KOG3088|consen 6 PNPFAEP 12 (313)
T ss_pred CCCCCCc
Confidence 4566665
No 15
>PRK07353 F0F1 ATP synthase subunit B'; Validated
Probab=56.69 E-value=76 Score=23.89 Aligned_cols=51 Identities=18% Similarity=0.176 Sum_probs=37.0
Q ss_pred HhHHHHHHhhHhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhHhhhhh
Q 029231 81 ALREWRRENAIRLEEKEKKEKEMLNQIIEEAEEYKLEFYRKSIVTRENNKA 131 (197)
Q Consensus 81 ~LREWRRQNAi~LEEKEk~EKE~r~QII~EAeeyK~eFYeKR~~n~EtnKa 131 (197)
.|.++|.+-...+++-.++-+..+++|+++|.+-....-+.=+.+++..+.
T Consensus 65 ~L~~a~~ea~~i~~~a~~~a~~~~~~~~~~a~~ea~~~~~~a~~~i~~e~~ 115 (140)
T PRK07353 65 QLASARKQAQAVIAEAEAEADKLAAEALAEAQAEAQASKEKARREIEQQKQ 115 (140)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 467777777777777777777788888888888877777666666555443
No 16
>KOG4672 consensus Uncharacterized conserved low complexity protein [Function unknown]
Probab=56.62 E-value=17 Score=35.30 Aligned_cols=48 Identities=21% Similarity=0.227 Sum_probs=37.2
Q ss_pred HHHHHHhhHhhHHHHHHHHHHHHHHHH-----HHHHHHHHHHHHhhhhHhhhhhc
Q 029231 83 REWRRENAIRLEEKEKKEKEMLNQIIE-----EAEEYKLEFYRKSIVTRENNKAS 132 (197)
Q Consensus 83 REWRRQNAi~LEEKEk~EKE~r~QII~-----EAeeyK~eFYeKR~~n~EtnKa~ 132 (197)
.+|.|+|.-.|+.|-|+-||-..+|+. +-+.|+.- +||++.-|.+|++
T Consensus 69 ~~~~~lnEkvLkdkrKK~rEtfer~~rlye~~~p~~~~~L--~r~eveye~kr~~ 121 (487)
T KOG4672|consen 69 IDVLRLNEKVLKDKRKKRRETFERGKRLYEATEPVMFSHL--QRREVEYEDKRPE 121 (487)
T ss_pred cchhhhHHHHHHHHHHHHHHHHHHHHHhhcccChHHHHHH--HHHhhhhhhhchh
Confidence 469999999999999999999999984 33345543 7777777776653
No 17
>CHL00019 atpF ATP synthase CF0 B subunit
Probab=56.48 E-value=66 Score=25.87 Aligned_cols=51 Identities=14% Similarity=-0.031 Sum_probs=32.2
Q ss_pred HhHHHHHHhhHhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhHhhhhh
Q 029231 81 ALREWRRENAIRLEEKEKKEKEMLNQIIEEAEEYKLEFYRKSIVTRENNKA 131 (197)
Q Consensus 81 ~LREWRRQNAi~LEEKEk~EKE~r~QII~EAeeyK~eFYeKR~~n~EtnKa 131 (197)
.|.++|.+-...+++-.++-...+.+|+++|..--....+.=+.+++..|.
T Consensus 84 ~L~~A~~ea~~ii~~A~~~ae~~~~~il~~A~~ea~~~~~~a~~~ie~Ek~ 134 (184)
T CHL00019 84 RLRQAELEADEIRVNGYSEIEREKENLINQAKEDLERLENYKNETIRFEQQ 134 (184)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 455666666666666666666667777777777766666655555554443
No 18
>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=56.28 E-value=29 Score=29.44 Aligned_cols=59 Identities=19% Similarity=0.240 Sum_probs=40.8
Q ss_pred cchhhHhH-HHHHHhhHhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhHhhhhhchh
Q 029231 76 PEEGFALR-EWRRENAIRLEEKEKKEKEMLNQIIEEAEEYKLEFYRKSIVTRENNKASNR 134 (197)
Q Consensus 76 ~EEG~~LR-EWRRQNAi~LEEKEk~EKE~r~QII~EAeeyK~eFYeKR~~n~EtnKa~NR 134 (197)
++---..| +|..+=+.+=++-+++.++++.+-.++-++|-+++=+|.+.+..+|++..-
T Consensus 111 ~e~ireWre~~~~~i~ekD~~e~~kk~e~~~~A~k~lddfY~~~~~k~e~~k~~nr~~ee 170 (225)
T PF01086_consen 111 PEAIREWREERDKRIEEKDAEEEEKKEEIKEKAKKELDDFYENRNEKKEKNKKQNREEEE 170 (225)
T ss_dssp TTHHHHHHHHHTTTSTHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTT-----
T ss_pred hHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 34444444 455555555555566777899999999999999999999999999988754
No 19
>CHL00118 atpG ATP synthase CF0 B' subunit; Validated
Probab=54.47 E-value=83 Score=24.71 Aligned_cols=48 Identities=19% Similarity=0.362 Sum_probs=29.7
Q ss_pred HhHHHHHHhhHhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhHhh
Q 029231 81 ALREWRRENAIRLEEKEKKEKEMLNQIIEEAEEYKLEFYRKSIVTREN 128 (197)
Q Consensus 81 ~LREWRRQNAi~LEEKEk~EKE~r~QII~EAeeyK~eFYeKR~~n~Et 128 (197)
.|.++|.+-...+++-.++-+..+.+++++|.+-...-.+.=+..++.
T Consensus 82 ~L~~A~~ea~~ii~~A~~~a~~~~~~~~~~A~~ea~~~~~~a~~~i~~ 129 (156)
T CHL00118 82 ELSKARKEAQLEITQSQKEAKEIVENELKQAQKYIDSLLNEATKQLEA 129 (156)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 456666666666666666666667777777777666655544444433
No 20
>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=54.31 E-value=51 Score=28.98 Aligned_cols=42 Identities=19% Similarity=0.246 Sum_probs=33.1
Q ss_pred HHHHHHhhHhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhh
Q 029231 83 REWRRENAIRLEEKEKKEKEMLNQIIEEAEEYKLEFYRKSIV 124 (197)
Q Consensus 83 REWRRQNAi~LEEKEk~EKE~r~QII~EAeeyK~eFYeKR~~ 124 (197)
.+||.+.+.+.++..++.+..+..++..||.|-.++...-.-
T Consensus 11 ~~~~~~~~~~~~~~k~~~~~~k~~~fkr~e~~~~~y~~~e~d 52 (235)
T TIGR01310 11 QELAVVRAKQAKAKKKRNKKKKKHYFKRAESFVHEYRKAERE 52 (235)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHH
Confidence 567777777777777777888999999999999998754433
No 21
>KOG1318 consensus Helix loop helix transcription factor EB [Transcription]
Probab=51.52 E-value=2e+02 Score=27.50 Aligned_cols=119 Identities=18% Similarity=0.149 Sum_probs=57.0
Q ss_pred CCcccccccccCCchhHhhhhccCCCCCCCCCC--CccCCCccccCCccCCCCCC--CCCCCCCCC-CCCCCCcchhhHh
Q 029231 8 DSVPVAEYTHSFDDTAEQLNSAVDLSDDNNNSS--FQSGDDAFASQTSVYGEYAD--GGSDGPILP-PPSDMVPEEGFAL 82 (197)
Q Consensus 8 ~s~~~~e~t~~fd~~~~~~ns~~g~~s~~~~~~--~~~~dDvf~s~~~~f~p~~n--g~sdGPiLP-pP~eM~~EEG~~L 82 (197)
|.+...+++.++--..+.+++-.| +-+.-++. ..+--|||.+...++.|... ..+.+-.+| -|.++. +-....
T Consensus 149 d~~~~~~~t~~~~~~~~~v~~~~~-~~~~~~~~~~s~~~~~~~~~~~~~~~~~~~~~~~s~~s~~~~~~rt~~-~~~~~~ 226 (411)
T KOG1318|consen 149 DDVISNIETLSASFPAQSVGSPAG-NGQTANTLTSSGASLNVYPSEGQFNVPMTGHDSASCPSQLSIGPRTHP-KTDATA 226 (411)
T ss_pred ccccccccccccccCccccCCCCc-CCcccceeeccchhcccccccCCCCCCCCccccccCccccCCCCCCCC-Ccccch
Confidence 334445555555444444555555 22211111 12224667665333333222 123333444 344443 223333
Q ss_pred HHHHHHhhHhhHHHHHHHHHHHH-----------------------HHHHHHHHHHHHHHHHhhhhHhh
Q 029231 83 REWRRENAIRLEEKEKKEKEMLN-----------------------QIIEEAEEYKLEFYRKSIVTREN 128 (197)
Q Consensus 83 REWRRQNAi~LEEKEk~EKE~r~-----------------------QII~EAeeyK~eFYeKR~~n~Et 128 (197)
-+|-||.-.-=.|=|||.++.-+ -|+..+-+|.++.-++++...|.
T Consensus 227 ~~rdr~Krd~HNeVERRRR~nIN~~IkeLg~liP~~~~~~~~~nKgtILk~s~dYIr~Lqq~~q~~~E~ 295 (411)
T KOG1318|consen 227 LERDRRKRDNHNEVERRRRENINDRIKELGQLIPKCNSEDMKSNKGTILKASCDYIRELQQTLQRAREL 295 (411)
T ss_pred hHHHHHHHhhhhHHHHHHHHHHHHHHHHHHHhCCCCCcchhhcccchhhHHHHHHHHHHHHHHHHHHHH
Confidence 45555443333444555554433 25667889999988887765554
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=50.10 E-value=1.1e+02 Score=23.30 Aligned_cols=51 Identities=24% Similarity=0.270 Sum_probs=34.0
Q ss_pred HhHHHHHHhhHhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhHhhhhh
Q 029231 81 ALREWRRENAIRLEEKEKKEKEMLNQIIEEAEEYKLEFYRKSIVTRENNKA 131 (197)
Q Consensus 81 ~LREWRRQNAi~LEEKEk~EKE~r~QII~EAeeyK~eFYeKR~~n~EtnKa 131 (197)
.|.++|.+-...+++-.++-...+++|+++|.+-....-++=+..+++.+.
T Consensus 55 ~l~~A~~ea~~i~~~a~~~a~~~~~~~~~~a~~e~~~~~~~a~~~i~~e~~ 105 (147)
T TIGR01144 55 ILKEAKDEAQEIIENANKRGSEILEEAKAEAREEREKIKAQARAEIEAEKE 105 (147)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 456666666666666667777777888888887777666655555554443
No 23
>COG0488 Uup ATPase components of ABC transporters with duplicated ATPase domains [General function prediction only]
Probab=49.50 E-value=40 Score=32.28 Aligned_cols=50 Identities=18% Similarity=0.167 Sum_probs=36.0
Q ss_pred hHHHHHHhhHhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhHhhhhhchhh
Q 029231 82 LREWRRENAIRLEEKEKKEKEMLNQIIEEAEEYKLEFYRKSIVTRENNKASNRE 135 (197)
Q Consensus 82 LREWRRQNAi~LEEKEk~EKE~r~QII~EAeeyK~eFYeKR~~n~EtnKa~NRE 135 (197)
.-.|.+|.++++ +.++++.+.+++-+++-+++...|...|... +|++.|.
T Consensus 235 y~~~~~~r~~~~-~~~~~~~~~~~~~~~~~~~~i~r~~~~~~~~---k~a~sr~ 284 (530)
T COG0488 235 YSSYLEQKAERL-RQEAAAYEKQQKELAKEQEWIRRGKAAASKA---KKAKSRI 284 (530)
T ss_pred HHHHHHHHHHHH-HHHHHHHHHHHHHHHHHHHHHHHHHhccchH---HHHHHHH
Confidence 457888888877 5555666667777888888999888887775 4455553
No 24
>PRK14474 F0F1 ATP synthase subunit B; Provisional
Probab=48.75 E-value=89 Score=26.85 Aligned_cols=50 Identities=14% Similarity=0.141 Sum_probs=33.8
Q ss_pred hHHHHHHhhHhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhHhhhhh
Q 029231 82 LREWRRENAIRLEEKEKKEKEMLNQIIEEAEEYKLEFYRKSIVTRENNKA 131 (197)
Q Consensus 82 LREWRRQNAi~LEEKEk~EKE~r~QII~EAeeyK~eFYeKR~~n~EtnKa 131 (197)
+.+++.+=...+++-.++-+..+++|+++|.+.-...-++-..+++..|.
T Consensus 66 l~~a~~ea~~ii~~A~~eA~~~~~~il~~A~~ea~~~~~~a~~~ie~Ek~ 115 (250)
T PRK14474 66 QQSLEQQRASFMAQAQEAADEQRQHLLNEAREDVATARDEWLEQLEREKQ 115 (250)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 55666666666666666667777888888887777776666655554443
No 25
>PF08404 Baculo_p74_N: Baculoviridae P74 N-terminal; InterPro: IPR013613 This domain is found at the N terminus of P74 occlusion-derived virus (ODV) envelope proteins which are required for oral infectivity. The envelope proteins are found in baculoviruses which are insect pathogens. The C terminus of P74 is anchored to the membrane whereas the N terminus is exposed to the virion surface. Furthermore P74 is unusual for a virus envelope protein as it lacks an N-terminal localisation signal sequence []. Also see IPR007663 from INTERPRO.
Probab=48.57 E-value=13 Score=34.09 Aligned_cols=22 Identities=50% Similarity=1.085 Sum_probs=17.3
Q ss_pred CCCCCCCCCCCcchhhHhHHHHHH
Q 029231 65 GPILPPPSDMVPEEGFALREWRRE 88 (197)
Q Consensus 65 GPiLPpP~eM~~EEG~~LREWRRQ 88 (197)
.|+||||.....++ .|.+||+.
T Consensus 242 S~~LP~~p~~d~~~--~L~~W~n~ 263 (301)
T PF08404_consen 242 SPILPPPPEVDSEK--TLEEWRNV 263 (301)
T ss_pred CccCCCCCCCchHH--HHHHHHHh
Confidence 45999998887555 99999863
No 26
>PRK06231 F0F1 ATP synthase subunit B; Validated
Probab=48.22 E-value=99 Score=25.84 Aligned_cols=51 Identities=6% Similarity=-0.001 Sum_probs=29.2
Q ss_pred HhHHHHHHhhHhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhHhhhhh
Q 029231 81 ALREWRRENAIRLEEKEKKEKEMLNQIIEEAEEYKLEFYRKSIVTRENNKA 131 (197)
Q Consensus 81 ~LREWRRQNAi~LEEKEk~EKE~r~QII~EAeeyK~eFYeKR~~n~EtnKa 131 (197)
.|.+||.+-...+++-.++-...+++|+++|.+--+..-++=+..++..|+
T Consensus 108 ~L~~A~~eA~~Ii~~A~~eAe~~~e~i~~~A~~eae~ii~~A~~~Ie~Ek~ 158 (205)
T PRK06231 108 RHENALAQAKEIIDQANYEALQLKSELEKEANRQANLIIFQARQEIEKERR 158 (205)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 455666665555555555555566777777766666555544444444333
No 27
>PF09753 Use1: Membrane fusion protein Use1; InterPro: IPR019150 This entry represents a family of proteins, approximately 300 residues in length, involved in vesicle transport. They have a single C-terminal transmembrane domain and a SNARE [soluble NSF (N-ethylmaleimide-sensitive fusion protein) attachment protein receptor] domain of approximately 60 residues. The SNARE domains are essential for membrane fusion and are conserved from yeasts to humans. Use1 is one of the three protein subunits that make up the SNARE complex and it is specifically required for Golgi-endoplasmic reticulum retrograde transport [].
Probab=47.63 E-value=1.2e+02 Score=25.55 Aligned_cols=7 Identities=29% Similarity=0.762 Sum_probs=3.5
Q ss_pred ccchhhh
Q 029231 161 CGCMHVM 167 (197)
Q Consensus 161 ~~~~~~~ 167 (197)
|||.-.|
T Consensus 226 ~~~~~~~ 232 (251)
T PF09753_consen 226 WGCWTWL 232 (251)
T ss_pred ccHHHHH
Confidence 4465444
No 28
>PRK14472 F0F1 ATP synthase subunit B; Provisional
Probab=47.40 E-value=1.2e+02 Score=24.23 Aligned_cols=50 Identities=16% Similarity=0.123 Sum_probs=28.5
Q ss_pred HhHHHHHHhhHhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhHhhhh
Q 029231 81 ALREWRRENAIRLEEKEKKEKEMLNQIIEEAEEYKLEFYRKSIVTRENNK 130 (197)
Q Consensus 81 ~LREWRRQNAi~LEEKEk~EKE~r~QII~EAeeyK~eFYeKR~~n~EtnK 130 (197)
.|.++|.+=...+++-.++-...+.+++++|.+--...-++-+.+++..|
T Consensus 78 ~L~~a~~ea~~ii~~A~~~a~~~~~~~~~~A~~ea~~~~~~a~~~I~~e~ 127 (175)
T PRK14472 78 LLAKADAEADKIIREGKEYAEKLRAEITEKAHTEAKKMIASAKEEIEQEK 127 (175)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 35555555555555555555566666666666666655555554444433
No 29
>PRK13453 F0F1 ATP synthase subunit B; Provisional
Probab=46.14 E-value=1.3e+02 Score=24.12 Aligned_cols=48 Identities=21% Similarity=0.194 Sum_probs=29.1
Q ss_pred HhHHHHHHhhHhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhHhh
Q 029231 81 ALREWRRENAIRLEEKEKKEKEMLNQIIEEAEEYKLEFYRKSIVTREN 128 (197)
Q Consensus 81 ~LREWRRQNAi~LEEKEk~EKE~r~QII~EAeeyK~eFYeKR~~n~Et 128 (197)
.|.++|.+=...+++-.++-+..+++|+++|.+-....-++=+..++.
T Consensus 78 ~l~~a~~ea~~ii~~a~~~a~~~~~~~~~~A~~ea~~~~~~A~~~I~~ 125 (173)
T PRK13453 78 KLKETQEEVQKILEDAKVQARQQQEQIIHEANVRANGMIETAQSEINS 125 (173)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 455666666666666666666677777777776666655544444433
No 30
>PRK14471 F0F1 ATP synthase subunit B; Provisional
Probab=45.30 E-value=1.4e+02 Score=23.31 Aligned_cols=50 Identities=24% Similarity=0.260 Sum_probs=27.6
Q ss_pred HhHHHHHHhhHhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhHhhhh
Q 029231 81 ALREWRRENAIRLEEKEKKEKEMLNQIIEEAEEYKLEFYRKSIVTRENNK 130 (197)
Q Consensus 81 ~LREWRRQNAi~LEEKEk~EKE~r~QII~EAeeyK~eFYeKR~~n~EtnK 130 (197)
.|.++|++-...+++-.+.-+..+.+++++|.+--...-++=+..++..|
T Consensus 68 ~l~~A~~ea~~ii~~A~~~a~~~~~~~~~~A~~ea~~~~~~a~~~i~~ek 117 (164)
T PRK14471 68 LLKEARAERDAILKEAREIKEKMIADAKEEAQVEGDKMIEQAKASIESEK 117 (164)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 34555555555555555555556666666666665555554444444433
No 31
>PF04521 Viral_P18: ssRNA positive strand viral 18kD cysteine rich protein; InterPro: IPR007609 This family represents the 18kDa cysteine-rich protein from ssRNA positive strand viruses.
Probab=45.08 E-value=47 Score=27.13 Aligned_cols=34 Identities=29% Similarity=0.495 Sum_probs=27.8
Q ss_pred HHH----HHhhHhhHHHHHHHHHHHHHHHHHHHHHHHH
Q 029231 84 EWR----RENAIRLEEKEKKEKEMLNQIIEEAEEYKLE 117 (197)
Q Consensus 84 EWR----RQNAi~LEEKEk~EKE~r~QII~EAeeyK~e 117 (197)
-|| +-=..+|+.=|++|..++.||+.--+.++..
T Consensus 68 a~r~~~l~~~~~~L~~Le~r~e~Lk~~~~~~~~~~~~~ 105 (120)
T PF04521_consen 68 AWRHAQLSDLNLELEKLERREEQLKTQIQVLTAAAKLA 105 (120)
T ss_pred HHhhhhhhhHHHHHHHHHHHHHHHHHHHHHHHHHhhHH
Confidence 577 6666789999999999999999876666643
No 32
>PF15466 DUF4635: Domain of unknown function (DUF4635)
Probab=43.45 E-value=80 Score=26.37 Aligned_cols=41 Identities=32% Similarity=0.409 Sum_probs=35.4
Q ss_pred hhHhHHHHHHhhHhhHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 029231 79 GFALREWRRENAIRLEEKEKKEKEMLNQIIEEAEEYKLEFY 119 (197)
Q Consensus 79 G~~LREWRRQNAi~LEEKEk~EKE~r~QII~EAeeyK~eFY 119 (197)
--++|-|-+.|.--+-||=.+|-.-+.|...+-|++..++.
T Consensus 85 ik~~r~WLkenLhvflEkLE~EvreLEQlV~DLE~WLDalL 125 (135)
T PF15466_consen 85 IKAIRNWLKENLHVFLEKLEKEVRELEQLVRDLEEWLDALL 125 (135)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence 35899999999999988888888888999999998887764
No 33
>PRK13461 F0F1 ATP synthase subunit B; Provisional
Probab=43.32 E-value=1.6e+02 Score=22.98 Aligned_cols=50 Identities=20% Similarity=0.281 Sum_probs=29.6
Q ss_pred HhHHHHHHhhHhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhHhhhh
Q 029231 81 ALREWRRENAIRLEEKEKKEKEMLNQIIEEAEEYKLEFYRKSIVTRENNK 130 (197)
Q Consensus 81 ~LREWRRQNAi~LEEKEk~EKE~r~QII~EAeeyK~eFYeKR~~n~EtnK 130 (197)
.|.++|.+=...+++-.++-+..+++|+++|.+--...-++=+..++..|
T Consensus 65 ~l~~a~~ea~~ii~~a~~~a~~~~~~i~~~A~~ea~~~~~~a~~~i~~e~ 114 (159)
T PRK13461 65 ELKNAKEEGKKIVEEYKSKAENVYEEIVKEAHEEADLIIERAKLEAQREK 114 (159)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 34555555445555555555566777777777777666665555555433
No 34
>PRK13428 F0F1 ATP synthase subunit delta; Provisional
Probab=43.01 E-value=1.1e+02 Score=28.41 Aligned_cols=49 Identities=14% Similarity=0.109 Sum_probs=35.1
Q ss_pred HhHHHHHHhhHhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhHhhh
Q 029231 81 ALREWRRENAIRLEEKEKKEKEMLNQIIEEAEEYKLEFYRKSIVTRENN 129 (197)
Q Consensus 81 ~LREWRRQNAi~LEEKEk~EKE~r~QII~EAeeyK~eFYeKR~~n~Etn 129 (197)
.|.++|.+-...+++-.++-++.+++|+++|++-.+...++=+.+++..
T Consensus 61 ~L~~Ak~ea~~Ii~~A~~~A~~~~~~~~~~A~~ea~~i~~~a~~~Ie~e 109 (445)
T PRK13428 61 AVEDAKAEAARVVEEAREDAERIAEQLRAQADAEAERIKVQGARQVQLL 109 (445)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 4777777777777777777788888888888887777665544444433
No 35
>PF15086 UPF0542: Uncharacterised protein family UPF0542
Probab=41.46 E-value=47 Score=25.30 Aligned_cols=31 Identities=35% Similarity=0.500 Sum_probs=25.6
Q ss_pred hHHHHHHhhHhhHHHHHHHHHHHHHHHHHHH
Q 029231 82 LREWRRENAIRLEEKEKKEKEMLNQIIEEAE 112 (197)
Q Consensus 82 LREWRRQNAi~LEEKEk~EKE~r~QII~EAe 112 (197)
+--|+-+.+|+-||||++-|+.|+.=|..+.
T Consensus 39 ~lSwkLaK~ie~~ere~K~k~Kr~~~i~k~r 69 (74)
T PF15086_consen 39 VLSWKLAKAIEKEEREKKKKAKRQANIAKAR 69 (74)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 4579999999999999999988887776654
No 36
>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=40.28 E-value=63 Score=28.30 Aligned_cols=53 Identities=32% Similarity=0.399 Sum_probs=25.0
Q ss_pred CCCCCCCCCCCCCCCCCCCCCc---chh---hHhHHHHHHhhHhhHHHHHHHHHHHHHHH
Q 029231 55 YGEYADGGSDGPILPPPSDMVP---EEG---FALREWRRENAIRLEEKEKKEKEMLNQII 108 (197)
Q Consensus 55 f~p~~ng~sdGPiLPpP~eM~~---EEG---~~LREWRRQNAi~LEEKEk~EKE~r~QII 108 (197)
||.. .|.+=|-..|.|++.+. |+- ..|.+=-..+...-++|+++..++..+|.
T Consensus 69 YG~a-SgV~P~~lwPt~eelee~e~Ee~~~~~sl~em~k~~~~~~~~k~~k~~~Rek~Ia 127 (217)
T PF10147_consen 69 YGLA-SGVDPGILWPTPEELEEQEYEEVEWPPSLQEMLKELREKKEEKEEKRLAREKEIA 127 (217)
T ss_pred hhhh-cCCChhhhCCCHHHHHHHHHHHHcCchHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 4444 33333555699987643 222 24444443333334444444444444443
No 37
>PRK13460 F0F1 ATP synthase subunit B; Provisional
Probab=40.24 E-value=1.7e+02 Score=23.34 Aligned_cols=47 Identities=15% Similarity=0.150 Sum_probs=26.1
Q ss_pred hHHHHHHhhHhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhHhh
Q 029231 82 LREWRRENAIRLEEKEKKEKEMLNQIIEEAEEYKLEFYRKSIVTREN 128 (197)
Q Consensus 82 LREWRRQNAi~LEEKEk~EKE~r~QII~EAeeyK~eFYeKR~~n~Et 128 (197)
|.++|.+=...+++-.++-..++.+|+++|.+.-...-+.-+.+++.
T Consensus 77 l~~a~~ea~~ii~~A~~ea~~~~~~~~~~A~~ea~~~~~~a~~~ie~ 123 (173)
T PRK13460 77 LNSAKDEANAIVAEAKSDALKLKNKLLEETNNEVKAQKDQAVKEIEL 123 (173)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 44555555555555555555566666666666666555544444443
No 38
>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=37.97 E-value=1.2e+02 Score=23.72 Aligned_cols=39 Identities=31% Similarity=0.322 Sum_probs=26.3
Q ss_pred cchhhHhHHHHHHhhHhhHHHHHHHHHHHHHHHHHHHHH
Q 029231 76 PEEGFALREWRRENAIRLEEKEKKEKEMLNQIIEEAEEY 114 (197)
Q Consensus 76 ~EEG~~LREWRRQNAi~LEEKEk~EKE~r~QII~EAeey 114 (197)
++|-.-.|++-++....|++|-++|.+...+=|++-++.
T Consensus 60 A~E~~Y~r~~EkEqL~~Lk~kl~~e~~~~~k~i~~le~~ 98 (100)
T PF04568_consen 60 AQEEQYFRKKEKEQLKKLKEKLKEEIEHHRKEIDELEKH 98 (100)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred hhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence 356666777777777777777777666666666655543
No 39
>PF04652 DUF605: Vta1 like; InterPro: IPR006745 This family contains proteins from the Eukaryota; functionally they are uncharacterised.; PDB: 2RKK_B 2RKL_B 3MHV_A.
Probab=37.27 E-value=1.1e+02 Score=26.70 Aligned_cols=42 Identities=19% Similarity=0.381 Sum_probs=32.5
Q ss_pred hhHhHHHHHHhhHhhHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 029231 79 GFALREWRRENAIRLEEKEKKEKEMLNQIIEEAEEYKLEFYR 120 (197)
Q Consensus 79 G~~LREWRRQNAi~LEEKEk~EKE~r~QII~EAeeyK~eFYe 120 (197)
+.-.|-|--|.++.+..+.++-++.+..+|+..|..|.+.-.
T Consensus 21 ~Y~c~~ya~~~~l~~~~~~~e~~~~~~~Ll~~lE~~K~~~~~ 62 (380)
T PF04652_consen 21 AYYCRLYAVEQILKLKLRSKECRQFLTSLLDKLEKMKAELGD 62 (380)
T ss_dssp HHHHHHHHHHHHTT-TT--HHHHHHHHHHHHHHHHHHHCT--
T ss_pred hHHHHHHHHHHHcCCCCCChhHHHHHHHHHHHHHHhhhccCc
Confidence 456889999999999888888899999999999988887663
No 40
>PRK14473 F0F1 ATP synthase subunit B; Provisional
Probab=36.16 E-value=2.1e+02 Score=22.37 Aligned_cols=48 Identities=17% Similarity=0.201 Sum_probs=28.2
Q ss_pred HhHHHHHHhhHhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhHhh
Q 029231 81 ALREWRRENAIRLEEKEKKEKEMLNQIIEEAEEYKLEFYRKSIVTREN 128 (197)
Q Consensus 81 ~LREWRRQNAi~LEEKEk~EKE~r~QII~EAeeyK~eFYeKR~~n~Et 128 (197)
.|.++|.+-...+++-.++-+..+++|+++|.+--...-+.=+.+++.
T Consensus 68 ~l~~A~~ea~~ii~~A~~~a~~~~~~~l~~A~~ea~~~~~~a~~~I~~ 115 (164)
T PRK14473 68 ELAKARQEAAKIVAQAQERARAQEAEIIAQARREAEKIKEEARAQAEQ 115 (164)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 455666655555555555556666777777776666555444444443
No 41
>cd02988 Phd_like_VIAF Phosducin (Phd)-like family, Viral inhibitor of apoptosis (IAP)-associated factor (VIAF) subfamily; VIAF is a Phd-like protein that functions in caspase activation during apoptosis. It was identified as an IAP binding protein through a screen of a human B-cell library using a prototype IAP. VIAF lacks a consensus IAP binding motif and while it does not function as an IAP antagonist, it still plays a regulatory role in the complete activation of caspases. VIAF itself is a substrate for IAP-mediated ubiquitination, suggesting that it may be a target of IAPs in the prevention of cell death. The similarity of VIAF to Phd points to a potential role distinct from apoptosis regulation. Phd functions as a cytosolic regulator of G protein by specifically binding to G protein betagamma (Gbg)-subunits. The C-terminal domain of Phd adopts a thioredoxin fold, but it does not contain a CXXC motif. Phd interacts with G protein beta mostly through the N-terminal helical domain.
Probab=35.19 E-value=90 Score=25.67 Aligned_cols=41 Identities=22% Similarity=0.259 Sum_probs=22.0
Q ss_pred HHHhhHhhHHHHHHHHHHHHHHHHHHH-HHHHHHHHHhhhhHhh
Q 029231 86 RRENAIRLEEKEKKEKEMLNQIIEEAE-EYKLEFYRKSIVTREN 128 (197)
Q Consensus 86 RRQNAi~LEEKEk~EKE~r~QII~EAe-eyK~eFYeKR~~n~Et 128 (197)
+++.+..|+.|.-.|-+.+.. ++-+ ++.+++=+||-..+.+
T Consensus 33 ~~~~~~~~e~~~~~el~~~~d--~~~d~~~Le~yR~kRl~el~~ 74 (192)
T cd02988 33 QEAHENALEKKLLDELDEELD--EEEDDRFLEEYRRKRLAEMKA 74 (192)
T ss_pred HHHHHhHhhhccHHHHHHhhc--ccccHHHHHHHHHHHHHHHHH
Confidence 444555666665444333221 1222 2777777888777655
No 42
>PF05499 DMAP1: DNA methyltransferase 1-associated protein 1 (DMAP1); InterPro: IPR008468 DNA methylation can contribute to transcriptional silencing through several transcriptionally repressive complexes, which include methyl-CpG binding domain proteins (MBDs) and histone deacetylases (HDACs). The chief enzyme that maintains mammalian DNA methylation, DNMT1, can also establish a repressive transcription complex. The non-catalytic N terminus of DNMT1 binds to HDAC2 and DMAP1 (for DNMT1 associated protein), and can mediate transcriptional repression. DMAP1 has intrinsic transcription repressive activity, and binds to the transcriptional co-repressor TSG101. DMAP1 is targeted to replication foci through interaction with the far N terminus of DNMT1 throughout S phase, whereas HDAC2 joins DNMT1 and DMAP1 only during late S phase, providing a platform for how histones may become deacetylated in heterochromatin following replication [].; GO: 0045892 negative regulation of transcription, DNA-dependent, 0005634 nucleus
Probab=35.06 E-value=38 Score=29.02 Aligned_cols=36 Identities=31% Similarity=0.513 Sum_probs=27.1
Q ss_pred chhhHhHHHHHHhhHhhHHHHHHHH-HHHHHHHHHHHHHH
Q 029231 77 EEGFALREWRRENAIRLEEKEKKEK-EMLNQIIEEAEEYK 115 (197)
Q Consensus 77 EEG~~LREWRRQNAi~LEEKEk~EK-E~r~QII~EAeeyK 115 (197)
||-.++-|.|+ |++.+|||+-| +=++++|..|++=.
T Consensus 1 EEe~Li~ELrK---IE~RKkEREKK~qDLqkLit~ad~~~ 37 (176)
T PF05499_consen 1 EEEMLIAELRK---IEARKKEREKKTQDLQKLITAADQQP 37 (176)
T ss_pred CHHHHHHHHHH---HHHHHHHHHHHHHHHHHHHhhccccC
Confidence 56677778776 77788888777 46788999988544
No 43
>KOG1144 consensus Translation initiation factor 5B (eIF-5B) [Translation, ribosomal structure and biogenesis]
Probab=33.24 E-value=1.4e+02 Score=31.75 Aligned_cols=36 Identities=28% Similarity=0.362 Sum_probs=19.3
Q ss_pred hHHHHHHhhHhhHHHHHHHHHHHHHHHHHHHHHHHH
Q 029231 82 LREWRRENAIRLEEKEKKEKEMLNQIIEEAEEYKLE 117 (197)
Q Consensus 82 LREWRRQNAi~LEEKEk~EKE~r~QII~EAeeyK~e 117 (197)
+|+-++.=|.+-|+.|++++|.-.++-.++++-++.
T Consensus 216 v~~~qe~La~~qe~eE~qkreeEE~~r~eeEEer~~ 251 (1064)
T KOG1144|consen 216 VRAMQEALAKRQEEEERQKREEEERLRREEEEERRR 251 (1064)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 555555555555555555555555555555554443
No 44
>PF10675 DUF2489: Protein of unknown function (DUF2489); InterPro: IPR019617 This entry represents bacterial uncharacterised proteins.
Probab=31.51 E-value=1e+02 Score=24.54 Aligned_cols=32 Identities=16% Similarity=0.358 Sum_probs=19.5
Q ss_pred hhHhHHHHHHhhHhhHHHHHHHHHHHHHHHHH
Q 029231 79 GFALREWRRENAIRLEEKEKKEKEMLNQIIEE 110 (197)
Q Consensus 79 G~~LREWRRQNAi~LEEKEk~EKE~r~QII~E 110 (197)
|.+|+.-|+|+....++-+...++++.+|++.
T Consensus 9 ~~Ll~~l~~q~~~~~~~~~~~~~~r~~~i~eS 40 (131)
T PF10675_consen 9 GYLLLKLKKQKEEQQQQQAQAIQERRARILES 40 (131)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 45667777777666555555555556666554
No 45
>COG3461 Uncharacterized conserved protein [Function unknown]
Probab=31.41 E-value=1.5e+02 Score=23.89 Aligned_cols=50 Identities=24% Similarity=0.273 Sum_probs=40.0
Q ss_pred HhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhh-----Hhhhhhchhhhhhhhch
Q 029231 91 IRLEEKEKKEKEMLNQIIEEAEEYKLEFYRKSIVT-----RENNKASNREREKVSGD 142 (197)
Q Consensus 91 i~LEEKEk~EKE~r~QII~EAeeyK~eFYeKR~~n-----~EtnKa~NREKEKly~~ 142 (197)
..|-+|-|.=..+++-+|+|+|. ..||..|-.. +-.-..+||.-||-+-+
T Consensus 10 eeLs~kirdf~Ra~~SLiEEiEA--~~wY~qR~~~tKD~~~r~ImehnrdeE~eHa~ 64 (103)
T COG3461 10 EELSEKIRDFSRARQSLIEEIEA--MMWYDQRADATKDEDLRAIMEHNRDEEKEHAA 64 (103)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHH--HHHHHHHhhccccHhHHHHHHHcccHHHHHHH
Confidence 46788899999999999999987 5799999653 44556799999987644
No 46
>KOG2357 consensus Uncharacterized conserved protein [Function unknown]
Probab=31.31 E-value=97 Score=30.10 Aligned_cols=38 Identities=21% Similarity=0.221 Sum_probs=25.3
Q ss_pred hHhHHHHHHhhHhh----------HHHHHHHHHHHHHHHHHHHHHHHH
Q 029231 80 FALREWRRENAIRL----------EEKEKKEKEMLNQIIEEAEEYKLE 117 (197)
Q Consensus 80 ~~LREWRRQNAi~L----------EEKEk~EKE~r~QII~EAeeyK~e 117 (197)
..+|+|+-+++..+ +.|+.++|+++.+|+.+.+.-|..
T Consensus 369 ~~~RQ~~~e~~~K~th~~rqEaaQ~kk~Ek~Ka~kekl~a~~d~Ek~r 416 (440)
T KOG2357|consen 369 DKNRQRVEEEFLKLTHAARQEAAQEKKAEKKKAEKEKLKASGDPEKQR 416 (440)
T ss_pred hhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhcCCHHHHH
Confidence 34688887776543 345566677788888877766654
No 47
>PRK05759 F0F1 ATP synthase subunit B; Validated
Probab=31.27 E-value=2.4e+02 Score=21.53 Aligned_cols=46 Identities=24% Similarity=0.256 Sum_probs=24.3
Q ss_pred hHHHHHHhhHhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhHh
Q 029231 82 LREWRRENAIRLEEKEKKEKEMLNQIIEEAEEYKLEFYRKSIVTRE 127 (197)
Q Consensus 82 LREWRRQNAi~LEEKEk~EKE~r~QII~EAeeyK~eFYeKR~~n~E 127 (197)
|.++|.+-...+++-..+-+..+.+++++|.+--+.-.++-...++
T Consensus 65 l~~a~~ea~~i~~~a~~ea~~~~~~~~~~a~~ea~~~~~~a~~~i~ 110 (156)
T PRK05759 65 LAEARAEAAEIIEQAKKRAAQIIEEAKAEAEAEAARIKAQAQAEIE 110 (156)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 4455555555555555555555566666665555554444433333
No 48
>PF09753 Use1: Membrane fusion protein Use1; InterPro: IPR019150 This entry represents a family of proteins, approximately 300 residues in length, involved in vesicle transport. They have a single C-terminal transmembrane domain and a SNARE [soluble NSF (N-ethylmaleimide-sensitive fusion protein) attachment protein receptor] domain of approximately 60 residues. The SNARE domains are essential for membrane fusion and are conserved from yeasts to humans. Use1 is one of the three protein subunits that make up the SNARE complex and it is specifically required for Golgi-endoplasmic reticulum retrograde transport [].
Probab=30.64 E-value=3.3e+02 Score=22.96 Aligned_cols=27 Identities=19% Similarity=0.399 Sum_probs=12.9
Q ss_pred HHhhHhhHHHHHHHHHHHHHHHHHHHH
Q 029231 87 RENAIRLEEKEKKEKEMLNQIIEEAEE 113 (197)
Q Consensus 87 RQNAi~LEEKEk~EKE~r~QII~EAee 113 (197)
++|++.....=++.+..+++..+-++.
T Consensus 180 K~~s~~~~~~l~~D~~~L~~~~~~~d~ 206 (251)
T PF09753_consen 180 KENSLAFSQILKEDNKVLDRTEEGLDR 206 (251)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 344555555555555554444444443
No 49
>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=30.52 E-value=2.1e+02 Score=20.74 Aligned_cols=48 Identities=23% Similarity=0.212 Sum_probs=30.4
Q ss_pred hHhHHHHHHhhHhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhHh
Q 029231 80 FALREWRRENAIRLEEKEKKEKEMLNQIIEEAEEYKLEFYRKSIVTRE 127 (197)
Q Consensus 80 ~~LREWRRQNAi~LEEKEk~EKE~r~QII~EAeeyK~eFYeKR~~n~E 127 (197)
..|.++|.+=...+++..++-+..+.+++.+|++....-.+.=...++
T Consensus 58 ~~l~~a~~ea~~i~~~a~~~a~~~~~~~~~ea~~~~~~~~~~a~~~i~ 105 (132)
T PF00430_consen 58 EKLAEAREEAQEIIEEAKEEAEKEKEEILAEAEKEAERIIEQAEAEIE 105 (132)
T ss_dssp HHHHHHHHHHCHHHHHHCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 346666666666666666666777777777777766665554444443
No 50
>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=30.40 E-value=1.9e+02 Score=23.32 Aligned_cols=29 Identities=34% Similarity=0.432 Sum_probs=12.9
Q ss_pred HHHhhHhhHHHHHHHHHHHHHHHHHHHHH
Q 029231 86 RRENAIRLEEKEKKEKEMLNQIIEEAEEY 114 (197)
Q Consensus 86 RRQNAi~LEEKEk~EKE~r~QII~EAeey 114 (197)
||++...++++.++-++...+-..+|++.
T Consensus 4 ~~~~~~~~~~~r~~~~~~~~~~r~eA~~~ 32 (151)
T PF11875_consen 4 RRRKKREIEEQREKNKEEIAEKRAEAESA 32 (151)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 33444444444444444444444455444
No 51
>PF10186 Atg14: UV radiation resistance protein and autophagy-related subunit 14; InterPro: IPR018791 Class III phosphatidylinositol 3-kinase (PI3-kinase) regulates multiple membrane trafficking. In yeast, two distinct PI3-kinase complexes are known: complex I (Vps34, Vps15, Vps30/Atg6, and Atg14) is involved in autophagy, and complex II (Vps34, Vps15, Vps30/Atg6, and Vps38) functions in the vacuolar protein sorting pathway. In mammals, the counterparts of Vps34, Vps15, and Vps30/Atg6 are Vps34, p150, and Beclin 1, respectively. Mammalian UV irradiation resistance-associated gene (UVRAG) has been identified as identical to yeast Vps38 []. The Atg14 (autophagy-related protein 14) proteins are hydrophilic proteins and have a coiled-coil motif at the N terminus region. Yeast cells with mutant Atg14 are defective not only in autophagy but also in sorting of carboxypeptidase Y (CPY), a vacuolar-soluble hydrolase, to the vacuole []. This entry represents Atg14 and UVRAG, which bind Beclin 1 to forms two distinct PI3-kinase complexes. This entry also includes Bakor (beclin-1-associated autophagy-related key regulator), also known as autophagy-related protein 14-like protein, which share sequence similarity to the yeast Atg14 protein []. Barkor positively regulates autophagy through its interaction with Beclin-1, with decreased levels of autophagosome formation observed when Barkor expression is eliminated []. Autophagy mediates the cellular response to nutrient deprivation, protein aggregation, and pathogen invasion in humans, and malfunction of autophagy has been implicated in multiple human diseases including cancer. ; GO: 0010508 positive regulation of autophagy
Probab=30.08 E-value=2.4e+02 Score=22.93 Aligned_cols=16 Identities=13% Similarity=0.227 Sum_probs=6.0
Q ss_pred HHHHHHHHHHHHHHHH
Q 029231 105 NQIIEEAEEYKLEFYR 120 (197)
Q Consensus 105 ~QII~EAeeyK~eFYe 120 (197)
.+|.++.++-+++..+
T Consensus 73 ~~l~~~i~~~~~~i~~ 88 (302)
T PF10186_consen 73 ERLRERIERLRKRIEQ 88 (302)
T ss_pred HHHHHHHHHHHHHHHH
Confidence 3333333333333333
No 52
>PF07768 PVL_ORF50: PVL ORF-50-like family; InterPro: IPR011688 This entry is represented by the Bacteriophage 69, Orf58. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. This is a family of sequences found in both bacteria and bacteriophages. This region is approximately 130 residues long and in some cases is found as part of the PVL (Panton-Valentine leukocidin) group of genes, which encode a member of the leukocidin group of bacterial toxins that kill leukocytes by creation of pores in the cell membrane []. PVL appears to be a virulence factor associated with a number of human diseases [].
Probab=29.81 E-value=1.4e+02 Score=24.04 Aligned_cols=34 Identities=26% Similarity=0.574 Sum_probs=17.7
Q ss_pred CCCCCCCCCCcchhhHhHHHHHHhhH-hhHHHHHHHHHHHHH
Q 029231 66 PILPPPSDMVPEEGFALREWRRENAI-RLEEKEKKEKEMLNQ 106 (197)
Q Consensus 66 PiLPpP~eM~~EEG~~LREWRRQNAi-~LEEKEk~EKE~r~Q 106 (197)
-+|++|-+|. +-||+-.-.. .|+ .|.+|++++.+
T Consensus 41 Eai~ap~g~~------~kE~~e~k~~~~l~-~e~~ERe~~r~ 75 (118)
T PF07768_consen 41 EAIEAPYGMR------RKEYKERKKMERLE-QERRERELERK 75 (118)
T ss_pred HHhccccccc------HHHHHHHHHHHHHH-HHHHHHHHHHH
Confidence 4677888776 4556543333 243 34555544433
No 53
>cd02987 Phd_like_Phd Phosducin (Phd)-like family, Phd subfamily; Phd is a cytosolic regulator of G protein functions. It specifically binds G protein betagamma (Gbg)-subunits with high affinity, resulting in the solubilization of Gbg from the plasma membrane. This impedes the formation of a functional G protein trimer (G protein alphabetagamma), thereby inhibiting G protein-mediated signal transduction. Phd also inhibits the GTPase activity of G protein alpha. Phd can be phosphorylated by protein kinase A and G protein-coupled receptor kinase 2, leading to its inactivation. Phd was originally isolated from the retina, where it is highly expressed and has been implicated to play an important role in light adaptation. It is also found in the pineal gland, liver, spleen, striated muscle and the brain. The C-terminal domain of Phd adopts a thioredoxin fold, but it does not contain a CXXC motif. Phd interacts with G protein beta mostly through the N-terminal helical domain.
Probab=29.60 E-value=95 Score=24.98 Aligned_cols=43 Identities=14% Similarity=0.353 Sum_probs=33.2
Q ss_pred HhHHHHHHhhHhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhHhhh
Q 029231 81 ALREWRRENAIRLEEKEKKEKEMLNQIIEEAEEYKLEFYRKSIVTRENN 129 (197)
Q Consensus 81 ~LREWRRQNAi~LEEKEk~EKE~r~QII~EAeeyK~eFYeKR~~n~Etn 129 (197)
.+..|||-+-+ ..|-+.++.+-++.|++.+.+=+||-..+.+.
T Consensus 12 v~~d~~~~~~~------~~~~~~~d~~~~~~e~~l~~~R~~R~~el~~~ 54 (175)
T cd02987 12 VINDWRKFKQL------KESEQEDDDDDEDKEEFLQQYREQRMQEMHAK 54 (175)
T ss_pred hHHHHHHHHhh------hchhhhhhhhhhhHHHHHHHHHHHHHHHHHHh
Confidence 46789987665 56666777777777889999888988888664
No 54
>PF14244 UBN2_3: gag-polypeptide of LTR copia-type
Probab=29.47 E-value=44 Score=25.64 Aligned_cols=26 Identities=35% Similarity=0.649 Sum_probs=17.1
Q ss_pred CCCCCCCCCCCCCcchhhHhHHHHHHhhHhh
Q 029231 63 SDGPILPPPSDMVPEEGFALREWRRENAIRL 93 (197)
Q Consensus 63 sdGPiLPpP~eM~~EEG~~LREWRRQNAi~L 93 (197)
=+|.+-|||.+- ....+|+++|++.+
T Consensus 38 i~g~~~~P~~~~-----~~~~~W~~~d~~v~ 63 (152)
T PF14244_consen 38 IDGTIPKPPETD-----PAYEKWERKDQLVL 63 (152)
T ss_pred ccCccccccccc-----hhhhhHHHhhhHHH
Confidence 346554443322 47899999999875
No 55
>PF07765 KIP1: KIP1-like protein; InterPro: IPR011684 This is a group of sequences found exclusively in plants. They are similar to kinase interacting protein 1 (KIP1), which has been found to interact with the kinase domain of PRK1, a receptor-like kinase []. This particular region contains two coiled-coils, which are described as motifs involved in protein-protein interactions []. It has also been suggested that the coiled-coils of the protein allow it to dimerise in vivo [].
Probab=29.45 E-value=79 Score=23.88 Aligned_cols=41 Identities=29% Similarity=0.529 Sum_probs=27.3
Q ss_pred HHHHHhhHhhHHHHHHHHHHHHHHHHHHHHHH---HHHHHHhhhhHh
Q 029231 84 EWRRENAIRLEEKEKKEKEMLNQIIEEAEEYK---LEFYRKSIVTRE 127 (197)
Q Consensus 84 EWRRQNAi~LEEKEk~EKE~r~QII~EAeeyK---~eFYeKR~~n~E 127 (197)
+|-..| |.+=|.+-|+|+.-|-++++.|- +-||+||..-+.
T Consensus 14 kWL~~~---l~dmd~kvk~mlklieedgdSfakrAEmyy~kRp~Li~ 57 (74)
T PF07765_consen 14 KWLQEN---LSDMDEKVKAMLKLIEEDGDSFAKRAEMYYKKRPELIS 57 (74)
T ss_pred HHHHHH---HHHHHHHHHHHHHHhccCcchHHHhhHHHhcccHHHHH
Confidence 577777 55556667788777766776653 357788765554
No 56
>COG2914 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=29.33 E-value=29 Score=27.67 Aligned_cols=21 Identities=38% Similarity=0.588 Sum_probs=15.8
Q ss_pred CCCCCCCCCCCcchhhHhHHHHHHhhHhhHHH
Q 029231 65 GPILPPPSDMVPEEGFALREWRRENAIRLEEK 96 (197)
Q Consensus 65 GPiLPpP~eM~~EEG~~LREWRRQNAi~LEEK 96 (197)
+|.|-.| .|||||+|.+-++.
T Consensus 75 RPLlaDP-----------KE~RR~Ra~~~~~~ 95 (99)
T COG2914 75 RPLLADP-----------KEARRKRAERAAAA 95 (99)
T ss_pred cccccCh-----------HHHHHHHHHHHHHh
Confidence 6777666 58999999875543
No 57
>PRK13455 F0F1 ATP synthase subunit B; Provisional
Probab=29.33 E-value=3e+02 Score=22.05 Aligned_cols=12 Identities=0% Similarity=0.003 Sum_probs=5.3
Q ss_pred hhhhhhhhchhh
Q 029231 133 NREREKVSGDFK 144 (197)
Q Consensus 133 NREKEKly~~~~ 144 (197)
.++|++.....+
T Consensus 133 ~~ek~~a~~~l~ 144 (184)
T PRK13455 133 ASAEAAAVKAVR 144 (184)
T ss_pred HHHHHHHHHHHH
Confidence 344444444443
No 58
>PF15046 DUF4532: Protein of unknown function (DUF4532)
Probab=29.17 E-value=46 Score=30.56 Aligned_cols=41 Identities=37% Similarity=0.364 Sum_probs=23.1
Q ss_pred CCCCCCCCCCCCCcc-------hhhH-hHHHHHHhhHhhHHHHHHHHHHH
Q 029231 63 SDGPILPPPSDMVPE-------EGFA-LREWRRENAIRLEEKEKKEKEML 104 (197)
Q Consensus 63 sdGPiLPpP~eM~~E-------EG~~-LREWRRQNAi~LEEKEk~EKE~r 104 (197)
..+|| |||+.|+.- ++-. +-.=||..+|.--.||-+|-+++
T Consensus 111 a~~PI-PPPSwMG~NTfl~FI~~~pif~D~~rK~qvI~rt~KELkE~~kL 159 (279)
T PF15046_consen 111 AEPPI-PPPSWMGDNTFLKFISCTPIFVDPNRKNQVILRTVKELKEFEKL 159 (279)
T ss_pred cCCCC-CChhhcCcchhhhhhhcccceechhhhhHHHHHHHHHHhhhHhh
Confidence 44675 999999842 2222 22335555555556666554443
No 59
>COG0359 RplI Ribosomal protein L9 [Translation, ribosomal structure and biogenesis]
Probab=28.91 E-value=1.2e+02 Score=25.09 Aligned_cols=35 Identities=23% Similarity=0.207 Sum_probs=27.6
Q ss_pred HHHhhHhhHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 029231 86 RRENAIRLEEKEKKEKEMLNQIIEEAEEYKLEFYR 120 (197)
Q Consensus 86 RRQNAi~LEEKEk~EKE~r~QII~EAeeyK~eFYe 120 (197)
-+.|...++.+.+++.....+.+++|+++++..-.
T Consensus 40 t~~n~~~~e~~r~~~e~~~~~~~~~a~~lk~~Le~ 74 (148)
T COG0359 40 TKGNLKLLEARRAKLEKKAAEELAEAEALKEKLEG 74 (148)
T ss_pred CHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhC
Confidence 35677788887777777788888999999888765
No 60
>PRK14145 heat shock protein GrpE; Provisional
Probab=28.90 E-value=1.2e+02 Score=25.99 Aligned_cols=14 Identities=14% Similarity=0.392 Sum_probs=8.4
Q ss_pred HHHHHHhhccceee
Q 029231 181 LMLVQIFSNFSIVQ 194 (197)
Q Consensus 181 ~~~~~~~~~~~~~~ 194 (197)
=.|..+|..+.|..
T Consensus 130 k~l~~vL~k~GVe~ 143 (196)
T PRK14145 130 RQFKKILDKFGVKE 143 (196)
T ss_pred HHHHHHHHHCCCEE
Confidence 34566777776654
No 61
>PF13256 DUF4047: Domain of unknown function (DUF4047)
Probab=26.22 E-value=1.4e+02 Score=24.72 Aligned_cols=31 Identities=39% Similarity=0.611 Sum_probs=23.0
Q ss_pred hHhHHHHHHhhHhhHHHHHHHHHHHHHHHHHHHHHH
Q 029231 80 FALREWRRENAIRLEEKEKKEKEMLNQIIEEAEEYK 115 (197)
Q Consensus 80 ~~LREWRRQNAi~LEEKEk~EKE~r~QII~EAeeyK 115 (197)
.++.+|+++ .||=.-|+|.|++|-.+-+.|-
T Consensus 64 q~~~~w~~~-----rEki~~e~eaLQ~IY~eie~~y 94 (125)
T PF13256_consen 64 QAIVEWKQG-----REKIVAEREALQNIYTEIEDYY 94 (125)
T ss_pred HHHHHHHHH-----HHHHHHHHHHHHHHHHHHHHHH
Confidence 356777765 5777788889999988877653
No 62
>PRK00137 rplI 50S ribosomal protein L9; Reviewed
Probab=26.15 E-value=1.6e+02 Score=23.62 Aligned_cols=34 Identities=18% Similarity=0.192 Sum_probs=24.4
Q ss_pred HHHhhHhhHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 029231 86 RRENAIRLEEKEKKEKEMLNQIIEEAEEYKLEFY 119 (197)
Q Consensus 86 RRQNAi~LEEKEk~EKE~r~QII~EAeeyK~eFY 119 (197)
-..|..+++.+.+...+...+.+++|++.+..+=
T Consensus 40 T~~~~~~~~~~~~~~~~~~~~~~~~a~~l~~~l~ 73 (147)
T PRK00137 40 TKGNLKQLEARRAELEAKAAEELAEAEALAEKLE 73 (147)
T ss_pred CHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhh
Confidence 3566677777777777777788888888776654
No 63
>PLN02316 synthase/transferase
Probab=25.59 E-value=1.8e+02 Score=30.64 Aligned_cols=79 Identities=23% Similarity=0.286 Sum_probs=0.0
Q ss_pred ccccCCccCC-CCCCCCCCCCCCCCCCCC------CcchhhHhHHHHHHhhHhhHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 029231 47 AFASQTSVYG-EYADGGSDGPILPPPSDM------VPEEGFALREWRRENAIRLEEKEKKEKEMLNQIIEEAEEYKLEFY 119 (197)
Q Consensus 47 vf~s~~~~f~-p~~ng~sdGPiLPpP~eM------~~EEG~~LREWRRQNAi~LEEKEk~EKE~r~QII~EAeeyK~eFY 119 (197)
||+..+|--. -..|+++.-=-+|.|..+ ..||-..+++-+.+.+++ ||-+|+..|++.+...|+.+=+.+=+
T Consensus 394 VFsdg~~~~~~~yDNn~~~Dyh~~v~~~~~~~~~~~~~~~~~~~~l~~~~~~~-~~~~r~k~~~~a~~~ae~k~~~~~~~ 472 (1036)
T PLN02316 394 VFADGPPGNARNYDNNGRQDFHAIVPNNIPEELYWVEEEHQIYRKLQEERRLR-EEAIRAKAEKTARMKAEMKEKTLKMF 472 (1036)
T ss_pred EEecCCcccccccccCCCcceeeecCCCCchhhhhHHHHHHHHHHHHHHHHhh-HHHHHHHHHHHHHHHHHHHHHHHHhh
Q ss_pred HHhhhhH
Q 029231 120 RKSIVTR 126 (197)
Q Consensus 120 eKR~~n~ 126 (197)
-+.+.++
T Consensus 473 l~~~~~~ 479 (1036)
T PLN02316 473 LLSQKHI 479 (1036)
T ss_pred hhccceE
No 64
>PF00664 ABC_membrane: ABC transporter transmembrane region; InterPro: IPR001140 ABC transporters belong to the ATP-Binding Cassette (ABC) superfamily, which uses the hydrolysis of ATP to energise diverse biological systems. ABC transporters minimally consist of two conserved regions: a highly conserved ATP binding cassette (ABC) and a less conserved transmembrane domain (TMD). These can be found on the same protein or on two different ones. Most ABC transporters function as a dimer and therefore are constituted of four domains, two ABC modules and two TMDs. ABC transporters are involved in the export or import of a wide variety of substrates ranging from small ions to macromolecules. The major function of ABC import systems is to provide essential nutrients to bacteria. They are found only in prokaryotes and their four constitutive domains are usually encoded by independent polypeptides (two ABC proteins and two TMD proteins). Prokaryotic importers require additional extracytoplasmic binding proteins (one or more per systems) for function. In contrast, export systems are involved in the extrusion of noxious substances, the export of extracellular toxins and the targeting of membrane components. They are found in all living organisms and in general the TMD is fused to the ABC module in a variety of combinations. Some eukaryotic exporters encode the four domains on the same polypeptide chain []. The ABC module (approximately two hundred amino acid residues) is known to bind and hydrolyse ATP, thereby coupling transport to ATP hydrolysis in a large number of biological processes. The cassette is duplicated in several subfamilies. Its primary sequence is highly conserved, displaying a typical phosphate-binding loop: Walker A, and a magnesium binding site: Walker B. Besides these two regions, three other conserved motifs are present in the ABC cassette: the switch region which contains a histidine loop, postulated to polarise the attaching water molecule for hydrolysis, the signature conserved motif (LSGGQ) specific to the ABC transporter, and the Q-motif (between Walker A and the signature), which interacts with the gamma phosphate through a water bond. The Walker A, Walker B, Q-loop and switch region form the nucleotide binding site [, , ]. The 3D structure of a monomeric ABC module adopts a stubby L-shape with two distinct arms. ArmI (mainly beta-strand) contains Walker A and Walker B. The important residues for ATP hydrolysis and/or binding are located in the P-loop. The ATP-binding pocket is located at the extremity of armI. The perpendicular armII contains mostly the alpha helical subdomain with the signature motif. It only seems to be required for structural integrity of the ABC module. ArmII is in direct contact with the TMD. The hinge between armI and armII contains both the histidine loop and the Q-loop, making contact with the gamma phosphate of the ATP molecule. ATP hydrolysis leads to a conformational change that could facilitate ADP release. In the dimer the two ABC cassettes contact each other through hydrophobic interactions at the antiparallel beta-sheet of armI by a two-fold axis [, , , , , ]. The ATP-Binding Cassette (ABC) superfamily forms one of the largest of all protein families with a diversity of physiological functions []. Several studies have shown that there is a correlation between the functional characterisation and the phylogenetic classification of the ABC cassette [, ]. More than 50 subfamilies have been described based on a phylogenetic and functional classification [, , ]; (for further information see http://www.tcdb.org/tcdb/index.php?tc=3.A.1). A variety of ATP-binding transport proteins have a six transmembrane helical region. They are all integral membrane proteins involved in a variety of transport systems. Members of this family include; the cystic fibrosis transmembrane conductance regulator (CFTR), bacterial leukotoxin secretion ATP-binding protein, multidrug resistance proteins, the yeast leptomycin B resistance protein, the mammalian sulphonylurea receptor and antigen peptide transporter 2. Many of these proteins have two such regions.; GO: 0005524 ATP binding, 0042626 ATPase activity, coupled to transmembrane movement of substances, 0006810 transport, 0055085 transmembrane transport, 0016021 integral to membrane; PDB: 3G61_B 3G5U_B 3G60_A 3B60_D 3QF4_B 2HYD_A 2ONJ_A 4A82_B 4AA3_A 2YL4_A.
Probab=25.51 E-value=2.7e+02 Score=20.36 Aligned_cols=18 Identities=11% Similarity=-0.114 Sum_probs=7.1
Q ss_pred HHHHHHHHHHHHHHHHHH
Q 029231 102 EMLNQIIEEAEEYKLEFY 119 (197)
Q Consensus 102 E~r~QII~EAeeyK~eFY 119 (197)
+..++......|.....-
T Consensus 174 ~~~~~~~~~~~e~l~g~~ 191 (275)
T PF00664_consen 174 EANSELNSFLSESLSGIR 191 (275)
T ss_dssp HHHHHHHHHHHHHHHTHH
T ss_pred ccccccccccccchhhhH
Confidence 333333444444443333
No 65
>COG3935 DnaD Putative primosome component and related proteins [DNA replication, recombination, and repair]
Probab=25.31 E-value=66 Score=28.58 Aligned_cols=25 Identities=24% Similarity=0.555 Sum_probs=14.9
Q ss_pred HhHHHHHHhhHhhHHHHHHHHHHHH
Q 029231 81 ALREWRRENAIRLEEKEKKEKEMLN 105 (197)
Q Consensus 81 ~LREWRRQNAi~LEEKEk~EKE~r~ 105 (197)
.||.||..|.-.++.-++++++.+.
T Consensus 185 IL~nW~k~gvkTv~dv~~~~~~~~~ 209 (246)
T COG3935 185 ILRNWKKNGVKTVEDVRAREEERRT 209 (246)
T ss_pred HHHHHHHcCCccHHHHHHHHHHHHH
Confidence 3566666666666665555555543
No 66
>PF05680 ATP-synt_E: ATP synthase E chain; InterPro: IPR008386 ATPases (or ATP synthases) are membrane-bound enzyme complexes/ion transporters that combine ATP synthesis and/or hydrolysis with the transport of protons across a membrane. ATPases can harness the energy from a proton gradient, using the flux of ions across the membrane via the ATPase proton channel to drive the synthesis of ATP. Some ATPases work in reverse, using the energy from the hydrolysis of ATP to create a proton gradient. There are different types of ATPases, which can differ in function (ATP synthesis and/or hydrolysis), structure (e.g., F-, V- and A-ATPases, which contain rotary motors) and in the type of ions they transport [, ]. The different types include: F-ATPases (F1F0-ATPases), which are found in mitochondria, chloroplasts and bacterial plasma membranes where they are the prime producers of ATP, using the proton gradient generated by oxidative phosphorylation (mitochondria) or photosynthesis (chloroplasts). V-ATPases (V1V0-ATPases), which are primarily found in eukaryotic vacuoles and catalyse ATP hydrolysis to transport solutes and lower pH in organelles. A-ATPases (A1A0-ATPases), which are found in Archaea and function like F-ATPases (though with respect to their structure and some inhibitor responses, A-ATPases are more closely related to the V-ATPases). P-ATPases (E1E2-ATPases), which are found in bacteria and in eukaryotic plasma membranes and organelles, and function to transport a variety of different ions across membranes. E-ATPases, which are cell-surface enzymes that hydrolyse a range of NTPs, including extracellular ATP. F-ATPases (also known as F1F0-ATPase, or H(+)-transporting two-sector ATPase) (3.6.3.14 from EC) are composed of two linked complexes: the F1 ATPase complex is the catalytic core and is composed of 5 subunits (alpha, beta, gamma, delta, epsilon), while the F0 ATPase complex is the membrane-embedded proton channel that is composed of at least 3 subunits (A-C), nine in mitochondria (A-G, F6, F8). Both the F1 and F0 complexes are rotary motors that are coupled back-to-back. In the F1 complex, the central gamma subunit forms the rotor inside the cylinder made of the alpha(3)beta(3) subunits, while in the F0 complex, the ring-shaped C subunits forms the rotor. The two rotors rotate in opposite directions, but the F0 rotor is usually stronger, using the force from the proton gradient to push the F1 rotor in reverse in order to drive ATP synthesis []. These ATPases can also work in reverse to hydrolyse ATP to create a proton gradient. This entry represents subunit E found in the F0 complex of F-ATPases. Mitochondrial F-ATPases can associate together to form dimeric or oligomeric complexes, such interactions involving the physical association of membrane-embedded F0 complexes. In yeast, the F0 complex E subunit appears to play an important role in supporting F-ATPase dimerisation. This subunit is anchored to the inner mitochondrial membrane via its N-terminal region, which is involved in stabilising subunits G and K of the F0 complex. The C-terminal region of subunit E is hydrophilic, protruding into the intermembrane space where it can also help stabilise the F-ATPase dimer complex []. More information about this protein can be found at Protein of the Month: ATP Synthases [].; GO: 0015078 hydrogen ion transmembrane transporter activity, 0015986 ATP synthesis coupled proton transport, 0000276 mitochondrial proton-transporting ATP synthase complex, coupling factor F(o)
Probab=24.91 E-value=1.6e+02 Score=22.16 Aligned_cols=29 Identities=21% Similarity=0.313 Sum_probs=19.3
Q ss_pred HHHHhhHh---hHHHHHHHHHHHHHHHHHHHH
Q 029231 85 WRRENAIR---LEEKEKKEKEMLNQIIEEAEE 113 (197)
Q Consensus 85 WRRQNAi~---LEEKEk~EKE~r~QII~EAee 113 (197)
|.+++.+. =++++.+|.+.+.++|++|..
T Consensus 26 ~~~~~~L~~~~~~~~~~~e~~~~eklie~AK~ 57 (86)
T PF05680_consen 26 AYHQRYLKAKAKKEAAEREYEAKEKLIEQAKA 57 (86)
T ss_pred HHHHHHHHhhHHHHHHHHHHHHHHHHHHHHHH
Confidence 45666665 455556677788888888743
No 67
>PRK14139 heat shock protein GrpE; Provisional
Probab=24.66 E-value=1.5e+02 Score=25.06 Aligned_cols=12 Identities=25% Similarity=0.321 Sum_probs=7.3
Q ss_pred HHHHHhhcccee
Q 029231 182 MLVQIFSNFSIV 193 (197)
Q Consensus 182 ~~~~~~~~~~~~ 193 (197)
.|..+|..+.|.
T Consensus 119 ~l~~vL~k~Gv~ 130 (185)
T PRK14139 119 QLTSAFEKGRVV 130 (185)
T ss_pred HHHHHHHHCCCc
Confidence 455667766654
No 68
>PF11166 DUF2951: Protein of unknown function (DUF2951); InterPro: IPR021337 This family of proteins has no known function. It has a highly conserved sequence.
Probab=24.66 E-value=2.8e+02 Score=22.22 Aligned_cols=60 Identities=27% Similarity=0.390 Sum_probs=33.6
Q ss_pred HHHHHhhHhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhH-------hhhhhchhhhhhhhchhhhHH
Q 029231 84 EWRRENAIRLEEKEKKEKEMLNQIIEEAEEYKLEFYRKSIVTR-------ENNKASNREREKVSGDFKILL 147 (197)
Q Consensus 84 EWRRQNAi~LEEKEk~EKE~r~QII~EAeeyK~eFYeKR~~n~-------EtnKa~NREKEKly~~~~~~~ 147 (197)
||| ..+||+-.+.-...+.+|.+--.. .+.-+.|=..|+ |-+|.+-++-.|-.++.|..+
T Consensus 10 e~R---i~rLEendk~i~~~L~~Ik~gq~~-qe~v~~kld~tlD~i~reRe~dee~k~~n~Knir~~Kmwi 76 (98)
T PF11166_consen 10 EWR---IRRLEENDKTIFNKLDEIKDGQHD-QELVNQKLDRTLDEINREREEDEENKKKNDKNIRDIKMWI 76 (98)
T ss_pred HHH---HHHHHHhhHHHHHHHHHHHHhHhh-HHHHHHHHHhhHHHHHHHHHHHHHHHHHHHhhHHHHHHHH
Confidence 676 357899888888888887654322 222333333322 333334444456566666544
No 69
>COG2825 HlpA Outer membrane protein [Cell envelope biogenesis, outer membrane]
Probab=24.62 E-value=2.5e+02 Score=23.17 Aligned_cols=42 Identities=10% Similarity=0.168 Sum_probs=22.9
Q ss_pred HhHHHHHHhhHhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Q 029231 81 ALREWRRENAIRLEEKEKKEKEMLNQIIEEAEEYKLEFYRKS 122 (197)
Q Consensus 81 ~LREWRRQNAi~LEEKEk~EKE~r~QII~EAeeyK~eFYeKR 122 (197)
..++|+++....=+...+++.+..+++.++....-+.+.++.
T Consensus 98 ~~~~~~~k~~~~~~~~~~~~~e~~~~~~~~i~~ai~~~a~~~ 139 (170)
T COG2825 98 LVNAFNKKQQEYEKDLNRREAEEEQKLLEKIQRAIESVAEKG 139 (170)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhC
Confidence 445555555555555555555555555555555555544443
No 70
>KOG4800 consensus Neuronal membrane glycoprotein/Myelin proteolipid protein [Function unknown]
Probab=24.49 E-value=32 Score=31.12 Aligned_cols=12 Identities=33% Similarity=0.775 Sum_probs=9.4
Q ss_pred cccccchhhhHH
Q 029231 158 KSHCGCMHVMFV 169 (197)
Q Consensus 158 ~~~~~~~~~~~~ 169 (197)
+--|||+|.|..
T Consensus 44 alfC~~gh~als 55 (248)
T KOG4800|consen 44 ALFCGCGHEALS 55 (248)
T ss_pred hhhhhhhHHHHH
Confidence 457999999853
No 71
>PF05313 Pox_P21: Poxvirus P21 membrane protein; InterPro: IPR007977 The p21 membrane protein of vaccinia virus, encoded by the A17L (or A18L) gene, has been reported to localise on the inner of the two membranes of the intracellular mature virus (IMV). It has also been shown that p21 acts as a membrane anchor for the externally located fusion protein P14 (A27L gene) [].; GO: 0016021 integral to membrane
Probab=24.11 E-value=36 Score=29.67 Aligned_cols=41 Identities=20% Similarity=0.373 Sum_probs=27.6
Q ss_pred hccCCCCCCCCCCCcc-C---CCcccc-CCccCCCCCCCCCCCCCCC
Q 029231 28 SAVDLSDDNNNSSFQS-G---DDAFAS-QTSVYGEYADGGSDGPILP 69 (197)
Q Consensus 28 s~~g~~s~~~~~~~~~-~---dDvf~s-~~~~f~p~~ng~sdGPiLP 69 (197)
||.-|-. +++|..++ | .++|+. |--.|=|..+|+.+||-.|
T Consensus 2 SYLsYYN-m~ddF~AGAGV~D~ELFT~EEq~sFlPk~~~~~~~~~~~ 47 (189)
T PF05313_consen 2 SYLSYYN-MFDDFSAGAGVSDEELFTEEEQESFLPKDGGGPGGPDFP 47 (189)
T ss_pred chhhhhc-chhhcccCCCCChhhhcCHHHHHccCCCCCCCCCCCCCc
Confidence 4555544 67765555 3 678876 4456779988888888755
No 72
>PF13904 DUF4207: Domain of unknown function (DUF4207)
Probab=24.08 E-value=3e+02 Score=23.90 Aligned_cols=29 Identities=21% Similarity=0.329 Sum_probs=19.4
Q ss_pred CCCCCCCcchhhHhHHHHHHhhHhhHHHH
Q 029231 69 PPPSDMVPEEGFALREWRRENAIRLEEKE 97 (197)
Q Consensus 69 PpP~eM~~EEG~~LREWRRQNAi~LEEKE 97 (197)
|++.....+--..+.+|.++....++++-
T Consensus 173 ~~~~~~~e~a~~~~q~W~~kK~~e~~~~r 201 (264)
T PF13904_consen 173 PEREVSQEEAKQRYQEWERKKKEEQQQKR 201 (264)
T ss_pred cccccCHHHHHHHHHHHHHHHHHHHHHHH
Confidence 55555553334799999998887666543
No 73
>PF10037 MRP-S27: Mitochondrial 28S ribosomal protein S27; InterPro: IPR019266 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 entry represents a family of small ribosomal proteins possessing one of three conserved sequence blocks found in proteins that stimulate the dissociation of guanine nucleotides from G-proteins. This leaves open the possibility that they may be functional partners of GTP-binding ribosomal proteins [].
Probab=23.98 E-value=3.5e+02 Score=25.67 Aligned_cols=61 Identities=21% Similarity=0.310 Sum_probs=37.5
Q ss_pred chhhHhHHHHHHhhHhhHHHHHHHHH----HHHHHHHHHHHHHHHHHHHhhhhHh--hh------hhchhhhhh
Q 029231 77 EEGFALREWRRENAIRLEEKEKKEKE----MLNQIIEEAEEYKLEFYRKSIVTRE--NN------KASNREREK 138 (197)
Q Consensus 77 EEG~~LREWRRQNAi~LEEKEk~EKE----~r~QII~EAeeyK~eFYeKR~~n~E--tn------Ka~NREKEK 138 (197)
+.+....+|..+=...++ .+-++-. ++.+-|++.+.-+.+++++|+..-. +. |.-.|||++
T Consensus 340 ~q~~~f~~W~~~rq~~~~-~q~~~l~~~~~~~~~rl~~ie~~~~~l~e~e~~lwffen~~~i~~~~~~~~kkk~ 412 (429)
T PF10037_consen 340 EQCERFQEWEEKRQSLLK-EQSERLLTLTQLRKERLEEIEKEDKELYEQEQQLWFFENEDKIQYPKRWQRKKKK 412 (429)
T ss_pred HHHHHHHHHHHHHHHHHH-HHHHHHhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhHHHHHHHHHhh
Confidence 566677889765443333 3333333 4677788888888899988876432 22 455666554
No 74
>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=23.75 E-value=1.1e+02 Score=22.49 Aligned_cols=27 Identities=22% Similarity=0.145 Sum_probs=19.4
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHhhh
Q 029231 98 KKEKEMLNQIIEEAEEYKLEFYRKSIV 124 (197)
Q Consensus 98 k~EKE~r~QII~EAeeyK~eFYeKR~~ 124 (197)
++.++.-.+-++++++|..++-+|.-+
T Consensus 87 ~~~~~~~~~~~~~~~~fla~n~k~~GV 113 (124)
T PF01346_consen 87 EKMAKAAEKNKAEGEAFLAENAKKEGV 113 (124)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHTSTTE
T ss_pred cchhhhhhhhHHHHHHHHHHHcCCCCC
Confidence 344556677789999999988776543
No 75
>PF02209 VHP: Villin headpiece domain; InterPro: IPR003128 Villin is an F-actin bundling protein involved in the maintenance of the microvilli of the absorptive epithelia. The villin-type "headpiece" domain is a modular motif found at the extreme C terminus of larger "core" domains in over 25 cytoskeletal proteins in plants and animals, often in assocation with the Gelsolin repeat. Although the headpiece is classified as an F-actin-binding domain, it has been shown that not all headpiece domains are intrinsically F-actin-binding motifs, surface charge distribution may be an important element for F-actin recognition []. An autonomously folding, 35 residue, thermostable subdomain (HP36) of the full-length 76 amino acid residue villin headpiece, is the smallest known example of a cooperatively folded domain of a naturally occurring protein. The structure of HP36, as determined by NMR spectroscopy, consists of three short helices surrounding a tightly packed hydrophobic core []. ; GO: 0003779 actin binding, 0007010 cytoskeleton organization; PDB: 1ZV6_A 1QZP_A 1UND_A 2PPZ_A 3TJW_B 1YU8_X 2JM0_A 1WY4_A 3MYC_A 1YU5_X ....
Probab=23.74 E-value=48 Score=21.68 Aligned_cols=18 Identities=33% Similarity=0.656 Sum_probs=13.3
Q ss_pred CCCcchhhHhHHHHHHhh
Q 029231 73 DMVPEEGFALREWRRENA 90 (197)
Q Consensus 73 eM~~EEG~~LREWRRQNA 90 (197)
.|..+|=..|-.|+|+|.
T Consensus 12 gm~~~eF~~lP~WKq~~l 29 (36)
T PF02209_consen 12 GMSREEFYKLPKWKQNNL 29 (36)
T ss_dssp SS-HHHHHHS-HHHHHHH
T ss_pred CCCHHHHHHChHHHHHHH
Confidence 377788889999999885
No 76
>PHA00452 T3/T7-like RNA polymerase
Probab=23.54 E-value=1.6e+02 Score=30.05 Aligned_cols=37 Identities=24% Similarity=0.449 Sum_probs=22.8
Q ss_pred hHhHHHHHHhhHhhH-HHHHH-HHHHHHHHHHHHHHHHH
Q 029231 80 FALREWRRENAIRLE-EKEKK-EKEMLNQIIEEAEEYKL 116 (197)
Q Consensus 80 ~~LREWRRQNAi~LE-EKEk~-EKE~r~QII~EAeeyK~ 116 (197)
..+++|+|+.+.... .+|.. .+--...+++-|..|+.
T Consensus 337 ~~~~~wk~~~~~~~~~~~~~~S~r~~~~~~l~iA~~f~~ 375 (807)
T PHA00452 337 EAFKAWKRAAAAWYTKEKERVSKRRRLEFMLRVANKFAD 375 (807)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcC
Confidence 678999998554332 22222 22234567788898887
No 77
>PF07261 DnaB_2: Replication initiation and membrane attachment; InterPro: IPR006343 This entry represents a domain found in several bacterial replication initiation and membrane attachment proteins, DnaB and DnaD. The DnaD protein is a component of the PriA primosome. The PriA primosome functions to recruit the replication fork helicase onto the DNA []. Members, both chromosomal or phage-associated, are found in the Bacillus/Clostridium group of Gram-positive bacteria []. The DnaB protein is essential for both replication initiation and membrane attachment of the origin region of the chromosome and Plasmid pUB110 in Bacillus subtilis. It is known that there are two different classes (DnaBI and DnaBII) in the DnaB mutants; DnaBI is essential for both chromosome and pUB110 replication, whereas DnaBII is necessary only for chromosome replication []. This domain tends to be found towards the C terminus of DnaB and DnaD proteins and is alpha helical in nature.; PDB: 2I5U_A 2ZC2_A.
Probab=23.29 E-value=20 Score=24.03 Aligned_cols=21 Identities=29% Similarity=0.612 Sum_probs=12.4
Q ss_pred HhHHHHHHhhHhhHHHHHHHH
Q 029231 81 ALREWRRENAIRLEEKEKKEK 101 (197)
Q Consensus 81 ~LREWRRQNAi~LEEKEk~EK 101 (197)
.|+.|++++...+|+-++.+|
T Consensus 56 Il~~W~~~gi~t~e~~~~~~k 76 (77)
T PF07261_consen 56 ILNNWKQKGIKTVEDAEEYEK 76 (77)
T ss_dssp HHHHHHHCT--SCCCCT----
T ss_pred HHHHHHHcCCCCHHHHHHHhh
Confidence 578899999888887766655
No 78
>PF07946 DUF1682: Protein of unknown function (DUF1682); InterPro: IPR012879 The members of this family are all hypothetical eukaryotic proteins of unknown function. One member (Q920S6 from SWISSPROT) is described as being an adipocyte-specific protein, but no evidence of this was found.
Probab=23.27 E-value=3.2e+02 Score=24.13 Aligned_cols=23 Identities=48% Similarity=0.387 Sum_probs=10.3
Q ss_pred HhhHHHHHHHHHHHHHHHHHHHH
Q 029231 91 IRLEEKEKKEKEMLNQIIEEAEE 113 (197)
Q Consensus 91 i~LEEKEk~EKE~r~QII~EAee 113 (197)
.+.++.++-.|+..++-.++|.+
T Consensus 263 ~R~~~~~~~~K~~~~~r~E~~~~ 285 (321)
T PF07946_consen 263 NREEEEEKILKEAHQERQEEAQE 285 (321)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHH
Confidence 34444444444444444444433
No 79
>PF12752 SUZ: SUZ domain; InterPro: IPR024771 The SUZ domain is a conserved RNA-binding domain found in eukaryotes and enriched in positively charged amino acids. It was first characterised in the Caenorhabditis elegans protein SZY-20 where it has been shown to bind RNA and allow their localization to the centrosome [].
Probab=23.11 E-value=26 Score=24.15 Aligned_cols=27 Identities=22% Similarity=0.307 Sum_probs=21.7
Q ss_pred HHHHhhHhhHHHHHHHHHHHHHHHHHH
Q 029231 85 WRRENAIRLEEKEKKEKEMLNQIIEEA 111 (197)
Q Consensus 85 WRRQNAi~LEEKEk~EKE~r~QII~EA 111 (197)
+..+....|||+|++=.+.|.+|...+
T Consensus 32 ~~~~~~kSlEERE~eY~~AR~RIFg~~ 58 (59)
T PF12752_consen 32 RKKRPSKSLEEREAEYAEARARIFGSS 58 (59)
T ss_pred ccccccCCHHHHHHHHHHHHHHHhCCC
Confidence 344567789999999999999997654
No 80
>PF08367 M16C_assoc: Peptidase M16C associated; InterPro: IPR013578 In the MEROPS database peptidases and peptidase homologues are grouped into clans and families. Clans are groups of families for which there is evidence of common ancestry based on a common structural fold: Each clan is identified with two letters, the first representing the catalytic type of the families included in the clan (with the letter 'P' being used for a clan containing families of more than one of the catalytic types serine, threonine and cysteine). Some families cannot yet be assigned to clans, and when a formal assignment is required, such a family is described as belonging to clan A-, C-, M-, N-, S-, T- or U-, according to the catalytic type. Some clans are divided into subclans because there is evidence of a very ancient divergence within the clan, for example MA(E), the gluzincins, and MA(M), the metzincins. Peptidase families are grouped by their catalytic type, the first character representing the catalytic type: A, aspartic; C, cysteine; G, glutamic acid; M, metallo; N, asparagine; S, serine; T, threonine; and U, unknown. The serine, threonine and cysteine peptidases utilise the amino acid as a nucleophile and form an acyl intermediate - these peptidases can also readily act as transferases. In the case of aspartic, glutamic and metallopeptidases, the nucleophile is an activated water molecule. In the case of the asparagine endopeptidases, the nucleophile is asparagine and all are self-processing endopeptidases. In many instances the structural protein fold that characterises the clan or family may have lost its catalytic activity, yet retain its function in protein recognition and binding. Metalloproteases are the most diverse of the four main types of protease, with more than 50 families identified to date. In these enzymes, a divalent cation, usually zinc, activates the water molecule. The metal ion is held in place by amino acid ligands, usually three in number. The known metal ligands are His, Glu, Asp or Lys and at least one other residue is required for catalysis, which may play an electrophillic role. Of the known metalloproteases, around half contain an HEXXH motif, which has been shown in crystallographic studies to form part of the metal-binding site []. The HEXXH motif is relatively common, but can be more stringently defined for metalloproteases as 'abXHEbbHbc', where 'a' is most often valine or threonine and forms part of the S1' subsite in thermolysin and neprilysin, 'b' is an uncharged residue, and 'c' a hydrophobic residue. Proline is never found in this site, possibly because it would break the helical structure adopted by this motif in metalloproteases []. This domain appears in eukaryotes as well as bacteria and tends to be found near the C terminus of metalloproteases and related sequences belonging to MEROPS peptidase family M16 (subfamily M16C, clan ME). These include: eupitrilysin, falcilysin, PreP peptidase, CYM1 peptidase and subfamily M16C non-peptidase homologues.; GO: 0008237 metallopeptidase activity, 0008270 zinc ion binding, 0006508 proteolysis; PDB: 2FGE_B 3S5I_A 3S5H_A 3S5M_A 3S5K_A.
Probab=23.00 E-value=1.4e+02 Score=24.89 Aligned_cols=18 Identities=33% Similarity=0.377 Sum_probs=11.2
Q ss_pred HHHHHHHHHHHHHHHHHH
Q 029231 99 KEKEMLNQIIEEAEEYKL 116 (197)
Q Consensus 99 ~EKE~r~QII~EAeeyK~ 116 (197)
-.++-+++|++++.+.++
T Consensus 26 Ls~~e~~~i~~~~~~L~~ 43 (248)
T PF08367_consen 26 LSEEEKEKIIEQTKELKE 43 (248)
T ss_dssp S-HHHHHHHHHHHHHHHH
T ss_pred CCHHHHHHHHHHHHHHHH
Confidence 345566777777777643
No 81
>PF10549 ORF11CD3: ORF11CD3 domain; InterPro: IPR018877 This entry represents the carboxy-terminal domain from ORF11 (Q9XJS9 from SWISSPROT), one of the proteins of Pseudomonas phage D3 (Bacteriophage D3). The function of these proteins are unknown [].
Probab=22.92 E-value=1e+02 Score=22.04 Aligned_cols=26 Identities=19% Similarity=0.392 Sum_probs=17.5
Q ss_pred hhHhHHHHHHhhHhhHHHHHHHHHHH
Q 029231 79 GFALREWRRENAIRLEEKEKKEKEML 104 (197)
Q Consensus 79 G~~LREWRRQNAi~LEEKEk~EKE~r 104 (197)
|-.|++||........+=++-+.++.
T Consensus 26 GrgL~~Wk~~Kp~l~~ki~~l~~~~Q 51 (57)
T PF10549_consen 26 GRGLNRWKWKKPQLEQKIEELEEQLQ 51 (57)
T ss_pred hHHHHHHHHhhHHHHHHHHHHHHHhh
Confidence 67799997777766665555555443
No 82
>KOG1029 consensus Endocytic adaptor protein intersectin [Signal transduction mechanisms; Intracellular trafficking, secretion, and vesicular transport]
Probab=22.83 E-value=2.8e+02 Score=29.69 Aligned_cols=26 Identities=42% Similarity=0.607 Sum_probs=11.7
Q ss_pred hhhHhHHHHHHhhHhhHHHHHHHHHHHHH
Q 029231 78 EGFALREWRRENAIRLEEKEKKEKEMLNQ 106 (197)
Q Consensus 78 EG~~LREWRRQNAi~LEEKEk~EKE~r~Q 106 (197)
-|-+=-|=|||= |+|.+++|+|.+.|
T Consensus 324 kGqaELerRRq~---leeqqqreree~eq 349 (1118)
T KOG1029|consen 324 KGQAELERRRQA---LEEQQQREREEVEQ 349 (1118)
T ss_pred hhhHHHHHHHHH---HHHHHHHHHHHHHH
Confidence 344444555553 34444444444433
No 83
>KOG2678 consensus Predicted membrane protein [Function unknown]
Probab=22.35 E-value=96 Score=28.11 Aligned_cols=22 Identities=27% Similarity=0.729 Sum_probs=14.7
Q ss_pred HHHHHHHHHHHHHHHHHHhhcc
Q 029231 169 VIIYVCFDLFMYLMLVQIFSNF 190 (197)
Q Consensus 169 ~~~~~~~~~~~~~~~~~~~~~~ 190 (197)
+||+||+-+..-+.+.|||.+-
T Consensus 222 miI~v~~sFVsMiliiqifkkl 243 (244)
T KOG2678|consen 222 MIIFVILSFVSMILIIQIFKKL 243 (244)
T ss_pred HHHHHHHHHHHHHHHHHHhhcc
Confidence 5666777665555567888763
No 84
>PF08592 DUF1772: Domain of unknown function (DUF1772); InterPro: IPR013901 This entry represents proteins of unknown function.
Probab=21.73 E-value=80 Score=23.01 Aligned_cols=23 Identities=26% Similarity=0.468 Sum_probs=16.7
Q ss_pred CCCCCCcch-hhHhHHHHHHhhHh
Q 029231 70 PPSDMVPEE-GFALREWRRENAIR 92 (197)
Q Consensus 70 pP~eM~~EE-G~~LREWRRQNAi~ 92 (197)
.|++...++ -..++.|.|-|..+
T Consensus 101 ~~~~~~~~~~~~l~~~W~~~n~vR 124 (139)
T PF08592_consen 101 SPEEAPADWVRALLDRWGRLNLVR 124 (139)
T ss_pred cccccchHHHHHHHHHHHHHHHHH
Confidence 344444456 67899999999876
No 85
>PF00855 PWWP: PWWP domain; InterPro: IPR000313 Upon characterisation of WHSC1, a gene mapping to the Wolf-Hirschhornsyndrome critical region and at its C terminus similar to the Drosophila melanogaster ASH1/trithorax group proteins, a novel protein domain designated PWWP domain was identified []. The PWWP domain is named after a conserved Pro-Trp-Trp-Pro motif. It is present in proteins of nuclear origin and plays a role in cell growth and differentiation. Due to its position, the composition of amino acids close to the PWWP motif and the pattern of other domains present it has been suggested that the domain is involved in protein-protein interactions [].; PDB: 3LYI_B 2L89_A 2NLU_A 1RI0_A 1KHC_A 3QKJ_C 2DAQ_A 1N27_A 3PFS_B 3QJ6_A ....
Probab=21.72 E-value=1.5e+02 Score=20.10 Aligned_cols=24 Identities=42% Similarity=0.591 Sum_probs=17.1
Q ss_pred HhhHHHHHHHHHHHHHHHHHHHHH
Q 029231 91 IRLEEKEKKEKEMLNQIIEEAEEY 114 (197)
Q Consensus 91 i~LEEKEk~EKE~r~QII~EAeey 114 (197)
..+.++.++.+....+-|++|++|
T Consensus 63 ~~~~~~~~~k~~~~~~Ai~eA~~~ 86 (86)
T PF00855_consen 63 EKLKKKKKKKRKSFRKAIEEAEEA 86 (86)
T ss_dssp HHHHHHHHHHSHHHHHHHHHHHHH
T ss_pred HHHHHhhccchHHHHHHHHHHHhC
Confidence 445555556667788888999876
No 86
>PF09403 FadA: Adhesion protein FadA; InterPro: IPR018543 FadA (Fusobacterium adhesin A) is an adhesin which forms two alpha helices. ; PDB: 3ETZ_B 3ETY_A 2GL2_B 3ETX_C 3ETW_A.
Probab=21.65 E-value=3e+02 Score=22.17 Aligned_cols=35 Identities=26% Similarity=0.127 Sum_probs=27.1
Q ss_pred HhhHhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Q 029231 88 ENAIRLEEKEKKEKEMLNQIIEEAEEYKLEFYRKS 122 (197)
Q Consensus 88 QNAi~LEEKEk~EKE~r~QII~EAeeyK~eFYeKR 122 (197)
.+..+|+.||....+...++.+.|+.-..+..+.+
T Consensus 34 ae~q~L~~kE~~r~~~~k~~ae~a~~~L~~~~~~~ 68 (126)
T PF09403_consen 34 AEYQQLEQKEEARYNEEKQEAEAAEAELAELKELY 68 (126)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 45677888888888888888888888777665544
No 87
>PRK00026 trmD tRNA (guanine-N(1)-)-methyltransferase; Reviewed
Probab=21.39 E-value=1.4e+02 Score=26.86 Aligned_cols=25 Identities=16% Similarity=0.457 Sum_probs=17.5
Q ss_pred CCCCCCcchhhHhHHHHHHhhHhhH
Q 029231 70 PPSDMVPEEGFALREWRRENAIRLE 94 (197)
Q Consensus 70 pP~eM~~EEG~~LREWRRQNAi~LE 94 (197)
.|+-+-.---....+|||+.++..-
T Consensus 192 VP~VLlSGnH~~I~~WR~~~sl~~T 216 (244)
T PRK00026 192 VPEVLLSGNHAKIARWRRKQSLERT 216 (244)
T ss_pred CcccccCCCHHHHHHHHHHHHHHHH
Confidence 5555544555678999999887543
No 88
>KOG3312 consensus Predicted membrane protein [Function unknown]
Probab=21.39 E-value=1.5e+02 Score=25.82 Aligned_cols=61 Identities=25% Similarity=0.241 Sum_probs=33.6
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHhhhhHhhhhhchhhhh--hhhchhhhHHHHHHhhhhccc
Q 029231 96 KEKKEKEMLNQIIEEAEEYKLEFYRKSIVTRENNKASNRERE--KVSGDFKILLVFVACFSFLNK 158 (197)
Q Consensus 96 KEk~EKE~r~QII~EAeeyK~eFYeKR~~n~EtnKa~NREKE--Kly~~~~~~~~~~~~~~~~~~ 158 (197)
|+-+.-|.+.++..+. -++.--+|-+..-|.-|++||+-- |.---|-|-|+|.|.++.+|.
T Consensus 45 K~sKKLE~~K~~~~~s--~~k~~kkKieR~Ee~LK~~nRDlSl~kmKsmfaigl~ftal~~~fNS 107 (186)
T KOG3312|consen 45 KQSKKLEKKKEENGDS--NDKSKKKKIERVEEKLKNNNRDLSLFKMKSMFAIGLAFTALLGMFNS 107 (186)
T ss_pred HHHHHHHHHhhhcccc--hhhHHHHHHHHHHHHHhccccchHHHHHHHHHHHHHHHHHHHHHHHh
Confidence 3333334444444443 223333344444556678888743 333456778888888887775
No 89
>PF03248 Rer1: Rer1 family; InterPro: IPR004932 RER1 family proteins are involved in involved in the retrieval of some endoplasmic reticulum membrane proteins from the early golgi compartment. The C terminus of yeast Rer1p interacts with a coatomer complex [].; GO: 0016021 integral to membrane
Probab=21.21 E-value=58 Score=27.75 Aligned_cols=33 Identities=18% Similarity=0.341 Sum_probs=21.8
Q ss_pred hhhhccCCCCCCCCCCCccCCCccccCCccCCCCCCCCCCCCCCCCC
Q 029231 25 QLNSAVDLSDDNNNSSFQSGDDAFASQTSVYGEYADGGSDGPILPPP 71 (197)
Q Consensus 25 ~~ns~~g~~s~~~~~~~~~~dDvf~s~~~~f~p~~ng~sdGPiLPpP 71 (197)
.+|...++-+|.+|.+... +++..+|||.||.+
T Consensus 59 lLnlfi~FltP~~Dp~l~~--------------~~~~~~~g~~Lp~~ 91 (176)
T PF03248_consen 59 LLNLFIAFLTPKFDPELEQ--------------DEEDEEEGPELPTT 91 (176)
T ss_pred HHHHHHHHhCCcCcccccc--------------ccccccccccCCCC
Confidence 3677888888877743322 22345789999986
No 90
>PF10661 EssA: WXG100 protein secretion system (Wss), protein EssA; InterPro: IPR018920 The Wss (WXG100 protein secretion system) in Staphylococcus aureus seems to be encoded by a locus of eight ORFs, called ess (eSAT-6 secretion system) []. This locus encodes, amongst several other proteins, EssA, a protein predicted to possess one transmembrane domain. Due to its predicted membrane location and its absolute requirement for WXG100 protein secretion, it has been speculated that EssA could form a secretion apparatus in conjunction with YukC and YukAB. Proteins homologous to EssA, YukC, EsaA and YukD were absent from mycobacteria []. Members of this family are associated with type VII secretion of WXG100 family targets in the Firmicutes, but not in the Actinobacteria. This highly divergent protein family consists largely of a central region of highly polar low-complexity sequence containing occasional LF motifs in weak repeats about 17 residues in length, flanked by hydrophobic N- and C-terminal regions.
Probab=20.24 E-value=4.8e+02 Score=21.19 Aligned_cols=12 Identities=17% Similarity=0.260 Sum_probs=8.2
Q ss_pred HHHHHHHHHHHH
Q 029231 110 EAEEYKLEFYRK 121 (197)
Q Consensus 110 EAeeyK~eFYeK 121 (197)
..+++|...|..
T Consensus 83 ~v~~~k~~LFs~ 94 (145)
T PF10661_consen 83 TVKETKDSLFSS 94 (145)
T ss_pred hHHHHHHHhhcc
Confidence 456777777764
No 91
>PRK08475 F0F1 ATP synthase subunit B; Validated
Probab=20.09 E-value=4.6e+02 Score=21.01 Aligned_cols=30 Identities=10% Similarity=0.142 Sum_probs=14.6
Q ss_pred hHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Q 029231 93 LEEKEKKEKEMLNQIIEEAEEYKLEFYRKS 122 (197)
Q Consensus 93 LEEKEk~EKE~r~QII~EAeeyK~eFYeKR 122 (197)
+++-.++-+..+.+|+++|.+-....-++-
T Consensus 94 i~~A~~eAe~~~~~ii~~A~~ea~~~~~~a 123 (167)
T PRK08475 94 VETAKKEAYILTQKIEKQTKDDIENLIKSF 123 (167)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 333334444455556665555555544433
Done!