Query 032335
Match_columns 143
No_of_seqs 42 out of 44
Neff 2.7
Searched_HMMs 46136
Date Fri Mar 29 12:45:02 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/032335.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/032335hhsearch_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 99.7 5.5E-17 1.2E-21 130.7 6.4 75 69-143 101-175 (225)
2 KOG4031 Vesicle coat protein c 99.1 1.8E-09 3.9E-14 89.5 12.3 101 37-139 63-165 (216)
3 PF08079 Ribosomal_L30_N: Ribo 89.8 2.9 6.2E-05 28.9 7.3 46 82-127 9-54 (71)
4 PF13019 Telomere_Sde2: Telome 76.5 3.9 8.6E-05 33.0 3.9 36 77-112 126-161 (162)
5 PRK07352 F0F1 ATP synthase sub 73.9 31 0.00067 26.5 8.1 55 80-134 78-132 (174)
6 KOG4031 Vesicle coat protein c 73.5 55 0.0012 28.0 10.0 82 45-132 79-162 (216)
7 TIGR03321 alt_F1F0_F0_B altern 70.7 35 0.00075 27.8 8.1 55 80-134 64-118 (246)
8 KOG4364 Chromatin assembly fac 68.7 61 0.0013 32.2 10.4 73 62-136 231-317 (811)
9 PRK13454 F0F1 ATP synthase sub 68.2 47 0.001 26.1 8.1 53 80-132 90-142 (181)
10 CHL00019 atpF ATP synthase CF0 68.2 48 0.001 25.7 8.1 54 81-134 84-137 (184)
11 TIGR01310 L7 60S ribosomal pro 66.7 34 0.00073 29.0 7.4 41 83-123 11-51 (235)
12 PRK14474 F0F1 ATP synthase sub 63.1 58 0.0013 27.0 8.1 52 81-132 65-116 (250)
13 PF15086 UPF0542: Uncharacteri 58.7 24 0.00052 25.7 4.5 33 82-114 39-71 (74)
14 CHL00118 atpG ATP synthase CF0 58.5 79 0.0017 24.0 8.1 53 80-132 81-133 (156)
15 PF10147 CR6_interact: Growth 57.2 31 0.00067 29.1 5.5 20 55-75 69-88 (217)
16 TIGR00570 cdk7 CDK-activating 57.1 70 0.0015 28.3 7.9 29 79-107 119-147 (309)
17 PRK06231 F0F1 ATP synthase sub 57.1 92 0.002 25.1 8.1 54 80-133 107-160 (205)
18 PF05553 DUF761: Cotton fibre 55.6 31 0.00067 21.9 4.1 27 105-131 3-29 (38)
19 PRK13453 F0F1 ATP synthase sub 54.4 99 0.0021 23.9 8.1 52 80-131 77-128 (173)
20 KOG1029 Endocytic adaptor prot 53.4 70 0.0015 32.6 8.0 25 88-112 342-366 (1118)
21 PRK14471 F0F1 ATP synthase sub 51.4 1E+02 0.0023 23.2 8.1 52 81-132 68-119 (164)
22 cd02987 Phd_like_Phd Phosducin 50.6 35 0.00076 26.5 4.6 43 81-129 12-54 (175)
23 COG5346 Predicted membrane pro 49.3 40 0.00087 27.0 4.8 56 67-124 37-94 (136)
24 PRK07353 F0F1 ATP synthase sub 49.3 1E+02 0.0022 22.4 8.1 53 80-132 64-116 (140)
25 PRK14472 F0F1 ATP synthase sub 48.7 1.2E+02 0.0026 23.2 8.1 53 80-132 77-129 (175)
26 PRK13428 F0F1 ATP synthase sub 48.2 1.3E+02 0.0027 27.1 8.2 51 81-131 61-111 (445)
27 PF08404 Baculo_p74_N: Baculov 48.1 14 0.0003 32.7 2.2 22 65-88 242-263 (301)
28 TIGR01144 ATP_synt_b ATP synth 45.6 1.2E+02 0.0026 22.2 8.0 52 81-132 55-106 (147)
29 PRK13460 F0F1 ATP synthase sub 44.7 1.4E+02 0.0031 22.9 8.0 51 81-131 76-126 (173)
30 PF00430 ATP-synt_B: ATP synth 44.7 1.1E+02 0.0024 21.5 7.1 51 80-130 58-108 (132)
31 PF15466 DUF4635: Domain of un 42.7 1.1E+02 0.0023 24.6 6.2 44 77-120 82-126 (135)
32 COG0488 Uup ATPase components 42.3 80 0.0017 29.3 6.2 43 82-125 235-277 (530)
33 PRK13461 F0F1 ATP synthase sub 41.5 1.5E+02 0.0033 22.2 8.0 53 80-132 64-116 (159)
34 COG3461 Uncharacterized conser 41.4 1E+02 0.0022 23.7 5.6 48 91-140 10-62 (103)
35 PF04568 IATP: Mitochondrial A 41.3 1.2E+02 0.0025 22.8 5.9 40 76-115 60-99 (100)
36 KOG3088 Secretory carrier memb 40.8 1.7E+02 0.0038 26.2 7.8 7 16-22 6-12 (313)
37 PF07768 PVL_ORF50: PVL ORF-50 40.4 90 0.002 24.0 5.4 33 66-105 41-74 (118)
38 PF07139 DUF1387: Protein of u 39.4 1.1E+02 0.0023 27.2 6.3 51 77-127 214-264 (302)
39 PRK14473 F0F1 ATP synthase sub 38.1 1.7E+02 0.0038 22.0 8.2 51 80-130 67-117 (164)
40 PF04521 Viral_P18: ssRNA posi 36.9 83 0.0018 24.7 4.7 34 83-116 67-104 (120)
41 COG2914 Uncharacterized protei 34.9 24 0.00053 26.9 1.5 21 65-96 75-95 (99)
42 PRK05759 F0F1 ATP synthase sub 33.6 2E+02 0.0042 21.2 7.8 49 81-129 64-112 (156)
43 TIGR01069 mutS2 MutS2 family p 31.3 2.9E+02 0.0062 26.8 8.2 39 85-123 540-578 (771)
44 COG2825 HlpA Outer membrane pr 30.5 2.5E+02 0.0054 22.2 6.6 42 81-122 98-139 (170)
45 KOG4752 Ribosomal protein L41 28.5 94 0.002 18.6 2.9 20 83-102 3-22 (26)
46 PF10675 DUF2489: Protein of u 28.3 1.5E+02 0.0032 22.7 4.8 32 79-110 9-40 (131)
47 PRK00026 trmD tRNA (guanine-N( 27.9 98 0.0021 26.7 4.1 36 70-111 192-227 (244)
48 PRK13455 F0F1 ATP synthase sub 27.0 3E+02 0.0064 21.3 8.0 34 82-115 88-121 (184)
49 PF10037 MRP-S27: Mitochondria 26.7 4.2E+02 0.0092 24.2 8.1 49 77-125 340-391 (429)
50 PF06528 Phage_P2_GpE: Phage P 26.2 27 0.00058 22.4 0.4 24 70-93 11-34 (39)
51 PF11831 Myb_Cef: pre-mRNA spl 26.1 1.5E+02 0.0033 24.4 4.8 23 87-109 109-131 (231)
52 PF05499 DMAP1: DNA methyltran 25.7 1.1E+02 0.0024 25.2 3.9 34 77-113 1-35 (176)
53 PF01346 FKBP_N: Domain amino 24.3 1.3E+02 0.0028 21.3 3.6 51 65-122 61-111 (124)
54 PF01086 Clathrin_lg_ch: Clath 24.1 1.8E+02 0.0038 23.8 4.9 54 81-134 117-170 (225)
55 PF05313 Pox_P21: Poxvirus P21 23.0 40 0.00087 28.2 0.9 41 28-69 2-47 (189)
56 PRK00409 recombination and DNA 22.9 5E+02 0.011 25.2 8.2 30 92-121 552-581 (782)
57 KOG1318 Helix loop helix trans 22.9 6.1E+02 0.013 23.5 11.1 23 107-129 274-296 (411)
58 PF15046 DUF4532: Protein of u 22.9 83 0.0018 27.8 2.8 40 63-103 111-158 (279)
59 KOG3184 60S ribosomal protein 22.8 2.2E+02 0.0048 24.2 5.3 46 82-127 11-56 (235)
60 PF04304 DUF454: Protein of un 21.8 42 0.00091 22.1 0.7 21 79-99 12-32 (71)
61 PRK09510 tolA cell envelope in 21.7 6E+02 0.013 23.1 8.1 28 61-91 43-70 (387)
62 PF11875 DUF3395: Domain of un 21.6 3.9E+02 0.0084 20.7 7.2 33 86-118 4-36 (151)
63 PF13904 DUF4207: Domain of un 21.6 4E+02 0.0087 22.3 6.6 29 69-97 173-201 (264)
64 PHA00452 T3/T7-like RNA polyme 21.4 2.2E+02 0.0048 28.1 5.6 40 77-116 334-375 (807)
65 PF10669 Phage_Gp23: Protein g 21.1 2.4E+02 0.0051 22.1 4.7 28 86-113 52-79 (121)
66 TIGR02606 antidote_CC2985 puta 20.9 2.2E+02 0.0048 19.3 4.1 25 79-107 27-51 (69)
67 PF03993 DUF349: Domain of Unk 20.7 2.5E+02 0.0054 18.1 4.7 28 89-116 21-48 (77)
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=99.68 E-value=5.5e-17 Score=130.65 Aligned_cols=75 Identities=36% Similarity=0.513 Sum_probs=58.2
Q ss_pred CCCCCCCcchhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhhhhhhhhhhccC
Q 032335 69 PPPSDMVPEEGFALREWRRENAIRLEEKEKKEKEMLNQIIEEAEEYKLEFYRKSIVTRENNKASNREREKSTEVS 143 (143)
Q Consensus 69 PpP~em~~EEg~~LREWRRqNA~~LeeKEk~EKe~r~qII~eAEeyk~eFYeKR~~~~E~nK~~NREkEk~fLAs 143 (143)
+++..+..|++.+||+||++++++|++|++++++++.+|+++|..+++.||++|+.+++++|+.||+.|+.||++
T Consensus 101 ~~~~~~~~E~~e~ireWre~~~~~i~ekD~~e~~kk~e~~~~A~k~lddfY~~~~~k~e~~k~~nr~~ee~fl~~ 175 (225)
T PF01086_consen 101 SPAPPVEEEEPEAIREWREERDKRIEEKDAEEEEKKEEIKEKAKKELDDFYENRNEKKEKNKKQNREEEEEFLAK 175 (225)
T ss_dssp ---STTTTS-TTHHHHHHHHHTTTSTHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTT----------
T ss_pred CccccccchhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHc
Confidence 344455655699999999999999999999999999999999999999999999999999999999999999974
No 2
>KOG4031 consensus Vesicle coat protein clathrin, light chain [Intracellular trafficking, secretion, and vesicular transport]
Probab=99.09 E-value=1.8e-09 Score=89.55 Aligned_cols=101 Identities=23% Similarity=0.309 Sum_probs=77.4
Q ss_pred CCCCCccCCCccccCCccCCCCCCCCCCCC--CCCCCCCCCcchhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 032335 37 NNSSFQSGDDAFASQTSVYGEYADGGSDGP--ILPPPSDMVPEEGFALREWRRENAIRLEEKEKKEKEMLNQIIEEAEEY 114 (143)
Q Consensus 37 ~~~~~~~~dd~f~s~~~~~~~~~ng~~dgp--ilPpP~em~~EEg~~LREWRRqNA~~LeeKEk~EKe~r~qII~eAEey 114 (143)
|..++..-|.+=.+....+.+..||-.+|+ |.++|. ..+|+..||.||.+++.+|++|+..++.++...+++|--.
T Consensus 63 ~e~~g~~~d~~~~~~~~~~f~~~nG~~d~~a~is~~~~--~~~epE~IRkWkeeQ~~rl~ekD~~sek~k~ElrekAkKe 140 (216)
T KOG4031|consen 63 FEESGPGIDALNGAVGGDVFQEDNGPADGYAGISQGPR--LRDEPEKIRKWKEEQMKRLQEKDEASEKLKEELREKAKKE 140 (216)
T ss_pred ccccCCCcchhhccccccccccCCCCcccccccCCCCC--cccChHHHHHHHHHHHHHHHHhhhhHHHHHHHHHHHHHHH
Confidence 333443333333333333446667755555 445555 4589999999999999999999999999999999999999
Q ss_pred HHHHHHHHHHHHHhhhhhhhhhhhh
Q 032335 115 KLEFYRKSIVTRENNKASNREREKS 139 (143)
Q Consensus 115 k~eFYeKR~~~~E~nK~~NREkEk~ 139 (143)
+++||..+..+++.+|.+||..|.-
T Consensus 141 lddwy~~~~ek~~k~~~~nk~eee~ 165 (216)
T KOG4031|consen 141 LDDWYDQQNEKLEKTKANNKAEEEA 165 (216)
T ss_pred HHHHHHHHHHHHHHHHHHhHHHHHH
Confidence 9999999999999999999765543
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=89.84 E-value=2.9 Score=28.86 Aligned_cols=46 Identities=22% Similarity=0.288 Sum_probs=39.0
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 032335 82 LREWRRENAIRLEEKEKKEKEMLNQIIEEAEEYKLEFYRKSIVTRE 127 (143)
Q Consensus 82 LREWRRqNA~~LeeKEk~EKe~r~qII~eAEeyk~eFYeKR~~~~E 127 (143)
..+|+...+....+.-..-+.+|..|+..|+.|..+|-..-...|.
T Consensus 9 ~~~~~~~~~~~~~~~k~~~~~~r~~~~kRAekY~kEYr~~erd~Ir 54 (71)
T PF08079_consen 9 NEKLKAKRAKKAAARKKKRKKKRKEIFKRAEKYVKEYRQKERDEIR 54 (71)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 3579999999999999999999999999999999998766555544
No 4
>PF13019 Telomere_Sde2: Telomere stability and silencing
Probab=76.50 E-value=3.9 Score=33.00 Aligned_cols=36 Identities=25% Similarity=0.458 Sum_probs=30.9
Q ss_pred chhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 032335 77 EEGFALREWRRENAIRLEEKEKKEKEMLNQIIEEAE 112 (143)
Q Consensus 77 EEg~~LREWRRqNA~~LeeKEk~EKe~r~qII~eAE 112 (143)
.+-..|.+|..+...+-+++.++.+++.++|++.+|
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 466789999999999888888888889999998886
No 5
>PRK07352 F0F1 ATP synthase subunit B; Validated
Probab=73.89 E-value=31 Score=26.47 Aligned_cols=55 Identities=9% Similarity=0.040 Sum_probs=44.2
Q ss_pred hHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhhhh
Q 032335 80 FALREWRRENAIRLEEKEKKEKEMLNQIIEEAEEYKLEFYRKSIVTRENNKASNR 134 (143)
Q Consensus 80 ~~LREWRRqNA~~LeeKEk~EKe~r~qII~eAEeyk~eFYeKR~~~~E~nK~~NR 134 (143)
..|.+||.+-...+.+-.+.-...+++|+.+|........++-...++..+..-+
T Consensus 78 ~~L~~a~~ea~~ii~~a~~~a~~~~~~~~~~A~~e~~~~~~~a~~~i~~e~~~a~ 132 (174)
T PRK07352 78 QKLAQAQQEAERIRADAKARAEAIRAEIEKQAIEDMARLKQTAAADLSAEQERVI 132 (174)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 3578888888888888778888889999999999999998888887777665433
No 6
>KOG4031 consensus Vesicle coat protein clathrin, light chain [Intracellular trafficking, secretion, and vesicular transport]
Probab=73.50 E-value=55 Score=27.96 Aligned_cols=82 Identities=24% Similarity=0.278 Sum_probs=55.6
Q ss_pred CCccccCCccCCCCCCCCCCCCCC-CCCCCCCcchhhHHHHHHHHHHHHHHHHH-HHHHHHHHHHHHHHHHHHHHHHHHH
Q 032335 45 DDAFASQTSVYGEYADGGSDGPIL-PPPSDMVPEEGFALREWRRENAIRLEEKE-KKEKEMLNQIIEEAEEYKLEFYRKS 122 (143)
Q Consensus 45 dd~f~s~~~~~~~~~ng~~dgpil-PpP~em~~EEg~~LREWRRqNA~~LeeKE-k~EKe~r~qII~eAEeyk~eFYeKR 122 (143)
-|||.-.--++..+ -|.+.||=+ =-|+- --.-||=++|.-.++-+++ +.+++.|++-|++-+++-+.|=+++
T Consensus 79 ~~~f~~~nG~~d~~-a~is~~~~~~~epE~-----IRkWkeeQ~~rl~ekD~~sek~k~ElrekAkKelddwy~~~~ek~ 152 (216)
T KOG4031|consen 79 GDVFQEDNGPADGY-AGISQGPRLRDEPEK-----IRKWKEEQMKRLQEKDEASEKLKEELREKAKKELDDWYDQQNEKL 152 (216)
T ss_pred ccccccCCCCcccc-cccCCCCCcccChHH-----HHHHHHHHHHHHHHhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 34665443333221 234555555 23333 3456777777777776554 4567899999999999999999999
Q ss_pred HHHHHhhhhh
Q 032335 123 IVTRENNKAS 132 (143)
Q Consensus 123 ~~~~E~nK~~ 132 (143)
..++..|++.
T Consensus 153 ~k~~~~nk~e 162 (216)
T KOG4031|consen 153 EKTKANNKAE 162 (216)
T ss_pred HHHHHHhHHH
Confidence 9999999764
No 7
>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=70.74 E-value=35 Score=27.76 Aligned_cols=55 Identities=15% Similarity=0.125 Sum_probs=44.0
Q ss_pred hHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhhhh
Q 032335 80 FALREWRRENAIRLEEKEKKEKEMLNQIIEEAEEYKLEFYRKSIVTRENNKASNR 134 (143)
Q Consensus 80 ~~LREWRRqNA~~LeeKEk~EKe~r~qII~eAEeyk~eFYeKR~~~~E~nK~~NR 134 (143)
..|.+|+.+-+..+++-.+.-+..+++|+.+|.+-.+...++-...+++.+..-+
T Consensus 64 ~~l~~a~~ea~~i~~~A~~eA~~~~~~i~~~A~~ea~~~~~~a~~~ie~E~~~a~ 118 (246)
T TIGR03321 64 EKNEELDQQREVLLTKAKEEAQAERQRLLDEAREEADEIREKWQEALRREQAALS 118 (246)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 3577888888888888888888889999999999988888877777776665443
No 8
>KOG4364 consensus Chromatin assembly factor-I [Chromatin structure and dynamics]
Probab=68.67 E-value=61 Score=32.19 Aligned_cols=73 Identities=21% Similarity=0.247 Sum_probs=40.2
Q ss_pred CCCCCCCCCCCCCCcchhhHHHHHHHHH--------------HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 032335 62 GSDGPILPPPSDMVPEEGFALREWRREN--------------AIRLEEKEKKEKEMLNQIIEEAEEYKLEFYRKSIVTRE 127 (143)
Q Consensus 62 ~~dgpilPpP~em~~EEg~~LREWRRqN--------------A~~LeeKEk~EKe~r~qII~eAEeyk~eFYeKR~~~~E 127 (143)
...-+++|-|+-. .++..+++-|..- +++-.-|+++.++...+|+++++..+.+=--++..+.+
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 3446778777654 4556665555111 11111234445566677888888777766655555555
Q ss_pred hhhhhhhhh
Q 032335 128 NNKASNRER 136 (143)
Q Consensus 128 ~nK~~NREk 136 (143)
....+-+++
T Consensus 309 qkekEkeEK 317 (811)
T KOG4364|consen 309 QKEKEKEEK 317 (811)
T ss_pred HHHHHHHHH
Confidence 554444433
No 9
>PRK13454 F0F1 ATP synthase subunit B'; Provisional
Probab=68.25 E-value=47 Score=26.05 Aligned_cols=53 Identities=19% Similarity=0.063 Sum_probs=39.6
Q ss_pred hHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhh
Q 032335 80 FALREWRRENAIRLEEKEKKEKEMLNQIIEEAEEYKLEFYRKSIVTRENNKAS 132 (143)
Q Consensus 80 ~~LREWRRqNA~~LeeKEk~EKe~r~qII~eAEeyk~eFYeKR~~~~E~nK~~ 132 (143)
..|.++|.+-...+++-.+.-+..+++|+.+|+........+-...++.-+..
T Consensus 90 ~~L~~Ar~EA~~ii~~A~~ea~~~~~~~~~~A~~e~~~~~aea~~~I~~~k~~ 142 (181)
T PRK13454 90 KALADARAEAQRIVAETRAEIQAELDVAIAKADAEIAAKAAESEKRIAEIRAG 142 (181)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 35777888888888877777788888999999888887777755555554443
No 10
>CHL00019 atpF ATP synthase CF0 B subunit
Probab=68.18 E-value=48 Score=25.72 Aligned_cols=54 Identities=13% Similarity=-0.047 Sum_probs=40.6
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhhhh
Q 032335 81 ALREWRRENAIRLEEKEKKEKEMLNQIIEEAEEYKLEFYRKSIVTRENNKASNR 134 (143)
Q Consensus 81 ~LREWRRqNA~~LeeKEk~EKe~r~qII~eAEeyk~eFYeKR~~~~E~nK~~NR 134 (143)
.|.++|.+-+..+++-.+.....+++|+.+|..-.+...+.=...++..+..-+
T Consensus 84 ~L~~A~~ea~~ii~~A~~~ae~~~~~il~~A~~ea~~~~~~a~~~ie~Ek~~a~ 137 (184)
T CHL00019 84 RLRQAELEADEIRVNGYSEIEREKENLINQAKEDLERLENYKNETIRFEQQRAI 137 (184)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 567777777777777777777888889988888888887777666666555433
No 11
>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=66.74 E-value=34 Score=28.96 Aligned_cols=41 Identities=20% Similarity=0.268 Sum_probs=32.6
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 032335 83 REWRRENAIRLEEKEKKEKEMLNQIIEEAEEYKLEFYRKSI 123 (143)
Q Consensus 83 REWRRqNA~~LeeKEk~EKe~r~qII~eAEeyk~eFYeKR~ 123 (143)
..||.+.+....++.++-+..+..|+..||.|..++...-.
T Consensus 11 ~~~~~~~~~~~~~~k~~~~~~k~~~fkr~e~~~~~y~~~e~ 51 (235)
T TIGR01310 11 QELAVVRAKQAKAKKKRNKKKKKHYFKRAESFVHEYRKAER 51 (235)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHH
Confidence 46777777777777777888899999999999999875443
No 12
>PRK14474 F0F1 ATP synthase subunit B; Provisional
Probab=63.11 E-value=58 Score=26.98 Aligned_cols=52 Identities=13% Similarity=0.134 Sum_probs=41.8
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhh
Q 032335 81 ALREWRRENAIRLEEKEKKEKEMLNQIIEEAEEYKLEFYRKSIVTRENNKAS 132 (143)
Q Consensus 81 ~LREWRRqNA~~LeeKEk~EKe~r~qII~eAEeyk~eFYeKR~~~~E~nK~~ 132 (143)
.|.+++.+-+..+++-.+.-...+++|+.+|.+..+..-++-...++..+..
T Consensus 65 ~l~~a~~ea~~ii~~A~~eA~~~~~~il~~A~~ea~~~~~~a~~~ie~Ek~~ 116 (250)
T PRK14474 65 KQQSLEQQRASFMAQAQEAADEQRQHLLNEAREDVATARDEWLEQLEREKQE 116 (250)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 4678888888888888888888899999999999888888777777665544
No 13
>PF15086 UPF0542: Uncharacterised protein family UPF0542
Probab=58.66 E-value=24 Score=25.70 Aligned_cols=33 Identities=33% Similarity=0.455 Sum_probs=28.3
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 032335 82 LREWRRENAIRLEEKEKKEKEMLNQIIEEAEEY 114 (143)
Q Consensus 82 LREWRRqNA~~LeeKEk~EKe~r~qII~eAEey 114 (143)
+--|+-..+++-+|||++-|++|+.-|.++..-
T Consensus 39 ~lSwkLaK~ie~~ere~K~k~Kr~~~i~k~rr~ 71 (74)
T PF15086_consen 39 VLSWKLAKAIEKEEREKKKKAKRQANIAKARRT 71 (74)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhh
Confidence 457999999999999999999999888877543
No 14
>CHL00118 atpG ATP synthase CF0 B' subunit; Validated
Probab=58.45 E-value=79 Score=23.96 Aligned_cols=53 Identities=19% Similarity=0.337 Sum_probs=38.4
Q ss_pred hHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhh
Q 032335 80 FALREWRRENAIRLEEKEKKEKEMLNQIIEEAEEYKLEFYRKSIVTRENNKAS 132 (143)
Q Consensus 80 ~~LREWRRqNA~~LeeKEk~EKe~r~qII~eAEeyk~eFYeKR~~~~E~nK~~ 132 (143)
..|.++|.+-...+++-.+.-+..+.+|+.+|.+-.+...+.=...+++-+..
T Consensus 81 ~~L~~A~~ea~~ii~~A~~~a~~~~~~~~~~A~~ea~~~~~~a~~~i~~ek~~ 133 (156)
T CHL00118 81 QELSKARKEAQLEITQSQKEAKEIVENELKQAQKYIDSLLNEATKQLEAQKEK 133 (156)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 35677888777777777777777888888888888777776666555554443
No 15
>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=57.21 E-value=31 Score=29.06 Aligned_cols=20 Identities=30% Similarity=0.637 Sum_probs=11.2
Q ss_pred CCCCCCCCCCCCCCCCCCCCC
Q 032335 55 YGEYADGGSDGPILPPPSDMV 75 (143)
Q Consensus 55 ~~~~~ng~~dgpilPpP~em~ 75 (143)
||.. .|.+=|-..|.|++.+
T Consensus 69 YG~a-SgV~P~~lwPt~eele 88 (217)
T PF10147_consen 69 YGLA-SGVDPGILWPTPEELE 88 (217)
T ss_pred hhhh-cCCChhhhCCCHHHHH
Confidence 4444 3434455569997764
No 16
>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=57.14 E-value=70 Score=28.28 Aligned_cols=29 Identities=10% Similarity=0.259 Sum_probs=20.5
Q ss_pred hhHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 032335 79 GFALREWRRENAIRLEEKEKKEKEMLNQI 107 (143)
Q Consensus 79 g~~LREWRRqNA~~LeeKEk~EKe~r~qI 107 (143)
-.-|+.|.+.|+..|.+...+.++-...|
T Consensus 119 e~~l~~y~~~n~~~I~~n~~~~~~e~~~~ 147 (309)
T TIGR00570 119 KKKIETYQKENKDVIQKNKEKSTREQEEL 147 (309)
T ss_pred HHHHHHHHHHhHHHHHHHHHHHHhHHHHH
Confidence 45799999999999987655554444433
No 17
>PRK06231 F0F1 ATP synthase subunit B; Validated
Probab=57.11 E-value=92 Score=25.05 Aligned_cols=54 Identities=6% Similarity=-0.034 Sum_probs=37.7
Q ss_pred hHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhhh
Q 032335 80 FALREWRRENAIRLEEKEKKEKEMLNQIIEEAEEYKLEFYRKSIVTRENNKASN 133 (143)
Q Consensus 80 ~~LREWRRqNA~~LeeKEk~EKe~r~qII~eAEeyk~eFYeKR~~~~E~nK~~N 133 (143)
..|.+||.+-+..+.+-.++-...+++|+.+|..-.+..-++=...++..++.-
T Consensus 107 ~~L~~A~~eA~~Ii~~A~~eAe~~~e~i~~~A~~eae~ii~~A~~~Ie~Ek~~a 160 (205)
T PRK06231 107 QRHENALAQAKEIIDQANYEALQLKSELEKEANRQANLIIFQARQEIEKERREL 160 (205)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 356777777777776666666677788888888877777776666666655543
No 18
>PF05553 DUF761: Cotton fibre expressed protein; InterPro: IPR008480 This family consists of several plant proteins of unknown function. Three of the sequences from Gossypium hirsutum (Upland cotton) in this family are described as G. hirsutum fibre expressed proteins []. The remaining sequences, found in Arabidopsis thaliana, are uncharacterised.
Probab=55.60 E-value=31 Score=21.90 Aligned_cols=27 Identities=19% Similarity=0.333 Sum_probs=21.7
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHhhhh
Q 032335 105 NQIIEEAEEYKLEFYRKSIVTRENNKA 131 (143)
Q Consensus 105 ~qII~eAEeyk~eFYeKR~~~~E~nK~ 131 (143)
.+|=..||+||..||+.-.+.......
T Consensus 3 ~evd~rAe~FI~~f~~qlrlqr~~S~~ 29 (38)
T PF05553_consen 3 DEVDRRAEEFIAKFREQLRLQRQESLQ 29 (38)
T ss_pred hHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 467789999999999988777666554
No 19
>PRK13453 F0F1 ATP synthase subunit B; Provisional
Probab=54.42 E-value=99 Score=23.87 Aligned_cols=52 Identities=21% Similarity=0.187 Sum_probs=36.9
Q ss_pred hHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhh
Q 032335 80 FALREWRRENAIRLEEKEKKEKEMLNQIIEEAEEYKLEFYRKSIVTRENNKA 131 (143)
Q Consensus 80 ~~LREWRRqNA~~LeeKEk~EKe~r~qII~eAEeyk~eFYeKR~~~~E~nK~ 131 (143)
..|.++|.+-...+++-.+.-+..+++|+.+|.+-.+..-+.=...++..+.
T Consensus 77 ~~l~~a~~ea~~ii~~a~~~a~~~~~~~~~~A~~ea~~~~~~A~~~I~~ek~ 128 (173)
T PRK13453 77 QKLKETQEEVQKILEDAKVQARQQQEQIIHEANVRANGMIETAQSEINSQKE 128 (173)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 4567777777777777777777888888888887777776665555554443
No 20
>KOG1029 consensus Endocytic adaptor protein intersectin [Signal transduction mechanisms; Intracellular trafficking, secretion, and vesicular transport]
Probab=53.43 E-value=70 Score=32.63 Aligned_cols=25 Identities=28% Similarity=0.363 Sum_probs=13.2
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHH
Q 032335 88 ENAIRLEEKEKKEKEMLNQIIEEAE 112 (143)
Q Consensus 88 qNA~~LeeKEk~EKe~r~qII~eAE 112 (143)
+.+++++.|||+|.+++++-..++|
T Consensus 342 reree~eqkEreE~ekkererqEqE 366 (1118)
T KOG1029|consen 342 REREEVEQKEREEEEKKERERQEQE 366 (1118)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 3445555566555555555444444
No 21
>PRK14471 F0F1 ATP synthase subunit B; Provisional
Probab=51.41 E-value=1e+02 Score=23.23 Aligned_cols=52 Identities=23% Similarity=0.255 Sum_probs=34.4
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhh
Q 032335 81 ALREWRRENAIRLEEKEKKEKEMLNQIIEEAEEYKLEFYRKSIVTRENNKAS 132 (143)
Q Consensus 81 ~LREWRRqNA~~LeeKEk~EKe~r~qII~eAEeyk~eFYeKR~~~~E~nK~~ 132 (143)
.|.++|.+-+..+.+-.+.-...+.+|+.+|..-.+..-++=...++..+..
T Consensus 68 ~l~~A~~ea~~ii~~A~~~a~~~~~~~~~~A~~ea~~~~~~a~~~i~~ek~~ 119 (164)
T PRK14471 68 LLKEARAERDAILKEAREIKEKMIADAKEEAQVEGDKMIEQAKASIESEKNA 119 (164)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 4667777766666666666666777777777777777666655555554443
No 22
>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=50.60 E-value=35 Score=26.48 Aligned_cols=43 Identities=14% Similarity=0.353 Sum_probs=31.3
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhh
Q 032335 81 ALREWRRENAIRLEEKEKKEKEMLNQIIEEAEEYKLEFYRKSIVTRENN 129 (143)
Q Consensus 81 ~LREWRRqNA~~LeeKEk~EKe~r~qII~eAEeyk~eFYeKR~~~~E~n 129 (143)
||.+||+-+.+ ..|-.+.+++-++.+++...+=++|-..+...
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 78999987776 55666677776666778877777777776553
No 23
>COG5346 Predicted membrane protein [Function unknown]
Probab=49.30 E-value=40 Score=26.97 Aligned_cols=56 Identities=16% Similarity=0.226 Sum_probs=28.0
Q ss_pred CCCCCCCCCcchhhHHHHHHHHHHHHHHHHHHH--HHHHHHHHHHHHHHHHHHHHHHHHH
Q 032335 67 ILPPPSDMVPEEGFALREWRRENAIRLEEKEKK--EKEMLNQIIEEAEEYKLEFYRKSIV 124 (143)
Q Consensus 67 ilPpP~em~~EEg~~LREWRRqNA~~LeeKEk~--EKe~r~qII~eAEeyk~eFYeKR~~ 124 (143)
+||||..+++=+.+.=--- +.-+.+.+||.+ -+-.+..|.-..-.++-+||..+-.
T Consensus 37 ~LPpp~~l~qYnsI~pnt~--~rimaMAekEQahrH~~~~k~~~~q~r~~~~~~~tril~ 94 (136)
T COG5346 37 ILPPPDLLSQYNSIYPNTL--QRIMAMAEKEQAHRHAIDLKNLKIQRRGQLYAKLTRILL 94 (136)
T ss_pred cCCCHHHHHHHHhhcCCHH--HHHHHHHHHHHHHHHHHHHhhhHHHHHHHHHHHHHHHHH
Confidence 8999987764443322211 222334444332 2233334444555666777766543
No 24
>PRK07353 F0F1 ATP synthase subunit B'; Validated
Probab=49.29 E-value=1e+02 Score=22.43 Aligned_cols=53 Identities=17% Similarity=0.160 Sum_probs=39.3
Q ss_pred hHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhh
Q 032335 80 FALREWRRENAIRLEEKEKKEKEMLNQIIEEAEEYKLEFYRKSIVTRENNKAS 132 (143)
Q Consensus 80 ~~LREWRRqNA~~LeeKEk~EKe~r~qII~eAEeyk~eFYeKR~~~~E~nK~~ 132 (143)
..|.++|.+-...+++-...-...+++|+.+|.+-.+..-+.=...++..+..
T Consensus 64 ~~L~~a~~ea~~i~~~a~~~a~~~~~~~~~~a~~ea~~~~~~a~~~i~~e~~~ 116 (140)
T PRK07353 64 QQLASARKQAQAVIAEAEAEADKLAAEALAEAQAEAQASKEKARREIEQQKQA 116 (140)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 35677887777777777777778888888888888888777666666655443
No 25
>PRK14472 F0F1 ATP synthase subunit B; Provisional
Probab=48.72 E-value=1.2e+02 Score=23.23 Aligned_cols=53 Identities=15% Similarity=0.087 Sum_probs=34.6
Q ss_pred hHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhh
Q 032335 80 FALREWRRENAIRLEEKEKKEKEMLNQIIEEAEEYKLEFYRKSIVTRENNKAS 132 (143)
Q Consensus 80 ~~LREWRRqNA~~LeeKEk~EKe~r~qII~eAEeyk~eFYeKR~~~~E~nK~~ 132 (143)
..|.++|.+-...+++-.+.-...+++++.+|.+-....-+.=...++.-+..
T Consensus 77 ~~L~~a~~ea~~ii~~A~~~a~~~~~~~~~~A~~ea~~~~~~a~~~I~~e~~~ 129 (175)
T PRK14472 77 ELLAKADAEADKIIREGKEYAEKLRAEITEKAHTEAKKMIASAKEEIEQEKRR 129 (175)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 34666777666666666666667777777777777776666655555554443
No 26
>PRK13428 F0F1 ATP synthase subunit delta; Provisional
Probab=48.23 E-value=1.3e+02 Score=27.07 Aligned_cols=51 Identities=16% Similarity=0.138 Sum_probs=38.4
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhh
Q 032335 81 ALREWRRENAIRLEEKEKKEKEMLNQIIEEAEEYKLEFYRKSIVTRENNKA 131 (143)
Q Consensus 81 ~LREWRRqNA~~LeeKEk~EKe~r~qII~eAEeyk~eFYeKR~~~~E~nK~ 131 (143)
.|.++|.+-+.-+++-.+..+..+++|+.+|.+..+...+.=..+++..+.
T Consensus 61 ~L~~Ak~ea~~Ii~~A~~~A~~~~~~~~~~A~~ea~~i~~~a~~~Ie~ek~ 111 (445)
T PRK13428 61 AVEDAKAEAARVVEEAREDAERIAEQLRAQADAEAERIKVQGARQVQLLRA 111 (445)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 477888888888888888888888999999888888777655555554443
No 27
>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=48.10 E-value=14 Score=32.69 Aligned_cols=22 Identities=50% Similarity=1.085 Sum_probs=17.2
Q ss_pred CCCCCCCCCCCcchhhHHHHHHHH
Q 032335 65 GPILPPPSDMVPEEGFALREWRRE 88 (143)
Q Consensus 65 gpilPpP~em~~EEg~~LREWRRq 88 (143)
.++||||.....+. +|.+||.-
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 45999998876554 99999964
No 28
>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=45.64 E-value=1.2e+02 Score=22.23 Aligned_cols=52 Identities=23% Similarity=0.266 Sum_probs=36.4
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhh
Q 032335 81 ALREWRRENAIRLEEKEKKEKEMLNQIIEEAEEYKLEFYRKSIVTRENNKAS 132 (143)
Q Consensus 81 ~LREWRRqNA~~LeeKEk~EKe~r~qII~eAEeyk~eFYeKR~~~~E~nK~~ 132 (143)
.|.++|.+-+..+++-.+.-...+++|+.+|..-....-++=...+++.+..
T Consensus 55 ~l~~A~~ea~~i~~~a~~~a~~~~~~~~~~a~~e~~~~~~~a~~~i~~e~~~ 106 (147)
T TIGR01144 55 ILKEAKDEAQEIIENANKRGSEILEEAKAEAREEREKIKAQARAEIEAEKEQ 106 (147)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 4666777766677776777777788888888888777776666666555443
No 29
>PRK13460 F0F1 ATP synthase subunit B; Provisional
Probab=44.72 E-value=1.4e+02 Score=22.88 Aligned_cols=51 Identities=16% Similarity=0.156 Sum_probs=33.9
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhh
Q 032335 81 ALREWRRENAIRLEEKEKKEKEMLNQIIEEAEEYKLEFYRKSIVTRENNKA 131 (143)
Q Consensus 81 ~LREWRRqNA~~LeeKEk~EKe~r~qII~eAEeyk~eFYeKR~~~~E~nK~ 131 (143)
.|.+++.+-...+++-.+.-...+++|+.+|.+..+..-+.-...++..+.
T Consensus 76 ~l~~a~~ea~~ii~~A~~ea~~~~~~~~~~A~~ea~~~~~~a~~~ie~e~~ 126 (173)
T PRK13460 76 RLNSAKDEANAIVAEAKSDALKLKNKLLEETNNEVKAQKDQAVKEIELAKG 126 (173)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 466666666666666666667777778888877777766665555554443
No 30
>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=44.66 E-value=1.1e+02 Score=21.52 Aligned_cols=51 Identities=24% Similarity=0.231 Sum_probs=35.1
Q ss_pred hHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhh
Q 032335 80 FALREWRRENAIRLEEKEKKEKEMLNQIIEEAEEYKLEFYRKSIVTRENNK 130 (143)
Q Consensus 80 ~~LREWRRqNA~~LeeKEk~EKe~r~qII~eAEeyk~eFYeKR~~~~E~nK 130 (143)
..|.++|.+-...+++..+.-+..+.+++.+|+...+.-...=...+++.+
T Consensus 58 ~~l~~a~~ea~~i~~~a~~~a~~~~~~~~~ea~~~~~~~~~~a~~~i~~e~ 108 (132)
T PF00430_consen 58 EKLAEAREEAQEIIEEAKEEAEKEKEEILAEAEKEAERIIEQAEAEIEQEK 108 (132)
T ss_dssp HHHHHHHHHHCHHHHHHCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 356777777777777777777777778888887777776665555554443
No 31
>PF15466 DUF4635: Domain of unknown function (DUF4635)
Probab=42.70 E-value=1.1e+02 Score=24.55 Aligned_cols=44 Identities=34% Similarity=0.483 Sum_probs=38.7
Q ss_pred chhh-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 032335 77 EEGF-ALREWRRENAIRLEEKEKKEKEMLNQIIEEAEEYKLEFYR 120 (143)
Q Consensus 77 EEg~-~LREWRRqNA~~LeeKEk~EKe~r~qII~eAEeyk~eFYe 120 (143)
+||. +||-|-+.|---+-||=++|-.-+.|.+..-|...+.+..
T Consensus 82 eEPik~~r~WLkenLhvflEkLE~EvreLEQlV~DLE~WLDalLg 126 (135)
T PF15466_consen 82 EEPIKAIRNWLKENLHVFLEKLEKEVRELEQLVRDLEEWLDALLG 126 (135)
T ss_pred cchHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhC
Confidence 5554 7999999999999999999999999999999999988754
No 32
>COG0488 Uup ATPase components of ABC transporters with duplicated ATPase domains [General function prediction only]
Probab=42.31 E-value=80 Score=29.27 Aligned_cols=43 Identities=14% Similarity=0.121 Sum_probs=34.0
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 032335 82 LREWRRENAIRLEEKEKKEKEMLNQIIEEAEEYKLEFYRKSIVT 125 (143)
Q Consensus 82 LREWRRqNA~~LeeKEk~EKe~r~qII~eAEeyk~eFYeKR~~~ 125 (143)
.-.|.++.++.+ +.++++.+++++-+.+-+.+++.|...+...
T Consensus 235 y~~~~~~r~~~~-~~~~~~~~~~~~~~~~~~~~i~r~~~~~~~~ 277 (530)
T COG0488 235 YSSYLEQKAERL-RQEAAAYEKQQKELAKEQEWIRRGKAAASKA 277 (530)
T ss_pred HHHHHHHHHHHH-HHHHHHHHHHHHHHHHHHHHHHHHHhccchH
Confidence 346888888777 6666667778888888999999999888774
No 33
>PRK13461 F0F1 ATP synthase subunit B; Provisional
Probab=41.54 E-value=1.5e+02 Score=22.24 Aligned_cols=53 Identities=19% Similarity=0.246 Sum_probs=35.8
Q ss_pred hHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhh
Q 032335 80 FALREWRRENAIRLEEKEKKEKEMLNQIIEEAEEYKLEFYRKSIVTRENNKAS 132 (143)
Q Consensus 80 ~~LREWRRqNA~~LeeKEk~EKe~r~qII~eAEeyk~eFYeKR~~~~E~nK~~ 132 (143)
..|.++|.+-...+++-.+.-+..+++|+.+|..-.+..-++=...+++.+..
T Consensus 64 ~~l~~a~~ea~~ii~~a~~~a~~~~~~i~~~A~~ea~~~~~~a~~~i~~e~~~ 116 (159)
T PRK13461 64 RELKNAKEEGKKIVEEYKSKAENVYEEIVKEAHEEADLIIERAKLEAQREKEK 116 (159)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 34666666666666666666666788888888888877777666666554443
No 34
>COG3461 Uncharacterized conserved protein [Function unknown]
Probab=41.37 E-value=1e+02 Score=23.72 Aligned_cols=48 Identities=25% Similarity=0.272 Sum_probs=38.2
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH-----HHHhhhhhhhhhhhhh
Q 032335 91 IRLEEKEKKEKEMLNQIIEEAEEYKLEFYRKSIV-----TRENNKASNREREKST 140 (143)
Q Consensus 91 ~~LeeKEk~EKe~r~qII~eAEeyk~eFYeKR~~-----~~E~nK~~NREkEk~f 140 (143)
.+|-+|.+.=..+|+-+|+++|.- .||..|.. .+..-+.+||+.|+..
T Consensus 10 eeLs~kirdf~Ra~~SLiEEiEA~--~wY~qR~~~tKD~~~r~ImehnrdeE~eH 62 (103)
T COG3461 10 EELSEKIRDFSRARQSLIEEIEAM--MWYDQRADATKDEDLRAIMEHNRDEEKEH 62 (103)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHH--HHHHHHhhccccHhHHHHHHHcccHHHHH
Confidence 467788888889999999999874 79999964 3445567899998864
No 35
>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=41.28 E-value=1.2e+02 Score=22.75 Aligned_cols=40 Identities=30% Similarity=0.297 Sum_probs=29.8
Q ss_pred cchhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 032335 76 PEEGFALREWRRENAIRLEEKEKKEKEMLNQIIEEAEEYK 115 (143)
Q Consensus 76 ~EEg~~LREWRRqNA~~LeeKEk~EKe~r~qII~eAEeyk 115 (143)
+.|-.-+|++-+++-..|++|-+.+.+...+=|++-++.|
T Consensus 60 A~E~~Y~r~~EkEqL~~Lk~kl~~e~~~~~k~i~~le~~I 99 (100)
T PF04568_consen 60 AQEEQYFRKKEKEQLKKLKEKLKEEIEHHRKEIDELEKHI 99 (100)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred hhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhc
Confidence 4677778888888888888888777777777777666655
No 36
>KOG3088 consensus Secretory carrier membrane protein [Intracellular trafficking, secretion, and vesicular transport]
Probab=40.76 E-value=1.7e+02 Score=26.24 Aligned_cols=7 Identities=14% Similarity=0.534 Sum_probs=3.7
Q ss_pred ccCCcch
Q 032335 16 THSFDDT 22 (143)
Q Consensus 16 ~~~fd~~ 22 (143)
+.+|+|.
T Consensus 6 ~NPFadp 12 (313)
T KOG3088|consen 6 PNPFAEP 12 (313)
T ss_pred CCCCCCc
Confidence 3456554
No 37
>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=40.38 E-value=90 Score=24.02 Aligned_cols=33 Identities=24% Similarity=0.533 Sum_probs=19.8
Q ss_pred CCCCCCCCCCcchhhHHHHHHHHHHHH-HHHHHHHHHHHHH
Q 032335 66 PILPPPSDMVPEEGFALREWRRENAIR-LEEKEKKEKEMLN 105 (143)
Q Consensus 66 pilPpP~em~~EEg~~LREWRRqNA~~-LeeKEk~EKe~r~ 105 (143)
-+|++|-.|. +.||+.....+ | +.+.+|++++-
T Consensus 41 Eai~ap~g~~------~kE~~e~k~~~~l-~~e~~ERe~~r 74 (118)
T PF07768_consen 41 EAIEAPYGMR------RKEYKERKKMERL-EQERRERELER 74 (118)
T ss_pred HHhccccccc------HHHHHHHHHHHHH-HHHHHHHHHHH
Confidence 3677888776 57787766555 4 33444444433
No 38
>PF07139 DUF1387: Protein of unknown function (DUF1387); InterPro: IPR009816 This family represents a conserved region approximately 300 residues long within a number of hypothetical proteins of unknown function that seem to be restricted to mammals.
Probab=39.39 E-value=1.1e+02 Score=27.21 Aligned_cols=51 Identities=16% Similarity=0.208 Sum_probs=42.8
Q ss_pred chhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 032335 77 EEGFALREWRRENAIRLEEKEKKEKEMLNQIIEEAEEYKLEFYRKSIVTRE 127 (143)
Q Consensus 77 EEg~~LREWRRqNA~~LeeKEk~EKe~r~qII~eAEeyk~eFYeKR~~~~E 127 (143)
+|...|-.+|.+.|++|+..-...-.|-+.=+.+--.-|+.|...|+.--|
T Consensus 214 ~EAmeiL~aRqkkAeeLkrltd~A~~MsE~Ql~ELRadIK~fvs~rk~de~ 264 (302)
T PF07139_consen 214 AEAMEILDARQKKAEELKRLTDRASQMSEEQLAELRADIKHFVSERKYDEE 264 (302)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHhhcCHHHHHHHHHHHHHHhhhhhhHHH
Confidence 677888899999999999988888888888788888888999999886543
No 39
>PRK14473 F0F1 ATP synthase subunit B; Provisional
Probab=38.06 E-value=1.7e+02 Score=22.00 Aligned_cols=51 Identities=16% Similarity=0.197 Sum_probs=33.0
Q ss_pred hHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhh
Q 032335 80 FALREWRRENAIRLEEKEKKEKEMLNQIIEEAEEYKLEFYRKSIVTRENNK 130 (143)
Q Consensus 80 ~~LREWRRqNA~~LeeKEk~EKe~r~qII~eAEeyk~eFYeKR~~~~E~nK 130 (143)
..|.++|.+-...+++-.+.-+..+++|+.+|..-....-+.=...+++.+
T Consensus 67 ~~l~~A~~ea~~ii~~A~~~a~~~~~~~l~~A~~ea~~~~~~a~~~I~~ek 117 (164)
T PRK14473 67 AELAKARQEAAKIVAQAQERARAQEAEIIAQARREAEKIKEEARAQAEQER 117 (164)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 356677777666666666666667778888777777666655444444433
No 40
>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=36.87 E-value=83 Score=24.69 Aligned_cols=34 Identities=29% Similarity=0.474 Sum_probs=28.2
Q ss_pred HHHH----HHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 032335 83 REWR----RENAIRLEEKEKKEKEMLNQIIEEAEEYKL 116 (143)
Q Consensus 83 REWR----RqNA~~LeeKEk~EKe~r~qII~eAEeyk~ 116 (143)
=-|| +-...+|+.=|+++..++.+|+..-..++-
T Consensus 67 la~r~~~l~~~~~~L~~Le~r~e~Lk~~~~~~~~~~~~ 104 (120)
T PF04521_consen 67 LAWRHAQLSDLNLELEKLERREEQLKTQIQVLTAAAKL 104 (120)
T ss_pred HHHhhhhhhhHHHHHHHHHHHHHHHHHHHHHHHHHhhH
Confidence 3588 888899999999999999999986655543
No 41
>COG2914 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=34.87 E-value=24 Score=26.89 Aligned_cols=21 Identities=38% Similarity=0.588 Sum_probs=15.9
Q ss_pred CCCCCCCCCCCcchhhHHHHHHHHHHHHHHHH
Q 032335 65 GPILPPPSDMVPEEGFALREWRRENAIRLEEK 96 (143)
Q Consensus 65 gpilPpP~em~~EEg~~LREWRRqNA~~LeeK 96 (143)
+|+|-.| +|||||+|..-++.
T Consensus 75 RPLlaDP-----------KE~RR~Ra~~~~~~ 95 (99)
T COG2914 75 RPLLADP-----------KEARRKRAERAAAA 95 (99)
T ss_pred cccccCh-----------HHHHHHHHHHHHHh
Confidence 6777666 68999999876543
No 42
>PRK05759 F0F1 ATP synthase subunit B; Validated
Probab=33.61 E-value=2e+02 Score=21.23 Aligned_cols=49 Identities=22% Similarity=0.250 Sum_probs=28.8
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhh
Q 032335 81 ALREWRRENAIRLEEKEKKEKEMLNQIIEEAEEYKLEFYRKSIVTRENN 129 (143)
Q Consensus 81 ~LREWRRqNA~~LeeKEk~EKe~r~qII~eAEeyk~eFYeKR~~~~E~n 129 (143)
.|.+++.+-...+++-...-+..+++|+..|.+-...-.++-...+++.
T Consensus 64 ~l~~a~~ea~~i~~~a~~ea~~~~~~~~~~a~~ea~~~~~~a~~~i~~e 112 (156)
T PRK05759 64 QLAEARAEAAEIIEQAKKRAAQIIEEAKAEAEAEAARIKAQAQAEIEQE 112 (156)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 4556666666666666666666666666666666655555544444443
No 43
>TIGR01069 mutS2 MutS2 family protein. Function of MutS2 is unknown. It should not be considered a DNA mismatch repair protein. It is likely a DNA mismatch binding protein of unknown cellular function.
Probab=31.30 E-value=2.9e+02 Score=26.78 Aligned_cols=39 Identities=18% Similarity=0.003 Sum_probs=19.4
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 032335 85 WRRENAIRLEEKEKKEKEMLNQIIEEAEEYKLEFYRKSI 123 (143)
Q Consensus 85 WRRqNA~~LeeKEk~EKe~r~qII~eAEeyk~eFYeKR~ 123 (143)
..++...+|+++.++-++.+.+|+.+|.+-..+.+++=+
T Consensus 540 e~~~~~~~l~~~~~~l~~~~~~~~~~a~~ea~~~~~~a~ 578 (771)
T TIGR01069 540 EQEKLKKELEQEMEELKERERNKKLELEKEAQEALKALK 578 (771)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 333334445555555455566666555555555444433
No 44
>COG2825 HlpA Outer membrane protein [Cell envelope biogenesis, outer membrane]
Probab=30.48 E-value=2.5e+02 Score=22.25 Aligned_cols=42 Identities=10% Similarity=0.168 Sum_probs=36.0
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 032335 81 ALREWRRENAIRLEEKEKKEKEMLNQIIEEAEEYKLEFYRKS 122 (143)
Q Consensus 81 ~LREWRRqNA~~LeeKEk~EKe~r~qII~eAEeyk~eFYeKR 122 (143)
...+|++++..-=+...+++.+.++.++++....+..+.++.
T Consensus 98 ~~~~~~~k~~~~~~~~~~~~~e~~~~~~~~i~~ai~~~a~~~ 139 (170)
T COG2825 98 LVNAFNKKQQEYEKDLNRREAEEEQKLLEKIQRAIESVAEKG 139 (170)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhC
Confidence 667888888888888888899999999999999988887765
No 45
>KOG4752 consensus Ribosomal protein L41 [Translation, ribosomal structure and biogenesis]
Probab=28.46 E-value=94 Score=18.62 Aligned_cols=20 Identities=30% Similarity=0.685 Sum_probs=15.8
Q ss_pred HHHHHHHHHHHHHHHHHHHH
Q 032335 83 REWRRENAIRLEEKEKKEKE 102 (143)
Q Consensus 83 REWRRqNA~~LeeKEk~EKe 102 (143)
-.||.+....|+.|.++-+.
T Consensus 3 ~kwrkkrmrrlkrkrr~~~~ 22 (26)
T KOG4752|consen 3 AKWRKKRMRRLKRKRRKMRA 22 (26)
T ss_pred hHHHHHHHHHHHHHHHHHHh
Confidence 36999999999888776554
No 46
>PF10675 DUF2489: Protein of unknown function (DUF2489); InterPro: IPR019617 This entry represents bacterial uncharacterised proteins.
Probab=28.27 E-value=1.5e+02 Score=22.74 Aligned_cols=32 Identities=16% Similarity=0.358 Sum_probs=21.2
Q ss_pred hhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 032335 79 GFALREWRRENAIRLEEKEKKEKEMLNQIIEE 110 (143)
Q Consensus 79 g~~LREWRRqNA~~LeeKEk~EKe~r~qII~e 110 (143)
+.+|+.-++|+....++.+..-++++..|++.
T Consensus 9 ~~Ll~~l~~q~~~~~~~~~~~~~~r~~~i~eS 40 (131)
T PF10675_consen 9 GYLLLKLKKQKEEQQQQQAQAIQERRARILES 40 (131)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 34566677777666666666677777777553
No 47
>PRK00026 trmD tRNA (guanine-N(1)-)-methyltransferase; Reviewed
Probab=27.93 E-value=98 Score=26.66 Aligned_cols=36 Identities=17% Similarity=0.416 Sum_probs=23.8
Q ss_pred CCCCCCcchhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 032335 70 PPSDMVPEEGFALREWRRENAIRLEEKEKKEKEMLNQIIEEA 111 (143)
Q Consensus 70 pP~em~~EEg~~LREWRRqNA~~LeeKEk~EKe~r~qII~eA 111 (143)
.|+-+-.---..|.+||+++++. +.+.+|-+++..+
T Consensus 192 VP~VLlSGnH~~I~~WR~~~sl~------~T~~~RPDL~~~~ 227 (244)
T PRK00026 192 VPEVLLSGNHAKIARWRRKQSLE------RTKLRRPDLLEKL 227 (244)
T ss_pred CcccccCCCHHHHHHHHHHHHHH------HHHHhChhHHhhc
Confidence 45555444567899999999875 3455566665543
No 48
>PRK13455 F0F1 ATP synthase subunit B; Provisional
Probab=27.02 E-value=3e+02 Score=21.27 Aligned_cols=34 Identities=12% Similarity=0.081 Sum_probs=13.9
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 032335 82 LREWRRENAIRLEEKEKKEKEMLNQIIEEAEEYK 115 (143)
Q Consensus 82 LREWRRqNA~~LeeKEk~EKe~r~qII~eAEeyk 115 (143)
|.++|.+-+.-+++-.++-...+++++.+|..-.
T Consensus 88 L~~A~~ea~~Ii~~A~~~a~~~~e~~~~~a~~ea 121 (184)
T PRK13455 88 QREVQEQADRIVAAAKDEAQAAAEQAKADLEASI 121 (184)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 3444444444444333333333444444444433
No 49
>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=26.68 E-value=4.2e+02 Score=24.22 Aligned_cols=49 Identities=20% Similarity=0.346 Sum_probs=33.1
Q ss_pred chhhHHHHHHHHHHHHHHHHHHHHH---HHHHHHHHHHHHHHHHHHHHHHHH
Q 032335 77 EEGFALREWRRENAIRLEEKEKKEK---EMLNQIIEEAEEYKLEFYRKSIVT 125 (143)
Q Consensus 77 EEg~~LREWRRqNA~~LeeKEk~EK---e~r~qII~eAEeyk~eFYeKR~~~ 125 (143)
+......+|..+-...++..-+.-- .++.+-|.+.+.-+.++|++|...
T Consensus 340 ~q~~~f~~W~~~rq~~~~~q~~~l~~~~~~~~~rl~~ie~~~~~l~e~e~~l 391 (429)
T PF10037_consen 340 EQCERFQEWEEKRQSLLKEQSERLLTLTQLRKERLEEIEKEDKELYEQEQQL 391 (429)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHhhhHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 4455667999887777665443322 346777788888888888877653
No 50
>PF06528 Phage_P2_GpE: Phage P2 GpE; InterPro: IPR009493 This entry is represented by Burkholderia phage phiE202, Gp27. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. This family consists of several phage and bacterial proteins which are closely related to the GpE tail protein from Phage P2.
Probab=26.17 E-value=27 Score=22.40 Aligned_cols=24 Identities=33% Similarity=0.488 Sum_probs=17.5
Q ss_pred CCCCCCcchhhHHHHHHHHHHHHH
Q 032335 70 PPSDMVPEEGFALREWRRENAIRL 93 (143)
Q Consensus 70 pP~em~~EEg~~LREWRRqNA~~L 93 (143)
||++|.+=.-.-|.+||.|-..+.
T Consensus 11 ~Pse~~~m~l~El~~Wre~A~~R~ 34 (39)
T PF06528_consen 11 PPSEMDAMSLDELMDWRERARRRS 34 (39)
T ss_pred CHHHHhcCCHHHHHHHHHHHHHHh
Confidence 577777666677899998855543
No 51
>PF11831 Myb_Cef: pre-mRNA splicing factor component; InterPro: IPR021786 This domain is functionally uncharacterised. This domain is found in bacteria. This presumed domain is typically between 73 to 279 amino acids in length.
Probab=26.07 E-value=1.5e+02 Score=24.42 Aligned_cols=23 Identities=26% Similarity=0.352 Sum_probs=15.8
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHH
Q 032335 87 RENAIRLEEKEKKEKEMLNQIIE 109 (143)
Q Consensus 87 RqNA~~LeeKEk~EKe~r~qII~ 109 (143)
++.+++.+++++++..+|.|+|.
T Consensus 109 ~r~~~~~~~~e~~e~~rRSqvvQ 131 (231)
T PF11831_consen 109 ARERAEREEEEEKELKRRSQVVQ 131 (231)
T ss_pred HHHHHHHHHHHHHHHHHhhHHHH
Confidence 34455667777778888888764
No 52
>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=25.73 E-value=1.1e+02 Score=25.22 Aligned_cols=34 Identities=32% Similarity=0.565 Sum_probs=25.7
Q ss_pred chhhHHHHHHHHHHHHHHHHHHHHH-HHHHHHHHHHHH
Q 032335 77 EEGFALREWRRENAIRLEEKEKKEK-EMLNQIIEEAEE 113 (143)
Q Consensus 77 EEg~~LREWRRqNA~~LeeKEk~EK-e~r~qII~eAEe 113 (143)
||-.+|-|.|+ |++.+|||+-| .=++++|..|++
T Consensus 1 EEe~Li~ELrK---IE~RKkEREKK~qDLqkLit~ad~ 35 (176)
T PF05499_consen 1 EEEMLIAELRK---IEARKKEREKKTQDLQKLITAADQ 35 (176)
T ss_pred CHHHHHHHHHH---HHHHHHHHHHHHHHHHHHHhhccc
Confidence 46667777764 78888888777 467889999884
No 53
>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=24.30 E-value=1.3e+02 Score=21.34 Aligned_cols=51 Identities=14% Similarity=0.106 Sum_probs=26.4
Q ss_pred CCCCCCCCCCCcchhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 032335 65 GPILPPPSDMVPEEGFALREWRRENAIRLEEKEKKEKEMLNQIIEEAEEYKLEFYRKS 122 (143)
Q Consensus 65 gpilPpP~em~~EEg~~LREWRRqNA~~LeeKEk~EKe~r~qII~eAEeyk~eFYeKR 122 (143)
++.+.++++|+ .+|..+..+-....+ ++.++.-.+.+.+++.|+.+|-.+.
T Consensus 61 ~~~~l~~~e~~----~~l~~~~~~~~~~~~---~~~~~~~~~~~~~~~~fla~n~k~~ 111 (124)
T PF01346_consen 61 KKPKLSDEEAQ----EALQAFQQKMQAKQQ---EKMAKAAEKNKAEGEAFLAENAKKE 111 (124)
T ss_dssp T--SS-HHHHH----HHHHHHHHHHHHHHH---HHHHHHHHHHHHHHHHHHHHHHTST
T ss_pred CCcCCCHHHHH----HHHHHHHHHHHHHhh---cchhhhhhhhHHHHHHHHHHHcCCC
Confidence 34444444443 344454444333333 3344556677788888888876553
No 54
>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=24.14 E-value=1.8e+02 Score=23.83 Aligned_cols=54 Identities=15% Similarity=0.182 Sum_probs=36.2
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhhhh
Q 032335 81 ALREWRRENAIRLEEKEKKEKEMLNQIIEEAEEYKLEFYRKSIVTRENNKASNR 134 (143)
Q Consensus 81 ~LREWRRqNA~~LeeKEk~EKe~r~qII~eAEeyk~eFYeKR~~~~E~nK~~NR 134 (143)
-+.+|..+-+.+=++-+++.++++.+-..+-++|-.++=++...++..|+....
T Consensus 117 Wre~~~~~i~ekD~~e~~kk~e~~~~A~k~lddfY~~~~~k~e~~k~~nr~~ee 170 (225)
T PF01086_consen 117 WREERDKRIEEKDAEEEEKKEEIKEKAKKELDDFYENRNEKKEKNKKQNREEEE 170 (225)
T ss_dssp HHHHHTTTSTHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTT-----
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 334444444444445555666788888899999999999999999999988754
No 55
>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=22.96 E-value=40 Score=28.24 Aligned_cols=41 Identities=20% Similarity=0.373 Sum_probs=27.6
Q ss_pred hccCCCCCCCCCCCcc-C---CCcccc-CCccCCCCCCCCCCCCCCC
Q 032335 28 SAVDLSDDNNNSSFQS-G---DDAFAS-QTSVYGEYADGGSDGPILP 69 (143)
Q Consensus 28 ~~~g~~~~~~~~~~~~-~---dd~f~s-~~~~~~~~~ng~~dgpilP 69 (143)
||+-|-. +|++..++ | .++|+. |--.|=|..+|+.++|-.|
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 5555544 77766555 3 678876 4456778888877787755
No 56
>PRK00409 recombination and DNA strand exchange inhibitor protein; Reviewed
Probab=22.88 E-value=5e+02 Score=25.18 Aligned_cols=30 Identities=33% Similarity=0.440 Sum_probs=13.7
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 032335 92 RLEEKEKKEKEMLNQIIEEAEEYKLEFYRK 121 (143)
Q Consensus 92 ~LeeKEk~EKe~r~qII~eAEeyk~eFYeK 121 (143)
+|+++.++=++.+.+|+.+|.+--.+.+++
T Consensus 552 ~l~~~~~~l~~~~~~~~~~~~~~a~~~l~~ 581 (782)
T PRK00409 552 ELEEKKEKLQEEEDKLLEEAEKEAQQAIKE 581 (782)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 344444444444555555554444444433
No 57
>KOG1318 consensus Helix loop helix transcription factor EB [Transcription]
Probab=22.86 E-value=6.1e+02 Score=23.46 Aligned_cols=23 Identities=22% Similarity=0.271 Sum_probs=17.3
Q ss_pred HHHHHHHHHHHHHHHHHHHHHhh
Q 032335 107 IIEEAEEYKLEFYRKSIVTRENN 129 (143)
Q Consensus 107 II~eAEeyk~eFYeKR~~~~E~n 129 (143)
|++.+-+||.+.-++++...|.-
T Consensus 274 ILk~s~dYIr~Lqq~~q~~~E~~ 296 (411)
T KOG1318|consen 274 ILKASCDYIRELQQTLQRARELE 296 (411)
T ss_pred hhHHHHHHHHHHHHHHHHHHHHH
Confidence 66788999999888777555543
No 58
>PF15046 DUF4532: Protein of unknown function (DUF4532)
Probab=22.85 E-value=83 Score=27.81 Aligned_cols=40 Identities=35% Similarity=0.334 Sum_probs=21.8
Q ss_pred CCCCCCCCCCCCCc-------chhhH-HHHHHHHHHHHHHHHHHHHHHH
Q 032335 63 SDGPILPPPSDMVP-------EEGFA-LREWRRENAIRLEEKEKKEKEM 103 (143)
Q Consensus 63 ~dgpilPpP~em~~-------EEg~~-LREWRRqNA~~LeeKEk~EKe~ 103 (143)
..+|| |||+-|+. .++-+ +-.=||.+.|.--.||-+|-++
T Consensus 111 a~~PI-PPPSwMG~NTfl~FI~~~pif~D~~rK~qvI~rt~KELkE~~k 158 (279)
T PF15046_consen 111 AEPPI-PPPSWMGDNTFLKFISCTPIFVDPNRKNQVILRTVKELKEFEK 158 (279)
T ss_pred cCCCC-CChhhcCcchhhhhhhcccceechhhhhHHHHHHHHHHhhhHh
Confidence 34675 99999985 22222 2334455555555555555433
No 59
>KOG3184 consensus 60S ribosomal protein L7 [Translation, ribosomal structure and biogenesis]
Probab=22.79 E-value=2.2e+02 Score=24.17 Aligned_cols=46 Identities=17% Similarity=0.199 Sum_probs=37.5
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 032335 82 LREWRRENAIRLEEKEKKEKEMLNQIIEEAEEYKLEFYRKSIVTRE 127 (143)
Q Consensus 82 LREWRRqNA~~LeeKEk~EKe~r~qII~eAEeyk~eFYeKR~~~~E 127 (143)
..+++.+.+...-++.+..|..+..+...|+.|..+|+..+...+.
T Consensus 11 ~~~~~~~~~~~~~~~k~~~k~~~~~~~~~~e~~~~~~~~~~r~~i~ 56 (235)
T KOG3184|consen 11 QAELATQALRKLLAKKEIRKKKRKLFLKKAKHYHKEYRQKYRTEIR 56 (235)
T ss_pred HHHHHHHHHHHHHHHHHHHhccchhHHHHHHHHHHHHHhhhhHHHH
Confidence 5677888888888888888888999999999999999887665543
No 60
>PF04304 DUF454: Protein of unknown function (DUF454); InterPro: IPR007401 This is a predicted membrane protein.
Probab=21.76 E-value=42 Score=22.12 Aligned_cols=21 Identities=24% Similarity=0.479 Sum_probs=16.7
Q ss_pred hhHHHHHHHHHHHHHHHHHHH
Q 032335 79 GFALREWRRENAIRLEEKEKK 99 (143)
Q Consensus 79 g~~LREWRRqNA~~LeeKEk~ 99 (143)
|-.|++|+++.++-++.|=..
T Consensus 12 g~~I~~w~~~r~i~~k~K~~a 32 (71)
T PF04304_consen 12 GPYIRNWEEHRGIPRKAKIRA 32 (71)
T ss_pred HHHHHHHHHCCCcCHHHHHHH
Confidence 456899999999998887543
No 61
>PRK09510 tolA cell envelope integrity inner membrane protein TolA; Provisional
Probab=21.73 E-value=6e+02 Score=23.14 Aligned_cols=28 Identities=25% Similarity=0.616 Sum_probs=14.6
Q ss_pred CCCCCCCCCCCCCCCcchhhHHHHHHHHHHH
Q 032335 61 GGSDGPILPPPSDMVPEEGFALREWRRENAI 91 (143)
Q Consensus 61 g~~dgpilPpP~em~~EEg~~LREWRRqNA~ 91 (143)
||++|+++. .-|. +-|.+.-+|-|++..
T Consensus 43 gg~~g~~i~--AVmv-D~~~v~~q~~~~q~q 70 (387)
T PRK09510 43 GGGGGSVID--AVMV-DPGAVVEQYNRQQQQ 70 (387)
T ss_pred CCCCccccc--ceec-ChHHHHHHHHHHHHh
Confidence 344555431 2233 566777777665443
No 62
>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=21.62 E-value=3.9e+02 Score=20.69 Aligned_cols=33 Identities=30% Similarity=0.319 Sum_probs=16.9
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 032335 86 RRENAIRLEEKEKKEKEMLNQIIEEAEEYKLEF 118 (143)
Q Consensus 86 RRqNA~~LeeKEk~EKe~r~qII~eAEeyk~eF 118 (143)
|+++...++++.++-++...+-..+|++.+..-
T Consensus 4 ~~~~~~~~~~~r~~~~~~~~~~r~eA~~~~~lm 36 (151)
T PF11875_consen 4 RRRKKREIEEQREKNKEEIAEKRAEAESAIELM 36 (151)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 344444455555555555555555666555443
No 63
>PF13904 DUF4207: Domain of unknown function (DUF4207)
Probab=21.57 E-value=4e+02 Score=22.26 Aligned_cols=29 Identities=21% Similarity=0.329 Sum_probs=19.5
Q ss_pred CCCCCCCcchhhHHHHHHHHHHHHHHHHH
Q 032335 69 PPPSDMVPEEGFALREWRRENAIRLEEKE 97 (143)
Q Consensus 69 PpP~em~~EEg~~LREWRRqNA~~LeeKE 97 (143)
|++.....+=-..+.+|.++..++++++-
T Consensus 173 ~~~~~~~e~a~~~~q~W~~kK~~e~~~~r 201 (264)
T PF13904_consen 173 PEREVSQEEAKQRYQEWERKKKEEQQQKR 201 (264)
T ss_pred cccccCHHHHHHHHHHHHHHHHHHHHHHH
Confidence 55555553334899999998887766553
No 64
>PHA00452 T3/T7-like RNA polymerase
Probab=21.36 E-value=2.2e+02 Score=28.08 Aligned_cols=40 Identities=25% Similarity=0.389 Sum_probs=26.1
Q ss_pred chhhHHHHHHHHHHH-HHHHHHHHHHHHH-HHHHHHHHHHHH
Q 032335 77 EEGFALREWRRENAI-RLEEKEKKEKEML-NQIIEEAEEYKL 116 (143)
Q Consensus 77 EEg~~LREWRRqNA~-~LeeKEk~EKe~r-~qII~eAEeyk~ 116 (143)
+....++.|+++.+. .-+.++..++.+. ..+++-|..|++
T Consensus 334 ~~~~~~~~wk~~~~~~~~~~~~~~S~r~~~~~~l~iA~~f~~ 375 (807)
T PHA00452 334 ENEEAFKAWKRAAAAWYTKEKERVSKRRRLEFMLRVANKFAD 375 (807)
T ss_pred cCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcC
Confidence 445789999987543 3344555555554 446677888876
No 65
>PF10669 Phage_Gp23: Protein gp23 (Bacteriophage A118); InterPro: IPR018926 This entry is represented by the major tail subunit protein, Gp23 of Listeria phage A118 and prophage found in Bacilli. The function is currently unknown.
Probab=21.15 E-value=2.4e+02 Score=22.14 Aligned_cols=28 Identities=11% Similarity=0.226 Sum_probs=12.1
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 032335 86 RRENAIRLEEKEKKEKEMLNQIIEEAEE 113 (143)
Q Consensus 86 RRqNA~~LeeKEk~EKe~r~qII~eAEe 113 (143)
|.+-.++-++|++++++-|++.|..-++
T Consensus 52 R~K~E~~~q~r~rES~~Er~K~~~s~~~ 79 (121)
T PF10669_consen 52 RSKKEEKRQKRNRESKRERQKFIWSMNK 79 (121)
T ss_pred HHHHHHHHHHHhhhhHHHHHhHHhhhhH
Confidence 3333334444444444444444444443
No 66
>TIGR02606 antidote_CC2985 putative addiction module antidote protein, CC2985 family. This bacterial protein family has a very similar seed alignment to that of Pfam model pfam03693 but is a more stringent model with higher cutoff scores. Proteins that score above the trusted cutoff to this model almost invariably are found adjacent to a ParE family protein (pfam05016), where ParE is the killing partner of an addiction module for plasmid stabilization. Members of this family, therefore, are putative addiction module antidote proteins. Some are encoded on plasmids or in prophage regions, but others appear chromosomal. A genome may contain several identical copies, such as the four in Magnetococcus sp. MC-1. This family is named for one member, CC2985 of Caulobacter crescentus CB15.
Probab=20.95 E-value=2.2e+02 Score=19.31 Aligned_cols=25 Identities=32% Similarity=0.347 Sum_probs=13.6
Q ss_pred hhHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 032335 79 GFALREWRRENAIRLEEKEKKEKEMLNQI 107 (143)
Q Consensus 79 g~~LREWRRqNA~~LeeKEk~EKe~r~qI 107 (143)
..++|+.-| .|++++.+..++|..|
T Consensus 27 SEVir~aLR----~le~~e~~~~~Lr~~i 51 (69)
T TIGR02606 27 SEVVRAALR----LLEERETKLQALRDAI 51 (69)
T ss_pred HHHHHHHHH----HHHHHHHHHHHHHHHH
Confidence 356666665 4455554455555554
No 67
>PF03993 DUF349: Domain of Unknown Function (DUF349); InterPro: IPR007139 This motif is found singly or as up to five tandem repeats in a small set of bacterial proteins. There are two or three alpha-helices, and possibly a beta-strand.
Probab=20.72 E-value=2.5e+02 Score=18.10 Aligned_cols=28 Identities=21% Similarity=0.166 Sum_probs=18.7
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 032335 89 NAIRLEEKEKKEKEMLNQIIEEAEEYKL 116 (143)
Q Consensus 89 NA~~LeeKEk~EKe~r~qII~eAEeyk~ 116 (143)
--..+.+....-.+.+..||++|+....
T Consensus 21 ~~~~~~~~~~~n~~~K~~Li~~~~~l~~ 48 (77)
T PF03993_consen 21 FFEEQDAEREENLEKKEALIEEAEALAE 48 (77)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHhcc
Confidence 3344555555667788888888877653
Done!