Query psy5990
Match_columns 119
No_of_seqs 102 out of 163
Neff 3.8
Searched_HMMs 46136
Date Fri Aug 16 23:45:58 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy5990.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/5990hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG2062|consensus 100.0 6.6E-44 1.4E-48 321.5 10.8 113 1-115 3-115 (929)
2 COG5116 RPN2 26S proteasome re 100.0 2.7E-35 5.9E-40 262.9 7.6 113 1-115 3-115 (926)
3 PF12895 Apc3: Anaphase-promot 85.8 1.1 2.3E-05 28.9 3.1 44 38-81 6-49 (84)
4 PF13646 HEAT_2: HEAT repeats; 82.0 2.7 5.9E-05 26.6 3.7 54 6-65 3-57 (88)
5 PF07719 TPR_2: Tetratricopept 79.0 1.8 3.9E-05 23.0 1.9 21 63-83 7-27 (34)
6 PF13432 TPR_16: Tetratricopep 78.8 8.6 0.00019 23.2 5.1 42 38-81 14-55 (65)
7 PF02985 HEAT: HEAT repeat; I 77.2 4.6 9.9E-05 22.3 3.2 27 5-31 3-29 (31)
8 PF10193 Telomere_reg-2: Telom 76.6 5.1 0.00011 28.8 4.1 61 6-66 7-79 (114)
9 PF13925 Katanin_con80: con80 72.7 6.1 0.00013 29.8 3.9 67 7-76 74-141 (164)
10 PF13181 TPR_8: Tetratricopept 72.4 4.5 9.7E-05 21.6 2.4 19 62-80 6-24 (34)
11 PF13424 TPR_12: Tetratricopep 70.0 9.6 0.00021 23.7 3.8 22 62-83 51-72 (78)
12 PF13646 HEAT_2: HEAT repeats; 69.9 22 0.00047 22.3 5.5 50 4-59 33-83 (88)
13 PF14853 Fis1_TPR_C: Fis1 C-te 66.6 3.9 8.4E-05 26.1 1.5 16 65-80 9-24 (53)
14 PRK10866 outer membrane biogen 64.0 46 0.00099 26.3 7.4 72 29-102 43-114 (243)
15 PF12755 Vac14_Fab1_bd: Vacuol 63.8 44 0.00095 23.3 6.5 58 5-62 30-91 (97)
16 PF12895 Apc3: Anaphase-promot 63.6 8.3 0.00018 24.7 2.6 22 58-79 59-80 (84)
17 PF01602 Adaptin_N: Adaptin N 62.6 25 0.00055 29.3 5.9 56 4-59 269-324 (526)
18 PF00515 TPR_1: Tetratricopept 62.4 5.6 0.00012 21.3 1.4 16 64-79 8-23 (34)
19 PF07539 DRIM: Down-regulated 61.9 15 0.00033 27.4 4.1 47 6-55 21-67 (141)
20 PF13374 TPR_10: Tetratricopep 61.4 7.4 0.00016 21.0 1.9 21 63-83 8-28 (42)
21 PF03810 IBN_N: Importin-beta 59.9 13 0.00028 23.2 3.0 32 5-36 17-50 (77)
22 cd00020 ARM Armadillo/beta-cat 59.8 44 0.00094 21.4 5.8 61 4-64 9-74 (120)
23 PF04733 Coatomer_E: Coatomer 59.7 6.3 0.00014 32.2 1.9 45 39-83 84-128 (290)
24 PF05131 Pep3_Vps18: Pep3/Vps1 59.5 6.4 0.00014 29.6 1.8 20 63-82 109-128 (147)
25 KOG3785|consensus 57.9 18 0.00038 32.8 4.5 54 58-113 58-111 (557)
26 PRK02603 photosystem I assembl 57.0 25 0.00053 25.5 4.4 32 52-83 67-98 (172)
27 PF09986 DUF2225: Uncharacteri 56.3 29 0.00062 27.4 5.0 43 38-80 142-188 (214)
28 PF13371 TPR_9: Tetratricopept 56.1 26 0.00056 21.3 3.9 42 33-79 10-51 (73)
29 smart00185 ARM Armadillo/beta- 55.7 23 0.00049 19.2 3.3 27 4-30 14-40 (41)
30 TIGR02795 tol_pal_ybgF tol-pal 55.4 37 0.00079 21.7 4.6 23 58-80 40-62 (119)
31 cd00864 PI3Ka Phosphoinositide 55.3 74 0.0016 23.8 6.9 58 3-63 70-129 (152)
32 PF13174 TPR_6: Tetratricopept 51.0 16 0.00034 18.9 2.0 20 61-80 4-23 (33)
33 PF13414 TPR_11: TPR repeat; P 50.6 19 0.00042 21.7 2.6 30 54-83 34-64 (69)
34 PF13176 TPR_7: Tetratricopept 50.4 12 0.00027 20.9 1.6 16 64-79 6-21 (36)
35 KOG3877|consensus 50.1 26 0.00056 30.8 4.1 76 38-116 127-211 (393)
36 PF14559 TPR_19: Tetratricopep 49.8 24 0.00053 21.1 3.0 43 39-83 9-51 (68)
37 PF09976 TPR_21: Tetratricopep 49.2 37 0.0008 23.9 4.2 43 38-80 65-108 (145)
38 KOG3364|consensus 49.2 30 0.00066 27.0 4.0 55 36-94 50-105 (149)
39 PF12717 Cnd1: non-SMC mitotic 49.1 53 0.0012 24.4 5.3 65 5-69 28-93 (178)
40 PF11815 DUF3336: Domain of un 47.4 60 0.0013 24.2 5.3 81 32-113 27-117 (145)
41 PF04826 Arm_2: Armadillo-like 47.1 88 0.0019 25.4 6.6 98 4-101 56-198 (254)
42 cd00872 PI3Ka_I Phosphoinositi 47.0 1.1E+02 0.0024 23.7 6.8 61 3-66 70-132 (171)
43 cd00020 ARM Armadillo/beta-cat 46.7 75 0.0016 20.3 6.0 59 4-62 51-114 (120)
44 PF09976 TPR_21: Tetratricopep 45.9 66 0.0014 22.6 5.1 47 31-79 24-70 (145)
45 PF00514 Arm: Armadillo/beta-c 45.6 46 0.00099 18.9 3.6 26 4-29 14-39 (41)
46 TIGR02521 type_IV_pilW type IV 42.2 67 0.0015 22.1 4.6 25 59-83 171-195 (234)
47 PRK13800 putative oxidoreducta 42.1 66 0.0014 30.2 5.7 54 4-63 623-676 (897)
48 PF11701 UNC45-central: Myosin 41.7 1E+02 0.0022 22.8 5.7 61 6-66 90-157 (157)
49 PF12348 CLASP_N: CLASP N term 40.6 1E+02 0.0023 23.0 5.7 71 7-77 136-215 (228)
50 PF07721 TPR_4: Tetratricopept 40.4 43 0.00093 17.6 2.7 20 60-79 4-23 (26)
51 smart00028 TPR Tetratricopepti 39.9 41 0.00089 15.3 2.5 19 63-81 7-25 (34)
52 smart00145 PI3Ka Phosphoinosit 38.3 1.8E+02 0.0038 22.6 6.8 58 5-65 77-136 (184)
53 PF13935 Ead_Ea22: Ead/Ea22-li 37.4 59 0.0013 23.9 3.9 61 4-64 66-129 (139)
54 PF14689 SPOB_a: Sensor_kinase 37.2 1.1E+02 0.0023 19.6 4.6 40 20-79 6-45 (62)
55 PRK13800 putative oxidoreducta 36.8 1.4E+02 0.0029 28.2 6.9 42 7-52 747-788 (897)
56 PHA00510 transcriptional regul 36.7 18 0.00038 27.3 1.0 34 6-39 78-114 (125)
57 PRK09687 putative lyase; Provi 36.5 99 0.0021 25.1 5.4 57 3-65 24-80 (280)
58 PF10579 Rapsyn_N: Rapsyn N-te 36.3 26 0.00057 24.6 1.8 21 62-82 48-68 (80)
59 TIGR02521 type_IV_pilW type IV 35.5 88 0.0019 21.5 4.3 26 58-83 66-91 (234)
60 TIGR03302 OM_YfiO outer membra 34.2 87 0.0019 23.2 4.4 34 54-87 200-233 (235)
61 PF04826 Arm_2: Armadillo-like 33.9 2.6E+02 0.0056 22.7 7.9 35 14-48 107-143 (254)
62 PF13513 HEAT_EZ: HEAT-like re 32.7 72 0.0016 18.8 3.1 22 6-27 32-53 (55)
63 COG5096 Vesicle coat complex, 32.7 1.5E+02 0.0032 28.5 6.5 71 8-81 98-175 (757)
64 PRK00736 hypothetical protein; 32.5 99 0.0021 20.5 4.0 32 17-48 15-46 (68)
65 PF12719 Cnd3: Nuclear condens 32.4 2.1E+02 0.0046 23.0 6.6 103 8-114 70-188 (298)
66 KOG2019|consensus 31.2 43 0.00094 32.6 2.8 28 20-47 732-759 (998)
67 cd00189 TPR Tetratricopeptide 29.4 1.1E+02 0.0023 17.0 4.1 26 58-83 35-60 (100)
68 PF01602 Adaptin_N: Adaptin N 28.1 1.6E+02 0.0034 24.6 5.3 58 9-69 86-144 (526)
69 PF13133 DUF3949: Protein of u 28.1 55 0.0012 22.2 2.2 23 45-67 24-58 (62)
70 PF10363 DUF2435: Protein of u 27.9 66 0.0014 22.3 2.6 38 6-44 7-44 (92)
71 PRK09687 putative lyase; Provi 27.8 1.7E+02 0.0038 23.7 5.4 58 4-65 161-218 (280)
72 PF13428 TPR_14: Tetratricopep 27.6 79 0.0017 18.1 2.6 18 63-80 7-24 (44)
73 PF05464 Phi-29_GP4: Phi-29-li 27.4 11 0.00023 28.5 -1.5 34 6-39 78-114 (125)
74 PF13429 TPR_15: Tetratricopep 27.1 1.2E+02 0.0026 23.3 4.2 48 32-82 124-171 (280)
75 PF04102 SlyX: SlyX; InterPro 26.8 1.5E+02 0.0033 19.4 4.1 33 17-49 14-46 (69)
76 PF00613 PI3Ka: Phosphoinositi 26.3 3E+02 0.0066 21.1 6.5 58 3-63 76-135 (184)
77 PRK02119 hypothetical protein; 25.9 1.5E+02 0.0032 19.9 4.0 32 17-48 19-50 (73)
78 PF09295 ChAPs: ChAPs (Chs5p-A 25.6 66 0.0014 28.0 2.8 36 64-102 275-310 (395)
79 PRK00295 hypothetical protein; 25.0 1.6E+02 0.0035 19.4 4.0 32 17-48 15-46 (68)
80 PF11817 Foie-gras_1: Foie gra 24.6 83 0.0018 24.8 3.0 25 63-87 184-208 (247)
81 PF10020 DUF2262: Uncharacteri 24.1 57 0.0012 23.9 1.8 34 5-39 53-86 (150)
82 KOG1130|consensus 22.8 39 0.00085 31.2 0.9 15 65-79 63-77 (639)
83 COG2909 MalT ATP-dependent tra 22.8 3.4E+02 0.0073 26.8 7.0 75 10-86 265-376 (894)
84 PRK02793 phi X174 lysis protei 22.7 1.2E+02 0.0026 20.3 3.1 32 17-48 18-49 (72)
85 PF05004 IFRD: Interferon-rela 22.7 2.8E+02 0.006 23.0 5.8 67 5-71 46-118 (309)
86 PRK04406 hypothetical protein; 22.0 1.2E+02 0.0027 20.5 3.1 32 17-48 21-52 (75)
87 TIGR03302 OM_YfiO outer membra 21.8 3.3E+02 0.0072 20.0 5.7 58 32-91 47-104 (235)
88 PF03368 Dicer_dimer: Dicer di 21.8 61 0.0013 22.1 1.5 23 55-77 59-81 (90)
89 PRK00846 hypothetical protein; 21.3 2E+02 0.0043 19.9 4.0 33 17-49 23-55 (77)
90 PF05757 PsbQ: Oxygen evolving 21.2 1.1E+02 0.0024 24.6 3.0 56 23-78 112-176 (202)
91 cd00633 Secretoglobin Secretog 21.2 1.8E+02 0.0039 18.6 3.6 34 35-68 30-63 (67)
92 PF12688 TPR_5: Tetratrico pep 21.2 1.5E+02 0.0032 21.4 3.5 28 53-80 34-61 (120)
93 PRK04325 hypothetical protein; 20.4 2.2E+02 0.0047 19.1 4.0 31 17-47 19-49 (74)
94 PF12862 Apc5: Anaphase-promot 20.3 2.7E+02 0.0058 18.5 4.4 28 56-83 40-67 (94)
No 1
>KOG2062|consensus
Probab=100.00 E-value=6.6e-44 Score=321.51 Aligned_cols=113 Identities=50% Similarity=0.849 Sum_probs=111.1
Q ss_pred CCcHHHHHHhcCCCchHHHHHHHHHHhhhhhcchHHHHhhHHHHHHHhhCCCCCchhHHHHHHHHHhhhccChHHHHHHH
Q psy5990 1 MNTVAGVISLLDDPMIELKEFSLKKLNDIVDDFWPEVSEAIQKIEILHEDKGFPQYKLAALVASKVYFHLGSFSDSLQYA 80 (119)
Q Consensus 1 ~tSaag~laLL~E~d~~Lk~~AL~~L~~vVd~~W~EIsd~i~~IE~LyED~~F~~R~lAALvaSKVyyhLgey~~aL~yA 80 (119)
+|||+|+++||+||.|+||+|||.++|++||+|||||||++++||.||||++||+|++|||++||||||||+|++||+||
T Consensus 3 itsAa~lialL~e~~~~lk~~Al~~in~vVd~~WpEIsd~l~~IE~lyed~~F~er~~AaL~~SKVyy~Lgeye~Al~yA 82 (929)
T KOG2062|consen 3 ITSAAGLIALLREPEPSLKVHALFKINNVVDQFWPEISDSLPKIESLYEDETFPERQLAALLASKVYYYLGEYEDALEYA 82 (929)
T ss_pred ccchHHHHHHHhCCchHHHHHHHHHHHHHHHHhhHHhhhhHHHHHHHhccCCCchhHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 68999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HhCCCCCCCCCCChhHHHhhhhhhhhHHHHHhhhc
Q psy5990 81 LGAGDLFDVRNDTVYVKTIICKYFCISLSTYRYSN 115 (119)
Q Consensus 81 L~AG~lFdv~~~seYvetiisk~~cID~Yi~~~~~ 115 (119)
|+||+.|||+++|+|++|||+| |||+||+.++.
T Consensus 83 L~ag~~F~Vd~~S~y~etivak--~id~yi~~~~~ 115 (929)
T KOG2062|consen 83 LRAGDDFDVDENSDYVETIVAK--CIDMYIETASE 115 (929)
T ss_pred HcCCccccccCccchhhHHHHH--HHHHHHHHHHH
Confidence 9999999999999999999999 99999998764
No 2
>COG5116 RPN2 26S proteasome regulatory complex component [Posttranslational modification, protein turnover, chaperones]
Probab=100.00 E-value=2.7e-35 Score=262.88 Aligned_cols=113 Identities=35% Similarity=0.551 Sum_probs=110.3
Q ss_pred CCcHHHHHHhcCCCchHHHHHHHHHHhhhhhcchHHHHhhHHHHHHHhhCCCCCchhHHHHHHHHHhhhccChHHHHHHH
Q psy5990 1 MNTVAGVISLLDDPMIELKEFSLKKLNDIVDDFWPEVSEAIQKIEILHEDKGFPQYKLAALVASKVYFHLGSFSDSLQYA 80 (119)
Q Consensus 1 ~tSaag~laLL~E~d~~Lk~~AL~~L~~vVd~~W~EIsd~i~~IE~LyED~~F~~R~lAALvaSKVyyhLgey~~aL~yA 80 (119)
+|||+|+++||.|....++++||..+|..|||.||||||.+++||.||+|.+||.|++|||++|||||+||||++|+.||
T Consensus 3 ~tta~~L~all~e~~d~~~~~Al~~In~~vDqlwpeIsddl~~Ie~lydd~sf~~remaaL~~SKvYy~LgeY~~Ai~yA 82 (926)
T COG5116 3 MTTARILPALLAELRDGRESEALDVINAHVDQLWPEISDDLRYIEALYDDDSFDPREMAALCLSKVYYVLGEYQQAIEYA 82 (926)
T ss_pred cchhhhHHHHHHHHhhhhHHHHHHHHHHHHHHhhhhhhchhhHHHHhhccCCCCHHHHHHHHHHHHHHHHHhHHHHHHHH
Confidence 68999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HhCCCCCCCCCCChhHHHhhhhhhhhHHHHHhhhc
Q psy5990 81 LGAGDLFDVRNDTVYVKTIICKYFCISLSTYRYSN 115 (119)
Q Consensus 81 L~AG~lFdv~~~seYvetiisk~~cID~Yi~~~~~ 115 (119)
|.||+.|+++++|.|++|||.| |||+|++..+.
T Consensus 83 L~agdrfl~D~~S~y~etiv~k--~iem~vh~~~~ 115 (926)
T COG5116 83 LRAGDRFLVDDGSFYYETIVYK--SIEMYVHMMDS 115 (926)
T ss_pred HhcCCceeecCCccceehhHHh--HHHHHHHHHHH
Confidence 9999999999999999999999 99999987553
No 3
>PF12895 Apc3: Anaphase-promoting complex, cyclosome, subunit 3; PDB: 3KAE_D 3Q4A_B 2C2L_D 3Q47_B 3Q49_B 2XPI_A 3ULQ_A.
Probab=85.78 E-value=1.1 Score=28.89 Aligned_cols=44 Identities=18% Similarity=0.231 Sum_probs=24.0
Q ss_pred HhhHHHHHHHhhCCCCCchhHHHHHHHHHhhhccChHHHHHHHH
Q psy5990 38 SEAIQKIEILHEDKGFPQYKLAALVASKVYFHLGSFSDSLQYAL 81 (119)
Q Consensus 38 sd~i~~IE~LyED~~F~~R~lAALvaSKVyyhLgey~~aL~yAL 81 (119)
.++|...|.+++...........+-...+||++|+|++|+.+.-
T Consensus 6 ~~Ai~~~~k~~~~~~~~~~~~~~~~la~~~~~~~~y~~A~~~~~ 49 (84)
T PF12895_consen 6 ENAIKYYEKLLELDPTNPNSAYLYNLAQCYFQQGKYEEAIELLQ 49 (84)
T ss_dssp HHHHHHHHHHHHHHCGTHHHHHHHHHHHHHHHTTHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHCCCChhHHHHHHHHHHHHHCCCHHHHHHHHH
Confidence 34555555665544332233333335677777777777776653
No 4
>PF13646 HEAT_2: HEAT repeats; PDB: 1OYZ_A 3FGA_A 2PF4_C 2IAE_A 3B2A_A.
Probab=81.95 E-value=2.7 Score=26.61 Aligned_cols=54 Identities=22% Similarity=0.274 Sum_probs=41.2
Q ss_pred HHHHhc-CCCchHHHHHHHHHHhhhhhcchHHHHhhHHHHHHHhhCCCCCchhHHHHHHHH
Q psy5990 6 GVISLL-DDPMIELKEFSLKKLNDIVDDFWPEVSEAIQKIEILHEDKGFPQYKLAALVASK 65 (119)
Q Consensus 6 g~laLL-~E~d~~Lk~~AL~~L~~vVd~~W~EIsd~i~~IE~LyED~~F~~R~lAALvaSK 65 (119)
.++..| +++++.+|..|++-|-.+ +.+ +.++.+..+.+|++..-|.-|+.-..+
T Consensus 3 ~L~~~l~~~~~~~vr~~a~~~L~~~----~~~--~~~~~L~~~l~d~~~~vr~~a~~aL~~ 57 (88)
T PF13646_consen 3 ALLQLLQNDPDPQVRAEAARALGEL----GDP--EAIPALIELLKDEDPMVRRAAARALGR 57 (88)
T ss_dssp HHHHHHHTSSSHHHHHHHHHHHHCC----THH--HHHHHHHHHHTSSSHHHHHHHHHHHHC
T ss_pred HHHHHHhcCCCHHHHHHHHHHHHHc----CCH--hHHHHHHHHHcCCCHHHHHHHHHHHHH
Confidence 467777 999999999999998843 433 778888888888777667766655554
No 5
>PF07719 TPR_2: Tetratricopeptide repeat; InterPro: IPR013105 The tetratrico peptide repeat (TPR) is a structural motif present in a wide range of proteins [, , ]. It mediates protein-protein interactions and the assembly of multiprotein complexes []. The TPR motif consists of 3-16 tandem-repeats of 34 amino acids residues, although individual TPR motifs can be dispersed in the protein sequence. Sequence alignment of the TPR domains reveals a consensus sequence defined by a pattern of small and large amino acids. TPR motifs have been identified in various different organisms, ranging from bacteria to humans. Proteins containing TPRs are involved in a variety of biological processes, such as cell cycle regulation, transcriptional control, mitochondrial and peroxisomal protein transport, neurogenesis and protein folding. This repeat includes outlying Tetratricopeptide-like repeats (TPR) that are not matched by IPR001440 from INTERPRO.; PDB: 1XNF_B 3Q15_A 4ABN_A 1OUV_A 3U4T_A 3MA5_C 2KCV_A 2KCL_A 2XEV_A 3NF1_A ....
Probab=79.04 E-value=1.8 Score=22.96 Aligned_cols=21 Identities=24% Similarity=0.699 Sum_probs=16.3
Q ss_pred HHHHhhhccChHHHHHHHHhC
Q psy5990 63 ASKVYFHLGSFSDSLQYALGA 83 (119)
Q Consensus 63 aSKVyyhLgey~~aL~yAL~A 83 (119)
.+.+|+.+|+|++|+++-..|
T Consensus 7 lg~~~~~~~~~~~A~~~~~~a 27 (34)
T PF07719_consen 7 LGQAYYQLGNYEEAIEYFEKA 27 (34)
T ss_dssp HHHHHHHTT-HHHHHHHHHHH
T ss_pred HHHHHHHhCCHHHHHHHHHHH
Confidence 468999999999999876543
No 6
>PF13432 TPR_16: Tetratricopeptide repeat; PDB: 3CVP_A 3CVL_A 3CVQ_A 3CV0_A 2GW1_B 3CVN_A 3QKY_A 2PL2_B.
Probab=78.85 E-value=8.6 Score=23.15 Aligned_cols=42 Identities=21% Similarity=0.386 Sum_probs=30.5
Q ss_pred HhhHHHHHHHhhCCCCCchhHHHHHHHHHhhhccChHHHHHHHH
Q psy5990 38 SEAIQKIEILHEDKGFPQYKLAALVASKVYFHLGSFSDSLQYAL 81 (119)
Q Consensus 38 sd~i~~IE~LyED~~F~~R~lAALvaSKVyyhLgey~~aL~yAL 81 (119)
.+++...+.+.+.. |...-|-.....+++..|++++|+.+--
T Consensus 14 ~~A~~~~~~~l~~~--P~~~~a~~~lg~~~~~~g~~~~A~~~~~ 55 (65)
T PF13432_consen 14 DEAIAAFEQALKQD--PDNPEAWYLLGRILYQQGRYDEALAYYE 55 (65)
T ss_dssp HHHHHHHHHHHCCS--TTHHHHHHHHHHHHHHTT-HHHHHHHHH
T ss_pred HHHHHHHHHHHHHC--CCCHHHHHHHHHHHHHcCCHHHHHHHHH
Confidence 34555555555544 7788888888999999999999997643
No 7
>PF02985 HEAT: HEAT repeat; InterPro: IPR000357 The HEAT repeat is a tandemly repeated, 37-47 amino acid long module occurring in a number of cytoplasmic proteins, including the four name-giving proteins huntingtin, elongation factor 3 (EF3), the 65 Kd alpha regulatory subunit of protein phosphatase 2A (PP2A) and the yeast PI3-kinase TOR1 []. Arrays of HEAT repeats consists of 3 to 36 units forming a rod-like helical structure and appear to function as protein-protein interaction surfaces. It has been noted that many HEAT repeat-containing proteins are involved in intracellular transport processes. In the crystal structure of PP2A PR65/A [], the HEAT repeats consist of pairs of antiparallel alpha helices [].; GO: 0005515 protein binding; PDB: 3FGA_A 2PF4_C 2IAE_A 2BKU_D 3EA5_B 3ND2_A 2BPT_A 2NYL_A 2NPP_D 2PKG_B ....
Probab=77.17 E-value=4.6 Score=22.26 Aligned_cols=27 Identities=26% Similarity=0.443 Sum_probs=22.2
Q ss_pred HHHHHhcCCCchHHHHHHHHHHhhhhh
Q psy5990 5 AGVISLLDDPMIELKEFSLKKLNDIVD 31 (119)
Q Consensus 5 ag~laLL~E~d~~Lk~~AL~~L~~vVd 31 (119)
..++.+|+++++++|..|.+.|..+..
T Consensus 3 p~l~~~l~D~~~~VR~~a~~~l~~i~~ 29 (31)
T PF02985_consen 3 PILLQLLNDPSPEVRQAAAECLGAIAE 29 (31)
T ss_dssp HHHHHHHT-SSHHHHHHHHHHHHHHHH
T ss_pred HHHHHHcCCCCHHHHHHHHHHHHHHHh
Confidence 357899999999999999999887754
No 8
>PF10193 Telomere_reg-2: Telomere length regulation protein; InterPro: IPR019337 This entry represents a conserved domain found in a group of proteins called telomere-length regulation, or clock abnormal protein-2, which are conserved from plants to humans. These proteins regulate telomere length and contribute to silencing of sub-telomeric regions []. In vitro the protein binds to telomeric DNA repeats. ; PDB: 3O4Z_B.
Probab=76.57 E-value=5.1 Score=28.81 Aligned_cols=61 Identities=21% Similarity=0.288 Sum_probs=38.6
Q ss_pred HHHHhcCCC--chHHHHHHHHHHhhhh----------hcchHHHHhhHHHHHHHhhCCCCCchhHHHHHHHHH
Q psy5990 6 GVISLLDDP--MIELKEFSLKKLNDIV----------DDFWPEVSEAIQKIEILHEDKGFPQYKLAALVASKV 66 (119)
Q Consensus 6 g~laLL~E~--d~~Lk~~AL~~L~~vV----------d~~W~EIsd~i~~IE~LyED~~F~~R~lAALvaSKV 66 (119)
-++..|.++ +++-..-||+....+| .+++.|+...|-.++.=|+.++|.+....|+||-=|
T Consensus 7 Dll~~L~~~~~~~e~~e~aL~~a~~LIR~k~~fg~el~~~a~eL~~~Ll~L~~~f~~~~Fe~~R~~alval~v 79 (114)
T PF10193_consen 7 DLLEYLRSDDEDYEKFEAALKSAEKLIRRKPDFGTELSEYAEELLKALLHLQNKFDIENFEELRQNALVALVV 79 (114)
T ss_dssp HHHHHHT------S-SHHHHHHHHHHHHS-----SSHHHHHHHHHHHHHH---TT--TTTTHHHHHHHHHHHH
T ss_pred HHHHHHhcCcCCHHHHHHHHHHHHHHHhcCCCCcchHHHHHHHHHHHHhhccccCCccCHHHHHHHHHHHHHH
Confidence 356666654 4777888888877654 556777777777788889999999999999987655
No 9
>PF13925 Katanin_con80: con80 domain of Katanin
Probab=72.67 E-value=6.1 Score=29.78 Aligned_cols=67 Identities=15% Similarity=0.185 Sum_probs=45.0
Q ss_pred HHHhcCCCchHHHHHHHHHHhhhhhcchHHHHhhHHH-HHHHhhCCCCCchhHHHHHHHHHhhhccChHHH
Q psy5990 7 VISLLDDPMIELKEFSLKKLNDIVDDFWPEVSEAIQK-IEILHEDKGFPQYKLAALVASKVYFHLGSFSDS 76 (119)
Q Consensus 7 ~laLL~E~d~~Lk~~AL~~L~~vVd~~W~EIsd~i~~-IE~LyED~~F~~R~lAALvaSKVyyhLgey~~a 76 (119)
+-.||..+...-...||+-|..+++.||+.|.+.+.. -..---|-..++|.-- +.++|=+|.+.-.-
T Consensus 74 i~~LL~Sk~E~~i~~aL~~L~~i~~~f~~~I~~~~~~~~~~~gVDl~~EeR~~k---c~~c~~~L~~i~~~ 141 (164)
T PF13925_consen 74 IEELLQSKYESYISVALEMLRSILKKFGPVIRSNLSAPSPSIGVDLSAEERMEK---CQECYQQLRKIVQI 141 (164)
T ss_pred HHHHHhCCcHHHHHHHHHHHHHHHHHHHHHHHHHHHhcccccccccchHHHHHH---HHHHHHHHHHHHHH
Confidence 3467888888899999999999999999999988774 1223345555555422 23444455444433
No 10
>PF13181 TPR_8: Tetratricopeptide repeat; PDB: 3GW4_B 3MA5_C 2KCV_A 2KCL_A 3FP3_A 3LCA_A 3FP4_A 3FP2_A 1W3B_B 1ELW_A ....
Probab=72.40 E-value=4.5 Score=21.57 Aligned_cols=19 Identities=32% Similarity=0.698 Sum_probs=16.3
Q ss_pred HHHHHhhhccChHHHHHHH
Q psy5990 62 VASKVYFHLGSFSDSLQYA 80 (119)
Q Consensus 62 vaSKVyyhLgey~~aL~yA 80 (119)
..+++|..+|++++|+++-
T Consensus 6 ~lg~~y~~~~~~~~A~~~~ 24 (34)
T PF13181_consen 6 NLGKIYEQLGDYEEALEYF 24 (34)
T ss_dssp HHHHHHHHTTSHHHHHHHH
T ss_pred HHHHHHHHcCCHHHHHHHH
Confidence 4579999999999999874
No 11
>PF13424 TPR_12: Tetratricopeptide repeat; PDB: 3RO2_A 3Q15_A 3ASG_A 3ASD_A 3AS5_A 3AS4_A 3ASH_B 4A1S_B 3CEQ_B 3EDT_H ....
Probab=69.98 E-value=9.6 Score=23.70 Aligned_cols=22 Identities=27% Similarity=0.650 Sum_probs=18.1
Q ss_pred HHHHHhhhccChHHHHHHHHhC
Q psy5990 62 VASKVYFHLGSFSDSLQYALGA 83 (119)
Q Consensus 62 vaSKVyyhLgey~~aL~yAL~A 83 (119)
-.+.+|+.+|++++|+++--.|
T Consensus 51 ~lg~~~~~~g~~~~A~~~~~~a 72 (78)
T PF13424_consen 51 NLGECYYRLGDYEEALEYYQKA 72 (78)
T ss_dssp HHHHHHHHTTHHHHHHHHHHHH
T ss_pred HHHHHHHHcCCHHHHHHHHHHH
Confidence 3479999999999999986543
No 12
>PF13646 HEAT_2: HEAT repeats; PDB: 1OYZ_A 3FGA_A 2PF4_C 2IAE_A 3B2A_A.
Probab=69.93 E-value=22 Score=22.33 Aligned_cols=50 Identities=24% Similarity=0.220 Sum_probs=36.0
Q ss_pred HHHHHHhcCCCchHHHHHHHHHHhhhhhcchHHHHhhHHHHHHHhhCCCCCc-hhHH
Q psy5990 4 VAGVISLLDDPMIELKEFSLKKLNDIVDDFWPEVSEAIQKIEILHEDKGFPQ-YKLA 59 (119)
Q Consensus 4 aag~laLL~E~d~~Lk~~AL~~L~~vVd~~W~EIsd~i~~IE~LyED~~F~~-R~lA 59 (119)
...++.+|+.+++.+|..|+..|..+= -.+.++.+..+..|+.=+. |.-|
T Consensus 33 ~~~L~~~l~d~~~~vr~~a~~aL~~i~------~~~~~~~L~~~l~~~~~~~vr~~a 83 (88)
T PF13646_consen 33 IPALIELLKDEDPMVRRAAARALGRIG------DPEAIPALIKLLQDDDDEVVREAA 83 (88)
T ss_dssp HHHHHHHHTSSSHHHHHHHHHHHHCCH------HHHTHHHHHHHHTC-SSHHHHHHH
T ss_pred HHHHHHHHcCCCHHHHHHHHHHHHHhC------CHHHHHHHHHHHcCCCcHHHHHHH
Confidence 456888999999999999999998772 2557777777776654333 4433
No 13
>PF14853 Fis1_TPR_C: Fis1 C-terminal tetratricopeptide repeat; PDB: 1IYG_A 1PC2_A 1NZN_A 3UUX_C 1Y8M_A 2PQR_A 2PQN_A 3O48_A.
Probab=66.60 E-value=3.9 Score=26.07 Aligned_cols=16 Identities=19% Similarity=0.488 Sum_probs=13.1
Q ss_pred HHhhhccChHHHHHHH
Q psy5990 65 KVYFHLGSFSDSLQYA 80 (119)
Q Consensus 65 KVyyhLgey~~aL~yA 80 (119)
--+|.||+|++|++|.
T Consensus 9 ig~ykl~~Y~~A~~~~ 24 (53)
T PF14853_consen 9 IGHYKLGEYEKARRYC 24 (53)
T ss_dssp HHHHHTT-HHHHHHHH
T ss_pred HHHHHhhhHHHHHHHH
Confidence 4589999999999986
No 14
>PRK10866 outer membrane biogenesis protein BamD; Provisional
Probab=64.01 E-value=46 Score=26.35 Aligned_cols=72 Identities=11% Similarity=0.041 Sum_probs=52.4
Q ss_pred hhhcchHHHHhhHHHHHHHhhCCCCCchhHHHHHHHHHhhhccChHHHHHHHHhCCCCCCCCCCChhHHHhhhh
Q psy5990 29 IVDDFWPEVSEAIQKIEILHEDKGFPQYKLAALVASKVYFHLGSFSDSLQYALGAGDLFDVRNDTVYVKTIICK 102 (119)
Q Consensus 29 vVd~~W~EIsd~i~~IE~LyED~~F~~R~lAALvaSKVyyhLgey~~aL~yAL~AG~lFdv~~~seYvetiisk 102 (119)
+-..-|.+-.+...++...+-+. |....|.+-...+||.+|+|++|+.+.=..=..+--+++-+|+.=+++.
T Consensus 43 ~~~g~y~~Ai~~f~~l~~~yP~s--~~a~~a~l~la~ayy~~~~y~~A~~~~e~fi~~~P~~~~~~~a~Y~~g~ 114 (243)
T PRK10866 43 LQDGNWKQAITQLEALDNRYPFG--PYSQQVQLDLIYAYYKNADLPLAQAAIDRFIRLNPTHPNIDYVLYMRGL 114 (243)
T ss_pred HHCCCHHHHHHHHHHHHHhCCCC--hHHHHHHHHHHHHHHhcCCHHHHHHHHHHHHHhCcCCCchHHHHHHHHH
Confidence 44566776666666665544444 5666777888999999999999999887766666666777777777765
No 15
>PF12755 Vac14_Fab1_bd: Vacuolar 14 Fab1-binding region
Probab=63.77 E-value=44 Score=23.33 Aligned_cols=58 Identities=17% Similarity=0.157 Sum_probs=39.0
Q ss_pred HHHHHhcCCCchHHHHHHHHHHhhhhhcchHHHHhhHHH----HHHHhhCCCCCchhHHHHH
Q psy5990 5 AGVISLLDDPMIELKEFSLKKLNDIVDDFWPEVSEAIQK----IEILHEDKGFPQYKLAALV 62 (119)
Q Consensus 5 ag~laLL~E~d~~Lk~~AL~~L~~vVd~~W~EIsd~i~~----IE~LyED~~F~~R~lAALv 62 (119)
.++|..++++|+.++-+|.+.|.+++...=.++=.+.+. +-.+..|+.=.-|.-|.++
T Consensus 30 ~pVL~~~~D~d~rVRy~AcEaL~ni~k~~~~~~l~~f~~IF~~L~kl~~D~d~~Vr~~a~~L 91 (97)
T PF12755_consen 30 PPVLKCFDDQDSRVRYYACEALYNISKVARGEILPYFNEIFDALCKLSADPDENVRSAAELL 91 (97)
T ss_pred HHHHHHcCCCcHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCchhHHHHHHHH
Confidence 578999999999999999999999876554444333333 3345556555455544443
No 16
>PF12895 Apc3: Anaphase-promoting complex, cyclosome, subunit 3; PDB: 3KAE_D 3Q4A_B 2C2L_D 3Q47_B 3Q49_B 2XPI_A 3ULQ_A.
Probab=63.64 E-value=8.3 Score=24.67 Aligned_cols=22 Identities=9% Similarity=0.354 Sum_probs=17.0
Q ss_pred HHHHHHHHHhhhccChHHHHHH
Q psy5990 58 LAALVASKVYFHLGSFSDSLQY 79 (119)
Q Consensus 58 lAALvaSKVyyhLgey~~aL~y 79 (119)
-...+..++|+.||.|++|++.
T Consensus 59 ~~~~l~a~~~~~l~~y~eAi~~ 80 (84)
T PF12895_consen 59 DIHYLLARCLLKLGKYEEAIKA 80 (84)
T ss_dssp HHHHHHHHHHHHTT-HHHHHHH
T ss_pred HHHHHHHHHHHHhCCHHHHHHH
Confidence 4444558999999999999975
No 17
>PF01602 Adaptin_N: Adaptin N terminal region; InterPro: IPR002553 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. This traffic is bidirectional, to ensure that proteins required to form vesicles are recycled. Vesicles have specific coat proteins (such as clathrin or coatomer) that are important for cargo selection and direction of transfer []. Clathrin coats contain both clathrin 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 []. All AP complexes are heterotetramers composed of two large subunits (adaptins), a medium subunit (mu) and a small subunit (sigma). Each subunit has a specific function. Adaptin subunits recognise and bind to clathrin through their hinge region (clathrin box), and recruit accessory proteins that modulate AP function through their C-terminal appendage domains. By contrast, GGAs are monomers composed of four domains, which have functions similar to AP subunits: an N-terminal VHS (Vps27p/Hrs/Stam) domain, a GAT (GGA and Tom1) domain, a hinge region, and a C-terminal GAE (gamma-adaptin ear) domain. The GAE domain is similar to the AP gamma-adaptin ear domain, being responsible for the recruitment of accessory proteins that regulate clathrin-mediated endocytosis []. While clathrin mediates endocytic protein transport from ER to Golgi, coatomers (COPI, COPII) primarily mediate intra-Golgi transport, as well as the reverse Golgi to ER transport of dilysine-tagged proteins []. Coatomers reversibly associate with Golgi (non-clathrin-coated) vesicles to mediate protein transport and for budding from Golgi membranes []. Coatomer complexes are hetero-oligomers composed of at least an alpha, beta, beta', gamma, delta, epsilon and zeta subunits. This entry represents the N-terminal domain of various adaptins from different AP clathrin adaptor complexes (including AP1, AP2, AP3 and AP4), and from the beta and gamma subunits of various coatomer (COP) adaptors. This domain has a 2-layer alpha/alpha fold that forms a right-handed superhelix, and is a member of the ARM repeat superfamily []. The N-terminal region of the various AP adaptor proteins share strong sequence identity; by contrast, the C-terminal domains of different adaptins share similar structural folds, but have little sequence identity []. It has been proposed that the N-terminal domain interacts with another uniform component of the coated vesicles. More information about these proteins can be found at Protein of the Month: Clathrin [].; GO: 0006886 intracellular protein transport, 0016192 vesicle-mediated transport, 0030117 membrane coat; PDB: 1W63_C 2JKR_A 2JKT_A 2XA7_A 2VGL_B 3TJZ_E.
Probab=62.59 E-value=25 Score=29.32 Aligned_cols=56 Identities=20% Similarity=0.161 Sum_probs=43.7
Q ss_pred HHHHHHhcCCCchHHHHHHHHHHhhhhhcchHHHHhhHHHHHHHhhCCCCCchhHH
Q psy5990 4 VAGVISLLDDPMIELKEFSLKKLNDIVDDFWPEVSEAIQKIEILHEDKGFPQYKLA 59 (119)
Q Consensus 4 aag~laLL~E~d~~Lk~~AL~~L~~vVd~~W~EIsd~i~~IE~LyED~~F~~R~lA 59 (119)
...+..+|..+++.+|..||+.|..+.....+.+...-..+..+--|+.-.=|..|
T Consensus 269 ~~~L~~lL~s~~~nvr~~~L~~L~~l~~~~~~~v~~~~~~~~~l~~~~d~~Ir~~~ 324 (526)
T PF01602_consen 269 INPLIKLLSSSDPNVRYIALDSLSQLAQSNPPAVFNQSLILFFLLYDDDPSIRKKA 324 (526)
T ss_dssp HHHHHHHHTSSSHHHHHHHHHHHHHHCCHCHHHHGTHHHHHHHHHCSSSHHHHHHH
T ss_pred HHHHHHHhhcccchhehhHHHHHHHhhcccchhhhhhhhhhheecCCCChhHHHHH
Confidence 45688999999999999999999999999988888666667766635444444444
No 18
>PF00515 TPR_1: Tetratricopeptide repeat; InterPro: IPR001440 The tetratrico peptide repeat (TPR) is a structural motif present in a wide range of proteins [, , ]. It mediates protein-protein interactions and the assembly of multiprotein complexes []. The TPR motif consists of 3-16 tandem-repeats of 34 amino acids residues, although individual TPR motifs can be dispersed in the protein sequence. Sequence alignment of the TPR domains reveals a consensus sequence defined by a pattern of small and large amino acids. TPR motifs have been identified in various different organisms, ranging from bacteria to humans. Proteins containing TPRs are involved in a variety of biological processes, such as cell cycle regulation, transcriptional control, mitochondrial and peroxisomal protein transport, neurogenesis and protein folding. The X-ray structure of a domain containing three TPRs from protein phosphatase 5 revealed that TPR adopts a helix-turn-helix arrangement, with adjacent TPR motifs packing in a parallel fashion, resulting in a spiral of repeating anti-parallel alpha-helices []. The two helices are denoted helix A and helix B. The packing angle between helix A and helix B is ~24 degrees; within a single TPR and generates a right-handed superhelical shape. Helix A interacts with helix B and with helix A' of the next TPR. Two protein surfaces are generated: the inner concave surface is contributed to mainly by residue on helices A, and the other surface presents residues from both helices A and B. ; GO: 0005515 protein binding; PDB: 3SF4_C 2LNI_A 1ELW_A 2C0M_A 1FCH_B 3R9A_B 2J9Q_A 2C0L_A 1KT1_A 3FWV_A ....
Probab=62.38 E-value=5.6 Score=21.31 Aligned_cols=16 Identities=38% Similarity=1.061 Sum_probs=12.7
Q ss_pred HHHhhhccChHHHHHH
Q psy5990 64 SKVYFHLGSFSDSLQY 79 (119)
Q Consensus 64 SKVyyhLgey~~aL~y 79 (119)
-.+|+.+|+|++|+.+
T Consensus 8 g~~~~~~~~~~~A~~~ 23 (34)
T PF00515_consen 8 GNAYFQLGDYEEALEY 23 (34)
T ss_dssp HHHHHHTT-HHHHHHH
T ss_pred HHHHHHhCCchHHHHH
Confidence 3689999999999876
No 19
>PF07539 DRIM: Down-regulated in metastasis; InterPro: IPR011430 These eukaryotic proteins include DRIM (Down-Regulated In Metastasis) (O75691 from SWISSPROT), which is differentially expressed in metastatic and non-metastatic human breast carcinoma cells []. It is believed to be involved in processing of non-coding RNA [].
Probab=61.90 E-value=15 Score=27.40 Aligned_cols=47 Identities=26% Similarity=0.355 Sum_probs=38.4
Q ss_pred HHHHhcCCCchHHHHHHHHHHhhhhhcchHHHHhhHHHHHHHhhCCCCCc
Q psy5990 6 GVISLLDDPMIELKEFSLKKLNDIVDDFWPEVSEAIQKIEILHEDKGFPQ 55 (119)
Q Consensus 6 g~laLL~E~d~~Lk~~AL~~L~~vVd~~W~EIsd~i~~IE~LyED~~F~~ 55 (119)
-++.||..+|+++|..||+-|-.-=+ |.|..+=+.++.|.+|.+|.+
T Consensus 21 ~~~~LL~~~d~~vQklAL~cll~~k~---~~l~pY~d~L~~Lldd~~frd 67 (141)
T PF07539_consen 21 ALLRLLSSRDPEVQKLALDCLLTWKD---PYLTPYKDNLENLLDDKTFRD 67 (141)
T ss_pred HHHHHHcCCCHHHHHHHHHHHHHhCc---HHHHhHHHHHHHHcCcchHHH
Confidence 36889999999999999998876222 457778888899999998864
No 20
>PF13374 TPR_10: Tetratricopeptide repeat; PDB: 3CEQ_B 3EDT_H 3NF1_A.
Probab=61.41 E-value=7.4 Score=21.05 Aligned_cols=21 Identities=19% Similarity=0.347 Sum_probs=16.2
Q ss_pred HHHHhhhccChHHHHHHHHhC
Q psy5990 63 ASKVYFHLGSFSDSLQYALGA 83 (119)
Q Consensus 63 aSKVyyhLgey~~aL~yAL~A 83 (119)
.+.+|+..|+|++|+++.-.+
T Consensus 8 la~~~~~~g~~~~A~~~~~~a 28 (42)
T PF13374_consen 8 LANAYRAQGRYEEALELLEEA 28 (42)
T ss_dssp HHHHHHHCT-HHHHHHHHHHH
T ss_pred HHHHHHhhhhcchhhHHHHHH
Confidence 357899999999999986543
No 21
>PF03810 IBN_N: Importin-beta N-terminal domain; InterPro: IPR001494 Karyopherins are a group of proteins involved in transporting molecules through the pores of the nuclear envelope. Karyopherins, which may act as importins or exportins, are part of the Importin-beta super-family, which all share a similar three-dimensional structure. Members of the importin-beta (karyopherin-beta) family can bind and transport cargo by themselves, or can form heterodimers with importin-alpha. As part of a heterodimer, importin-beta mediates interactions with the pore complex, while importin-alpha acts as an adaptor protein to bind the nuclear localisation signal (NLS) on the cargo through the classical NLS import of proteins. Importin-beta is a helicoidal molecule constructed from 19 HEAT repeats. Many nuclear pore proteins contain FG sequence repeats that can bind to HEAT repeats within importins [, ], which is important for importin-beta mediated transport. Ran GTPase helps to control the unidirectional transfer of cargo. The cytoplasm contains primarily RanGDP and the nucleus RanGTP through the actions of RanGAP and RanGEF, respectively. In the nucleus, RanGTP binds to importin-beta within the importin/cargo complex, causing a conformational change in importin-beta that releases it from importin-alpha-bound cargo. As a result, the N-terminal auto-inhibitory region on importin-alpha is free to loop back and bind to the major NLS-binding site, causing the cargo to be released []. There are additional release factors as well. This entry represents the N-terminal domain of karyopherins that is important for the binding of the Ran protein []. More information about these proteins can be found at Protein of the Month: Importins [].; GO: 0008565 protein transporter activity, 0006886 intracellular protein transport; PDB: 3NC1_A 3NBY_D 3NBZ_D 3NC0_A 3GJX_D 1IBR_D 1QGR_A 3LWW_A 1F59_A 2Q5D_A ....
Probab=59.87 E-value=13 Score=23.24 Aligned_cols=32 Identities=13% Similarity=0.384 Sum_probs=26.1
Q ss_pred HHHHHhc-CC-CchHHHHHHHHHHhhhhhcchHH
Q psy5990 5 AGVISLL-DD-PMIELKEFSLKKLNDIVDDFWPE 36 (119)
Q Consensus 5 ag~laLL-~E-~d~~Lk~~AL~~L~~vVd~~W~E 36 (119)
..++.++ +. .++.+|.+|.--|...|...|..
T Consensus 17 ~~l~~il~~~~~~~~~R~~A~i~LKn~I~~~W~~ 50 (77)
T PF03810_consen 17 QYLLQILSSNSQDPEVRQLAAILLKNLIKKNWSP 50 (77)
T ss_dssp HHHHHHHHCTTSCHHHHHHHHHHHHHHHHHSGGH
T ss_pred HHHHHHHHccCCCHHHHHHHHHHHHHHHHHcCch
Confidence 4566677 33 37999999999999999999994
No 22
>cd00020 ARM Armadillo/beta-catenin-like repeats. An approximately 40 amino acid long tandemly repeated sequence motif first identified in the Drosophila segment polarity gene armadillo; these repeats were also found in the mammalian armadillo homolog beta-catenin, the junctional plaque protein plakoglobin, the adenomatous polyposis coli (APC) tumor suppressor protein, and a number of other proteins. ARM has been implicated in mediating protein-protein interactions, but no common features among the target proteins recognized by the ARM repeats have been identified; related to the HEAT domain; three consecutive copies of the repeat are represented by this alignment model.
Probab=59.77 E-value=44 Score=21.42 Aligned_cols=61 Identities=15% Similarity=0.130 Sum_probs=44.1
Q ss_pred HHHHHHhcCCCchHHHHHHHHHHhhhh---hcchHHHH--hhHHHHHHHhhCCCCCchhHHHHHHH
Q psy5990 4 VAGVISLLDDPMIELKEFSLKKLNDIV---DDFWPEVS--EAIQKIEILHEDKGFPQYKLAALVAS 64 (119)
Q Consensus 4 aag~laLL~E~d~~Lk~~AL~~L~~vV---d~~W~EIs--d~i~~IE~LyED~~F~~R~lAALvaS 64 (119)
...++.+|..+++.++..|+.-|-.+- ++.+.++- +.++.+..+..|+.-.-+.-|.-..+
T Consensus 9 i~~l~~~l~~~~~~~~~~a~~~l~~l~~~~~~~~~~~~~~~~i~~l~~~l~~~~~~v~~~a~~~L~ 74 (120)
T cd00020 9 LPALVSLLSSSDENVQREAAWALSNLSAGNNDNIQAVVEAGGLPALVQLLKSEDEEVVKAALWALR 74 (120)
T ss_pred hHHHHHHHHcCCHHHHHHHHHHHHHHhcCCHHHHHHHHHCCChHHHHHHHhCCCHHHHHHHHHHHH
Confidence 355789999999999999999988866 46677755 67888888888765444444443333
No 23
>PF04733 Coatomer_E: Coatomer epsilon subunit; InterPro: IPR006822 Proteins synthesised 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. This traffic is bidirectional, to ensure that proteins required to form vesicles are recycled. Vesicles have specific coat proteins (such as clathrin or coatomer) that are important for cargo selection and direction of transfer []. While clathrin mediates endocytic protein transport, and transport from ER to Golgi, coatomers primarily mediate intra-Golgi transport, as well as the reverse Golgi to ER transport of dilysine-tagged proteins []. For example, the coatomer COP1 (coat protein complex 1) is responsible for reverse transport of recycled proteins from Golgi and pre-Golgi compartments back to the ER, while COPII buds vesicles from the ER to the Golgi []. Coatomers reversibly associate with Golgi (non-clathrin-coated) vesicles to mediate protein transport and for budding from Golgi membranes []. Activated small guanine triphosphatases (GTPases) attract coat proteins to specific membrane export sites, thereby linking coatomers to export cargos. As coat proteins polymerise, vesicles are formed and budded from membrane-bound organelles. Coatomer complexes also influence Golgi structural integrity, as well as the processing, activity, and endocytic recycling of LDL receptors. In mammals, coatomer complexes can only be recruited by membranes associated to ADP-ribosylation factors (ARFs), which are small GTP-binding proteins. Coatomer complexes are hetero-oligomers composed of at least an alpha, beta, beta', gamma, delta, epsilon and zeta subunits. This entry represents the epsilon subunit of the coatomer complex, which is involved in the regulation of intracellular protein trafficking between the endoplasmic reticulum and the Golgi complex []. More information about these proteins can be found at Protein of the Month: Clathrin [].; GO: 0005198 structural molecule activity, 0006890 retrograde vesicle-mediated transport, Golgi to ER, 0030126 COPI vesicle coat; PDB: 3MV2_B 3MV3_F 3MKR_A.
Probab=59.74 E-value=6.3 Score=32.19 Aligned_cols=45 Identities=20% Similarity=0.417 Sum_probs=34.1
Q ss_pred hhHHHHHHHhhCCCCCchhHHHHHHHHHhhhccChHHHHHHHHhC
Q psy5990 39 EAIQKIEILHEDKGFPQYKLAALVASKVYFHLGSFSDSLQYALGA 83 (119)
Q Consensus 39 d~i~~IE~LyED~~F~~R~lAALvaSKVyyhLgey~~aL~yAL~A 83 (119)
..|.+++.+..+..-+...+.++++..+|+|-|++++||+..=+.
T Consensus 84 ~~l~~l~~~~~~~~~~~~~~~~~~~A~i~~~~~~~~~AL~~l~~~ 128 (290)
T PF04733_consen 84 SALEELKELLADQAGESNEIVQLLAATILFHEGDYEEALKLLHKG 128 (290)
T ss_dssp CHHHHHHHCCCTS---CHHHHHHHHHHHHCCCCHHHHHHCCCTTT
T ss_pred HHHHHHHHHHHhccccccHHHHHHHHHHHHHcCCHHHHHHHHHcc
Confidence 457777777777666667788999999999999999999876443
No 24
>PF05131 Pep3_Vps18: Pep3/Vps18/deep orange family; InterPro: IPR007810 This region is found in a number of proteins identified as being involved in Golgi function and vacuolar sorting. The molecular function of this region is unknown. Proteins containing this domain also contain a C-terminal ring finger domain.
Probab=59.54 E-value=6.4 Score=29.63 Aligned_cols=20 Identities=35% Similarity=0.690 Sum_probs=17.6
Q ss_pred HHHHhhhccChHHHHHHHHh
Q psy5990 63 ASKVYFHLGSFSDSLQYALG 82 (119)
Q Consensus 63 aSKVyyhLgey~~aL~yAL~ 82 (119)
+-|+|+..|+|++||+|+=.
T Consensus 109 vWk~yl~~~~fd~Al~~~~~ 128 (147)
T PF05131_consen 109 VWKIYLDKGDFDEALQYCKT 128 (147)
T ss_pred HHHHHHhcCcHHHHHHHccC
Confidence 46999999999999999744
No 25
>KOG3785|consensus
Probab=57.89 E-value=18 Score=32.83 Aligned_cols=54 Identities=17% Similarity=0.196 Sum_probs=34.0
Q ss_pred HHHHHHHHHhhhccChHHHHHHHHhCCCCCCCCCCChhHHHhhhhhhhhHHHHHhh
Q psy5990 58 LAALVASKVYFHLGSFSDSLQYALGAGDLFDVRNDTVYVKTIICKYFCISLSTYRY 113 (119)
Q Consensus 58 lAALvaSKVyyhLgey~~aL~yAL~AG~lFdv~~~seYvetiisk~~cID~Yi~~~ 113 (119)
---+-...+|||||+|++|+.-=-..-+ .-+.+++---.+-..+|-+-+|++..
T Consensus 58 ~~~lWia~C~fhLgdY~~Al~~Y~~~~~--~~~~~~el~vnLAcc~FyLg~Y~eA~ 111 (557)
T KOG3785|consen 58 SLQLWIAHCYFHLGDYEEALNVYTFLMN--KDDAPAELGVNLACCKFYLGQYIEAK 111 (557)
T ss_pred HHHHHHHHHHHhhccHHHHHHHHHHHhc--cCCCCcccchhHHHHHHHHHHHHHHH
Confidence 3456667999999999999964322222 22334444444555567788887754
No 26
>PRK02603 photosystem I assembly protein Ycf3; Provisional
Probab=57.04 E-value=25 Score=25.48 Aligned_cols=32 Identities=16% Similarity=0.137 Sum_probs=23.3
Q ss_pred CCCchhHHHHHHHHHhhhccChHHHHHHHHhC
Q psy5990 52 GFPQYKLAALVASKVYFHLGSFSDSLQYALGA 83 (119)
Q Consensus 52 ~F~~R~lAALvaSKVyyhLgey~~aL~yAL~A 83 (119)
..+....+......+|+++|+|++|+.+...|
T Consensus 67 ~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~a 98 (172)
T PRK02603 67 DPNDRSYILYNMGIIYASNGEHDKALEYYHQA 98 (172)
T ss_pred ccchHHHHHHHHHHHHHHcCCHHHHHHHHHHH
Confidence 33444566777788999999999998865544
No 27
>PF09986 DUF2225: Uncharacterized protein conserved in bacteria (DUF2225); InterPro: IPR018708 This conserved bacterial family has no known function.
Probab=56.34 E-value=29 Score=27.37 Aligned_cols=43 Identities=16% Similarity=0.288 Sum_probs=33.7
Q ss_pred HhhHHHHHHHhhCCCCCch----hHHHHHHHHHhhhccChHHHHHHH
Q psy5990 38 SEAIQKIEILHEDKGFPQY----KLAALVASKVYFHLGSFSDSLQYA 80 (119)
Q Consensus 38 sd~i~~IE~LyED~~F~~R----~lAALvaSKVyyhLgey~~aL~yA 80 (119)
..++..-+.-|+.++||.. ...-.+..-.++.||++++|+++-
T Consensus 142 ~~Al~~y~~a~~~e~~~~~~~~~~~l~YLigeL~rrlg~~~eA~~~f 188 (214)
T PF09986_consen 142 RKALEFYEEAYENEDFPIEGMDEATLLYLIGELNRRLGNYDEAKRWF 188 (214)
T ss_pred HHHHHHHHHHHHhCcCCCCCchHHHHHHHHHHHHHHhCCHHHHHHHH
Confidence 4567777889999999743 445566778899999999999874
No 28
>PF13371 TPR_9: Tetratricopeptide repeat
Probab=56.11 E-value=26 Score=21.26 Aligned_cols=42 Identities=21% Similarity=0.310 Sum_probs=26.9
Q ss_pred chHHHHhhHHHHHHHhhCCCCCchhHHHHHHHHHhhhccChHHHHHH
Q psy5990 33 FWPEVSEAIQKIEILHEDKGFPQYKLAALVASKVYFHLGSFSDSLQY 79 (119)
Q Consensus 33 ~W~EIsd~i~~IE~LyED~~F~~R~lAALvaSKVyyhLgey~~aL~y 79 (119)
-|.+--+.++.+=.+.-+....-+.+| .+|+.+|+|.+|++.
T Consensus 10 ~~~~A~~~~~~~l~~~p~~~~~~~~~a-----~~~~~~g~~~~A~~~ 51 (73)
T PF13371_consen 10 DYEEALEVLERALELDPDDPELWLQRA-----RCLFQLGRYEEALED 51 (73)
T ss_pred CHHHHHHHHHHHHHhCcccchhhHHHH-----HHHHHhccHHHHHHH
Confidence 455555555555555444444445554 899999999999764
No 29
>smart00185 ARM Armadillo/beta-catenin-like repeats. Approx. 40 amino acid repeat. Tandem repeats form superhelix of helices that is proposed to mediate interaction of beta-catenin with its ligands. Involved in transducing the Wingless/Wnt signal. In plakoglobin arm repeats bind alpha-catenin and N-cadherin.
Probab=55.72 E-value=23 Score=19.21 Aligned_cols=27 Identities=15% Similarity=0.204 Sum_probs=22.1
Q ss_pred HHHHHHhcCCCchHHHHHHHHHHhhhh
Q psy5990 4 VAGVISLLDDPMIELKEFSLKKLNDIV 30 (119)
Q Consensus 4 aag~laLL~E~d~~Lk~~AL~~L~~vV 30 (119)
...++.||..++++++..|+.-|..+.
T Consensus 14 i~~L~~ll~~~~~~i~~~a~~aL~nl~ 40 (41)
T smart00185 14 LPALVELLKSEDEEVVKEAAWALSNLS 40 (41)
T ss_pred HHHHHHHHcCCCHHHHHHHHHHHHHHc
Confidence 456888999999999999988876653
No 30
>TIGR02795 tol_pal_ybgF tol-pal system protein YbgF. Members of this protein family are the product of one of seven genes regularly clustered in operons to encode the proteins of the tol-pal system, which is critical for maintaining the integrity of the bacterial outer membrane. The gene for this periplasmic protein has been designated orf2 and ybgF. All members of the seed alignment were from unique tol-pal gene regions from completed bacterial genomes. The architecture of this protein is a signal sequence, a low-complexity region usually rich in Asn and Gln, a well-conserved region with tandem repeats that resemble the tetratricopeptide (TPR) repeat, involved in protein-protein interaction.
Probab=55.37 E-value=37 Score=21.67 Aligned_cols=23 Identities=17% Similarity=0.313 Sum_probs=12.0
Q ss_pred HHHHHHHHHhhhccChHHHHHHH
Q psy5990 58 LAALVASKVYFHLGSFSDSLQYA 80 (119)
Q Consensus 58 lAALvaSKVyyhLgey~~aL~yA 80 (119)
-+......+|+..|+|++|+++-
T Consensus 40 ~~~~~l~~~~~~~~~~~~A~~~~ 62 (119)
T TIGR02795 40 NAHYWLGEAYYAQGKYADAAKAF 62 (119)
T ss_pred HHHHHHHHHHHhhccHHHHHHHH
Confidence 33444455555555555555543
No 31
>cd00864 PI3Ka Phosphoinositide 3-kinase family, accessory domain (PIK domain); PIK domain is conserved in PI3 and PI4-kinases. Its role is unclear, but it has been suggested to be involved in substrate presentation. Phosphoinositide 3-kinases play an important role in a variety of fundamental cellular processes and can be divided into three main classes, defined by their substrate specificity and domain architecture.
Probab=55.28 E-value=74 Score=23.84 Aligned_cols=58 Identities=16% Similarity=0.251 Sum_probs=39.4
Q ss_pred cHHHHHHhcCC--CchHHHHHHHHHHhhhhhcchHHHHhhHHHHHHHhhCCCCCchhHHHHHH
Q psy5990 3 TVAGVISLLDD--PMIELKEFSLKKLNDIVDDFWPEVSEAIQKIEILHEDKGFPQYKLAALVA 63 (119)
Q Consensus 3 Saag~laLL~E--~d~~Lk~~AL~~L~~vVd~~W~EIsd~i~~IE~LyED~~F~~R~lAALva 63 (119)
+....|.||+. +++.++.||.+.|++.=|+ ++...++++=....-+.+....||-.+.
T Consensus 70 ~~~~aL~LL~~~~~~~~vr~yAv~~L~~~~~~---~l~~ylpQLVQaLkye~~~~~~L~~fLl 129 (152)
T cd00864 70 SPEDALELLSPKYPDPVVRQYAVRVLESASDD---ELLLYLPQLVQALKYEPYLDSYLARFLL 129 (152)
T ss_pred CHHHHHHHcCCcCCCHHHHHHHHHHHHhCCHH---HHHHHHHHHHHHHhccccCCCHHHHHHH
Confidence 34556788887 7899999999999985554 6666777665554444544555554443
No 32
>PF13174 TPR_6: Tetratricopeptide repeat; PDB: 3QKY_A 2XEV_A 3URZ_B 2Q7F_A.
Probab=51.02 E-value=16 Score=18.92 Aligned_cols=20 Identities=20% Similarity=0.743 Sum_probs=15.9
Q ss_pred HHHHHHhhhccChHHHHHHH
Q psy5990 61 LVASKVYFHLGSFSDSLQYA 80 (119)
Q Consensus 61 LvaSKVyyhLgey~~aL~yA 80 (119)
+-...+|+.+|++++|+++-
T Consensus 4 ~~~a~~~~~~g~~~~A~~~~ 23 (33)
T PF13174_consen 4 YRLARCYYKLGDYDEAIEYF 23 (33)
T ss_dssp HHHHHHHHHHCHHHHHHHHH
T ss_pred HHHHHHHHHccCHHHHHHHH
Confidence 44568899999999998753
No 33
>PF13414 TPR_11: TPR repeat; PDB: 2HO1_B 2FI7_B 2DBA_A 3Q4A_B 2C2L_D 3Q47_B 3Q49_B 2PL2_B 3IEG_B 2FBN_A ....
Probab=50.60 E-value=19 Score=21.69 Aligned_cols=30 Identities=20% Similarity=0.302 Sum_probs=23.1
Q ss_pred CchhHHHHHHHHHhhhcc-ChHHHHHHHHhC
Q psy5990 54 PQYKLAALVASKVYFHLG-SFSDSLQYALGA 83 (119)
Q Consensus 54 ~~R~lAALvaSKVyyhLg-ey~~aL~yAL~A 83 (119)
|+...+-.-.+.+|+.+| ++++|+++...|
T Consensus 34 p~~~~~~~~~g~~~~~~~~~~~~A~~~~~~a 64 (69)
T PF13414_consen 34 PNNAEAYYNLGLAYMKLGKDYEEAIEDFEKA 64 (69)
T ss_dssp TTHHHHHHHHHHHHHHTTTHHHHHHHHHHHH
T ss_pred CCCHHHHHHHHHHHHHhCccHHHHHHHHHHH
Confidence 444556677789999999 799999987653
No 34
>PF13176 TPR_7: Tetratricopeptide repeat; PDB: 3SF4_C 3RO3_A 3RO2_A.
Probab=50.42 E-value=12 Score=20.92 Aligned_cols=16 Identities=19% Similarity=0.764 Sum_probs=13.1
Q ss_pred HHHhhhccChHHHHHH
Q psy5990 64 SKVYFHLGSFSDSLQY 79 (119)
Q Consensus 64 SKVyyhLgey~~aL~y 79 (119)
..+|..+|+|++|+++
T Consensus 6 g~~~~~~g~~~~Ai~~ 21 (36)
T PF13176_consen 6 GRIYRQQGDYEKAIEY 21 (36)
T ss_dssp HHHHHHCT-HHHHHHH
T ss_pred HHHHHHcCCHHHHHHH
Confidence 3789999999999986
No 35
>KOG3877|consensus
Probab=50.11 E-value=26 Score=30.78 Aligned_cols=76 Identities=14% Similarity=0.159 Sum_probs=55.2
Q ss_pred HhhHHHHHHHhhCCCCCchhHHHHHHHHHhh-hccChHHHHHHHHhCCCCCC--CCCCChhH--HHhhhhh----hhhHH
Q psy5990 38 SEAIQKIEILHEDKGFPQYKLAALVASKVYF-HLGSFSDSLQYALGAGDLFD--VRNDTVYV--KTIICKY----FCISL 108 (119)
Q Consensus 38 sd~i~~IE~LyED~~F~~R~lAALvaSKVyy-hLgey~~aL~yAL~AG~lFd--v~~~seYv--etiisk~----~cID~ 108 (119)
+..++.|+..|.|+ +.+++|.+-+.+|- .+..|-+||.--|.-|.--= -+.-|+|| |.|-.+- -|.++
T Consensus 127 ~cr~~di~~Fy~dP---S~dlsa~~Q~r~y~~R~~QY~dAL~HiL~TGQGVVLERsp~SDFVF~eAM~~qgyi~~~~~~h 203 (393)
T KOG3877|consen 127 RCRLPDISMFYKDP---SGDLSAAMQDRIYNCRFDQYLDALAHILNTGQGVVLERSPHSDFVFAEAMRDQGYIGHEYFKH 203 (393)
T ss_pred ccCchhHHHhccCC---CccHHHHHHHHHHHhHHHHHHHHHHHHHhcCCeEEEecCcchhHHHHHHHHhcCcchhHHHHH
Confidence 35678899999998 55699999999985 58899999999998887432 22334443 4443221 28999
Q ss_pred HHHhhhcc
Q psy5990 109 STYRYSNV 116 (119)
Q Consensus 109 Yi~~~~~~ 116 (119)
|-.+|+|.
T Consensus 204 Ynevr~nt 211 (393)
T KOG3877|consen 204 YNEVRKNT 211 (393)
T ss_pred HHHHHhhh
Confidence 99999874
No 36
>PF14559 TPR_19: Tetratricopeptide repeat; PDB: 2R5S_A 3QDN_B 3QOU_A 3ASG_A 3ASD_A 3AS5_A 3AS4_A 3ASH_B 3FP3_A 3LCA_A ....
Probab=49.84 E-value=24 Score=21.06 Aligned_cols=43 Identities=21% Similarity=0.302 Sum_probs=27.1
Q ss_pred hhHHHHHHHhhCCCCCchhHHHHHHHHHhhhccChHHHHHHHHhC
Q psy5990 39 EAIQKIEILHEDKGFPQYKLAALVASKVYFHLGSFSDSLQYALGA 83 (119)
Q Consensus 39 d~i~~IE~LyED~~F~~R~lAALvaSKVyyhLgey~~aL~yAL~A 83 (119)
+++...+.+.+ .+|+..-+-+...++|+..|++++|.+.--..
T Consensus 9 ~A~~~~~~~l~--~~p~~~~~~~~la~~~~~~g~~~~A~~~l~~~ 51 (68)
T PF14559_consen 9 EAIELLEKALQ--RNPDNPEARLLLAQCYLKQGQYDEAEELLERL 51 (68)
T ss_dssp HHHHHHHHHHH--HTTTSHHHHHHHHHHHHHTT-HHHHHHHHHCC
T ss_pred HHHHHHHHHHH--HCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHH
Confidence 44444444442 13444455556679999999999999875544
No 37
>PF09976 TPR_21: Tetratricopeptide repeat; InterPro: IPR018704 This domain, found in various hypothetical prokaryotic proteins, has no known function.
Probab=49.18 E-value=37 Score=23.91 Aligned_cols=43 Identities=19% Similarity=0.237 Sum_probs=30.5
Q ss_pred HhhHHHHHHHhhCC-CCCchhHHHHHHHHHhhhccChHHHHHHH
Q psy5990 38 SEAIQKIEILHEDK-GFPQYKLAALVASKVYFHLGSFSDSLQYA 80 (119)
Q Consensus 38 sd~i~~IE~LyED~-~F~~R~lAALvaSKVyyhLgey~~aL~yA 80 (119)
.+++...+...++. .-+-+.+|.+=..+|++..|+|++|+...
T Consensus 65 ~~A~~~l~~~~~~~~d~~l~~~a~l~LA~~~~~~~~~d~Al~~L 108 (145)
T PF09976_consen 65 DEAKAALEKALANAPDPELKPLARLRLARILLQQGQYDEALATL 108 (145)
T ss_pred HHHHHHHHHHHhhCCCHHHHHHHHHHHHHHHHHcCCHHHHHHHH
Confidence 34555555555554 33456778887889999999999999885
No 38
>KOG3364|consensus
Probab=49.16 E-value=30 Score=26.96 Aligned_cols=55 Identities=22% Similarity=0.256 Sum_probs=38.9
Q ss_pred HHHhhHHHHHHHhh-CCCCCchhHHHHHHHHHhhhccChHHHHHHHHhCCCCCCCCCCCh
Q psy5990 36 EVSEAIQKIEILHE-DKGFPQYKLAALVASKVYFHLGSFSDSLQYALGAGDLFDVRNDTV 94 (119)
Q Consensus 36 EIsd~i~~IE~LyE-D~~F~~R~lAALvaSKVyyhLgey~~aL~yAL~AG~lFdv~~~se 94 (119)
+|-.-|.-+|++++ +..-..|+.--.+|- -+|.|++|+.|++|-=. +++.+.++.
T Consensus 50 dv~~GI~iLe~l~~~~~~~~rRe~lyYLAv-g~yRlkeY~~s~~yvd~---ll~~e~~n~ 105 (149)
T KOG3364|consen 50 DVQEGIVILEDLLKSAHPERRRECLYYLAV-GHYRLKEYSKSLRYVDA---LLETEPNNR 105 (149)
T ss_pred HHHHhHHHHHHHhhhcCcccchhhhhhhHH-HHHHHhhHHHHHHHHHH---HHhhCCCcH
Confidence 46677888999998 455557776666653 47899999999999532 555554443
No 39
>PF12717 Cnd1: non-SMC mitotic condensation complex subunit 1
Probab=49.12 E-value=53 Score=24.44 Aligned_cols=65 Identities=17% Similarity=0.092 Sum_probs=51.9
Q ss_pred HHHHHhcCCCchHHHHHHHHHHhhhhhcchHHHHhhH-HHHHHHhhCCCCCchhHHHHHHHHHhhh
Q psy5990 5 AGVISLLDDPMIELKEFSLKKLNDIVDDFWPEVSEAI-QKIEILHEDKGFPQYKLAALVASKVYFH 69 (119)
Q Consensus 5 ag~laLL~E~d~~Lk~~AL~~L~~vVd~~W~EIsd~i-~~IE~LyED~~F~~R~lAALvaSKVyyh 69 (119)
.-+...|.++++.+|..|+.-|..++-+-+--+-+.+ ..+-.+..|++=.=|+.|...-..+--.
T Consensus 28 ~~l~~~L~D~~~~VR~~al~~Ls~Li~~d~ik~k~~l~~~~l~~l~D~~~~Ir~~A~~~~~e~~~~ 93 (178)
T PF12717_consen 28 PNLYKCLRDEDPLVRKTALLVLSHLILEDMIKVKGQLFSRILKLLVDENPEIRSLARSFFSELLKK 93 (178)
T ss_pred HHHHHHHCCCCHHHHHHHHHHHHHHHHcCceeehhhhhHHHHHHHcCCCHHHHHHHHHHHHHHHHh
Confidence 3567889999999999999999999988777777777 7787888898877788887666555433
No 40
>PF11815 DUF3336: Domain of unknown function (DUF3336); InterPro: IPR021771 This family of proteins is characterised by an N-terminal domain that is found adjacent to the patatin/phospholipase A2-related domain (see PF01734 from PFAM). The family of proteins, which contain these two domains, have been characterised in Saccharomyces cerevisiae (Baker's yeast) as a bifunctional enzyme with triacylglycerol lipase and lysophosphatidic acid acyltransferase or lysophosphatidylethanolamine acyltransferase activity. They are generally involved in triacylglycerol mobilisation and localized to lipid particles [, ].
Probab=47.44 E-value=60 Score=24.18 Aligned_cols=81 Identities=16% Similarity=0.181 Sum_probs=50.2
Q ss_pred cchHHHHhhHHHHHHHh---hCCCC---CchhHHHHHHHHHhh-hccChHHHHHHHHhCC---CCCCCCCCChhHHHhhh
Q psy5990 32 DFWPEVSEAIQKIEILH---EDKGF---PQYKLAALVASKVYF-HLGSFSDSLQYALGAG---DLFDVRNDTVYVKTIIC 101 (119)
Q Consensus 32 ~~W~EIsd~i~~IE~Ly---ED~~F---~~R~lAALvaSKVyy-hLgey~~aL~yAL~AG---~lFdv~~~seYvetiis 101 (119)
+-|.++|..++.++-.- +++.. ..+..-..+..=--. .=|+. ..|-++|.+| ++.++....-|..+-+.
T Consensus 27 eEW~~~A~~LD~l~G~~~Wk~~~~s~~YD~~lI~~rl~~L~~aR~~~d~-~~l~~~Lr~~l~RNlggi~n~~LY~~s~~G 105 (145)
T PF11815_consen 27 EEWKEAAQELDELEGNDAWKEDDESDYYDYRLIRERLRELREARQSGDI-EALMFLLRTGLHRNLGGIGNPRLYSHSYSG 105 (145)
T ss_pred HHHHHHHHHHHHHcCcchhhcCCCCcccCHHHHHHHHHHHHHHHHcCCH-HHHHHHHHHHHhcCccccCCHHHHHHcccc
Confidence 67999999999885433 23332 222222111111111 11333 5677888876 57778889999998886
Q ss_pred hhhhhHHHHHhh
Q psy5990 102 KYFCISLSTYRY 113 (119)
Q Consensus 102 k~~cID~Yi~~~ 113 (119)
.-.+|+.||...
T Consensus 106 TK~lIe~Yi~ev 117 (145)
T PF11815_consen 106 TKRLIEEYIDEV 117 (145)
T ss_pred chHHHHHHHHHH
Confidence 667999999854
No 41
>PF04826 Arm_2: Armadillo-like; InterPro: IPR006911 This entry consists of mammalian proteins of unknown function.
Probab=47.10 E-value=88 Score=25.41 Aligned_cols=98 Identities=21% Similarity=0.258 Sum_probs=62.1
Q ss_pred HHHHHHhcCCCchHHHHHHHHHHhh--hhhcchHHHHhhHHHHHHHhhCCCC-CchhHHH--------------------
Q psy5990 4 VAGVISLLDDPMIELKEFSLKKLND--IVDDFWPEVSEAIQKIEILHEDKGF-PQYKLAA-------------------- 60 (119)
Q Consensus 4 aag~laLL~E~d~~Lk~~AL~~L~~--vVd~~W~EIsd~i~~IE~LyED~~F-~~R~lAA-------------------- 60 (119)
..-+..+|+.|++++|..||..|+. .-+++=..|..+|+++-..--...- ..=|+|+
T Consensus 56 i~lI~~lL~~p~~~vr~~AL~aL~Nls~~~en~~~Ik~~i~~Vc~~~~s~~lns~~Q~agLrlL~nLtv~~~~~~~l~~~ 135 (254)
T PF04826_consen 56 ISLIGSLLNDPNPSVREKALNALNNLSVNDENQEQIKMYIPQVCEETVSSPLNSEVQLAGLRLLTNLTVTNDYHHMLANY 135 (254)
T ss_pred HHHHHHHcCCCChHHHHHHHHHHHhcCCChhhHHHHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHccCCCcchhhhHHhh
Confidence 3447789999999999999999994 4445556788888877543222111 0111221
Q ss_pred ----------------HHHHHHhhhccChHHHHHHHHhCCCC------CCCCCCChhHHHhhh
Q psy5990 61 ----------------LVASKVYFHLGSFSDSLQYALGAGDL------FDVRNDTVYVKTIIC 101 (119)
Q Consensus 61 ----------------LvaSKVyyhLgey~~aL~yAL~AG~l------Fdv~~~seYvetiis 101 (119)
.-+.||..+|.+=++-.+..|+|+-+ ||.+++.+-...++.
T Consensus 136 i~~ll~LL~~G~~~~k~~vLk~L~nLS~np~~~~~Ll~~q~~~~~~~Lf~~~~~~~~l~~~l~ 198 (254)
T PF04826_consen 136 IPDLLSLLSSGSEKTKVQVLKVLVNLSENPDMTRELLSAQVLSSFLSLFNSSESKENLLRVLT 198 (254)
T ss_pred HHHHHHHHHcCChHHHHHHHHHHHHhccCHHHHHHHHhccchhHHHHHHccCCccHHHHHHHH
Confidence 12456677777777777777777654 676666665444443
No 42
>cd00872 PI3Ka_I Phosphoinositide 3-kinase (PI3K) class I, accessory domain ; PIK domain is conserved in all PI3 and PI4-kinases. Its role is unclear but it has been suggested to be involved in substrate presentation. In general, PI3K class I prefer phosphoinositol (4,5)-bisphosphate as a substrate. Mammalian members interact with active Ras. They form heterodimers with adapter molecules linking them to different signaling pathways.
Probab=46.99 E-value=1.1e+02 Score=23.69 Aligned_cols=61 Identities=18% Similarity=0.338 Sum_probs=46.1
Q ss_pred cHHHHHHhcCC--CchHHHHHHHHHHhhhhhcchHHHHhhHHHHHHHhhCCCCCchhHHHHHHHHH
Q psy5990 3 TVAGVISLLDD--PMIELKEFSLKKLNDIVDDFWPEVSEAIQKIEILHEDKGFPQYKLAALVASKV 66 (119)
Q Consensus 3 Saag~laLL~E--~d~~Lk~~AL~~L~~vVd~~W~EIsd~i~~IE~LyED~~F~~R~lAALvaSKV 66 (119)
+....|.||+. +|+.+|.||.+.|+..=|+ |+...++++=.--.-|.+.+..||-.+..+.
T Consensus 70 ~~~~aLeLL~~~f~d~~VR~yAV~~L~~~sd~---eL~~yL~QLVQaLKyE~~~ds~La~FLl~Ra 132 (171)
T cd00872 70 KPEQALELLDCNFPDEHVREFAVRCLEKLSDD---ELLQYLLQLVQVLKYEPYHDSDLVRFLLKRA 132 (171)
T ss_pred CHHHHHHHCCCcCCCHHHHHHHHHHHHhCCHH---HHHHHHHHHHHHHHcccccCCHHHHHHHHHH
Confidence 34456777876 6789999999999987664 6888999887777777777777777665554
No 43
>cd00020 ARM Armadillo/beta-catenin-like repeats. An approximately 40 amino acid long tandemly repeated sequence motif first identified in the Drosophila segment polarity gene armadillo; these repeats were also found in the mammalian armadillo homolog beta-catenin, the junctional plaque protein plakoglobin, the adenomatous polyposis coli (APC) tumor suppressor protein, and a number of other proteins. ARM has been implicated in mediating protein-protein interactions, but no common features among the target proteins recognized by the ARM repeats have been identified; related to the HEAT domain; three consecutive copies of the repeat are represented by this alignment model.
Probab=46.72 E-value=75 Score=20.27 Aligned_cols=59 Identities=15% Similarity=0.071 Sum_probs=41.3
Q ss_pred HHHHHHhcCCCchHHHHHHHHHHhhhhhcchHHH---H--hhHHHHHHHhhCCCCCchhHHHHH
Q psy5990 4 VAGVISLLDDPMIELKEFSLKKLNDIVDDFWPEV---S--EAIQKIEILHEDKGFPQYKLAALV 62 (119)
Q Consensus 4 aag~laLL~E~d~~Lk~~AL~~L~~vVd~~W~EI---s--d~i~~IE~LyED~~F~~R~lAALv 62 (119)
...++.+|..+++.++..|+.-|-.+......-. - +.++.+..+..+.+..-|+.|..+
T Consensus 51 i~~l~~~l~~~~~~v~~~a~~~L~~l~~~~~~~~~~~~~~g~l~~l~~~l~~~~~~~~~~a~~~ 114 (120)
T cd00020 51 LPALVQLLKSEDEEVVKAALWALRNLAAGPEDNKLIVLEAGGVPKLVNLLDSSNEDIQKNATGA 114 (120)
T ss_pred hHHHHHHHhCCCHHHHHHHHHHHHHHccCcHHHHHHHHHCCChHHHHHHHhcCCHHHHHHHHHH
Confidence 3457788999999999999999999988775321 1 236666666666655555555433
No 44
>PF09976 TPR_21: Tetratricopeptide repeat; InterPro: IPR018704 This domain, found in various hypothetical prokaryotic proteins, has no known function.
Probab=45.92 E-value=66 Score=22.61 Aligned_cols=47 Identities=17% Similarity=0.186 Sum_probs=32.7
Q ss_pred hcchHHHHhhHHHHHHHhhCCCCCchhHHHHHHHHHhhhccChHHHHHH
Q psy5990 31 DDFWPEVSEAIQKIEILHEDKGFPQYKLAALVASKVYFHLGSFSDSLQY 79 (119)
Q Consensus 31 d~~W~EIsd~i~~IE~LyED~~F~~R~lAALvaSKVyyhLgey~~aL~y 79 (119)
..-|..+...+..|.. +.++=+...+|.|...++++.-|+|++|...
T Consensus 24 ~~~~~~~~~~~~~l~~--~~~~s~ya~~A~l~lA~~~~~~g~~~~A~~~ 70 (145)
T PF09976_consen 24 AGDPAKAEAAAEQLAK--DYPSSPYAALAALQLAKAAYEQGDYDEAKAA 70 (145)
T ss_pred CCCHHHHHHHHHHHHH--HCCCChHHHHHHHHHHHHHHHCCCHHHHHHH
Confidence 3556666554444433 2333346689999999999999999998765
No 45
>PF00514 Arm: Armadillo/beta-catenin-like repeat; InterPro: IPR000225 The armadillo (Arm) repeat is an approximately 40 amino acid long tandemly repeated sequence motif first identified in the Drosophila melanogaster segment polarity gene armadillo involved in signal transduction through wingless. Animal Arm-repeat proteins function in various processes, including intracellular signalling and cytoskeletal regulation, and include such proteins as beta-catenin, the junctional plaque protein plakoglobin, the adenomatous polyposis coli (APC) tumour suppressor protein, and the nuclear transport factor importin-alpha, amongst others []. A subset of these proteins is conserved across eukaryotic kingdoms. In higher plants, some Arm-repeat proteins function in intracellular signalling like their mammalian counterparts, while others have novel functions []. The 3-dimensional fold of an armadillo repeat is known from the crystal structure of beta-catenin, where the 12 repeats form a superhelix of alpha helices with three helices per unit []. The cylindrical structure features a positively charged grove, which presumably interacts with the acidic surfaces of the known interaction partners of beta-catenin.; GO: 0005515 protein binding; PDB: 2Z6G_A 1IQ1_C 3RZX_A 2C1M_A 3BTR_C 3OQS_A 3TPO_A 1IAL_A 1Q1S_C 1PJM_B ....
Probab=45.57 E-value=46 Score=18.86 Aligned_cols=26 Identities=23% Similarity=0.385 Sum_probs=21.7
Q ss_pred HHHHHHhcCCCchHHHHHHHHHHhhh
Q psy5990 4 VAGVISLLDDPMIELKEFSLKKLNDI 29 (119)
Q Consensus 4 aag~laLL~E~d~~Lk~~AL~~L~~v 29 (119)
...++.||..++++++..|+-.|-.+
T Consensus 14 i~~Lv~ll~~~~~~v~~~a~~al~nl 39 (41)
T PF00514_consen 14 IPPLVQLLKSPDPEVQEEAAWALGNL 39 (41)
T ss_dssp HHHHHHHTTSSSHHHHHHHHHHHHHH
T ss_pred HHHHHHHHcCCCHHHHHHHHHHHHHH
Confidence 35689999999999999998877654
No 46
>TIGR02521 type_IV_pilW type IV pilus biogenesis/stability protein PilW. Members of this family are designated PilF in ref (PubMed:8973346) and PilW in ref (PubMed:15612916). This outer membrane protein is required both for pilus stability and for pilus function such as adherence to human cells. Members of this family contain copies of the TPR (tetratricopeptide repeat) domain.
Probab=42.20 E-value=67 Score=22.07 Aligned_cols=25 Identities=20% Similarity=0.397 Sum_probs=12.4
Q ss_pred HHHHHHHHhhhccChHHHHHHHHhC
Q psy5990 59 AALVASKVYFHLGSFSDSLQYALGA 83 (119)
Q Consensus 59 AALvaSKVyyhLgey~~aL~yAL~A 83 (119)
+......+|+..|++++|+++.-.+
T Consensus 171 ~~~~la~~~~~~~~~~~A~~~~~~~ 195 (234)
T TIGR02521 171 SLLELAELYYLRGQYKDARAYLERY 195 (234)
T ss_pred HHHHHHHHHHHcCCHHHHHHHHHHH
Confidence 3334445555555555555544333
No 47
>PRK13800 putative oxidoreductase/HEAT repeat-containing protein; Provisional
Probab=42.08 E-value=66 Score=30.25 Aligned_cols=54 Identities=19% Similarity=0.125 Sum_probs=39.2
Q ss_pred HHHHHHhcCCCchHHHHHHHHHHhhhhhcchHHHHhhHHHHHHHhhCCCCCchhHHHHHH
Q psy5990 4 VAGVISLLDDPMIELKEFSLKKLNDIVDDFWPEVSEAIQKIEILHEDKGFPQYKLAALVA 63 (119)
Q Consensus 4 aag~laLL~E~d~~Lk~~AL~~L~~vVd~~W~EIsd~i~~IE~LyED~~F~~R~lAALva 63 (119)
...++.+|+++++.+|..|++.|-..- + .+.++.|..+.+|+.-.-|.-|+--.
T Consensus 623 ~~~L~~~L~D~d~~VR~~Av~~L~~~~----~--~~~~~~L~~aL~D~d~~VR~~Aa~aL 676 (897)
T PRK13800 623 VAELAPYLADPDPGVRRTAVAVLTETT----P--PGFGPALVAALGDGAAAVRRAAAEGL 676 (897)
T ss_pred HHHHHHHhcCCCHHHHHHHHHHHhhhc----c--hhHHHHHHHHHcCCCHHHHHHHHHHH
Confidence 457888999999999999999887643 3 34567777777777766666554433
No 48
>PF11701 UNC45-central: Myosin-binding striated muscle assembly central; InterPro: IPR024660 The UNC-45 or small muscle protein 1 of Caenorhabditis elegans is expressed in two forms from different genomic positions in mammals: as a general tissue protein (UNC-45a) and as a specific form (UNC-45b) expressed only in striated and skeletal muscle. Myofibril formation requires both UNC-45 forms, consistent with the fact that the cytoskeleton is necessary for the development and maintenance of organised myofibrils []. Rng3 (Ring assembly protein 3), the homologue in Schizosaccharomyces pombe, is crucial for cell shape, normal actin cytoskeleton, and contractile ring assembly, and is essential for assembly of the myosin II-containing progenitors of the contractile ring. Widespread defects in the cytoskeleton are found in null mutants of all three fungal proteins []. Mammalian Unc45 is found to act as a specific chaperone during the folding of myosin and the assembly of striated muscle by forming a stable complex with the general chaperone Hsp90 []. All members carry up to three amino-terminal tetratricopeptide repeat (TPR) and a UCS domain at the C terminus that contains a number of Arm repeats. ; PDB: 3OPB_A 3NOW_A.
Probab=41.70 E-value=1e+02 Score=22.85 Aligned_cols=61 Identities=15% Similarity=0.120 Sum_probs=46.1
Q ss_pred HHHHhcC--CCchHHHHHHHHHHhh-hhhcchHH--HHhhHHHHHHHhhCCCCC--chhHHHHHHHHH
Q psy5990 6 GVISLLD--DPMIELKEFSLKKLND-IVDDFWPE--VSEAIQKIEILHEDKGFP--QYKLAALVASKV 66 (119)
Q Consensus 6 g~laLL~--E~d~~Lk~~AL~~L~~-vVd~~W~E--Isd~i~~IE~LyED~~F~--~R~lAALvaSKV 66 (119)
.++.+.. .++..++.-+|+-|+. ++|.-=.+ ..+.++-+|.+|....=+ -|-+|+++..|.
T Consensus 90 ~l~~~~~~~~~~~~~~~~~lell~aAc~d~~~r~~I~~~~~~~L~~~~~~~~~~~~ir~~A~v~L~Kl 157 (157)
T PF11701_consen 90 SLLPLASRKSKDRKVQKAALELLSAACIDKSCRTFISKNYVSWLKELYKNSKDDSEIRVLAAVGLCKL 157 (157)
T ss_dssp HHHHHHH-CTS-HHHHHHHHHHHHHHTTSHHHHHCCHHHCHHHHHHHTTTCC-HH-CHHHHHHHHHHC
T ss_pred HHHHHHhcccCCHHHHHHHHHHHHHHHccHHHHHHHHHHHHHHHHHHHccccchHHHHHHHHHHHhcC
Confidence 3555666 7888889999999985 88877777 568899999999655543 488999888773
No 49
>PF12348 CLASP_N: CLASP N terminal; InterPro: IPR024395 This domain is found in the N-terminal region of CLIP-associated proteins (CLASPs), which are widely conserved microtubule plus-end-tracking proteins that regulate the stability of dynamic microtubules [, ]. The domain is also found in other proteins involved in microtubule binding, including STU1, MOR1 and spindle pole body component Alp14.; PDB: 2QK2_A.
Probab=40.64 E-value=1e+02 Score=22.95 Aligned_cols=71 Identities=14% Similarity=0.108 Sum_probs=50.3
Q ss_pred HHHhcCCCchHHHHHHHHHHhhhhhcch---HHH------HhhHHHHHHHhhCCCCCchhHHHHHHHHHhhhccChHHHH
Q psy5990 7 VISLLDDPMIELKEFSLKKLNDIVDDFW---PEV------SEAIQKIEILHEDKGFPQYKLAALVASKVYFHLGSFSDSL 77 (119)
Q Consensus 7 ~laLL~E~d~~Lk~~AL~~L~~vVd~~W---~EI------sd~i~~IE~LyED~~F~~R~lAALvaSKVyyhLgey~~aL 77 (119)
+...+..+.+.+|..+++-|..++..++ +.+ ..-++.|-.+.+|.+=.-|+.|--+....+-|.|+-.+++
T Consensus 136 l~~~~~~Kn~~vR~~~~~~l~~~l~~~~~~~~~l~~~~~~~~l~~~l~~~l~D~~~~VR~~Ar~~~~~l~~~~~~~a~~~ 215 (228)
T PF12348_consen 136 LSQGLKSKNPQVREECAEWLAIILEKWGSDSSVLQKSAFLKQLVKALVKLLSDADPEVREAARECLWALYSHFPERAESI 215 (228)
T ss_dssp HHHHTT-S-HHHHHHHHHHHHHHHTT-----GGG--HHHHHHHHHHHHHHHTSS-HHHHHHHHHHHHHHHHHH-HHH---
T ss_pred HHHHHhCCCHHHHHHHHHHHHHHHHHccchHhhhcccchHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHCCHhhccc
Confidence 4456788999999999999999999888 333 4456667778899999999999988888888887765544
No 50
>PF07721 TPR_4: Tetratricopeptide repeat; InterPro: IPR011717 This entry includes tetratricopeptide-like repeats not detected by the IPR001440 from INTERPRO, IPR013105 from INTERPRO and IPR011716 from INTERPRO models. The tetratricopeptide repeat (TPR) motif is a protein-protein interaction module found in multiple copies in a number of functionally different proteins that facilitates specific interactions with a partner protein(s) [].; GO: 0042802 identical protein binding
Probab=40.42 E-value=43 Score=17.58 Aligned_cols=20 Identities=10% Similarity=0.204 Sum_probs=16.2
Q ss_pred HHHHHHHhhhccChHHHHHH
Q psy5990 60 ALVASKVYFHLGSFSDSLQY 79 (119)
Q Consensus 60 ALvaSKVyyhLgey~~aL~y 79 (119)
.+....+++..|++++|...
T Consensus 4 ~~~la~~~~~~G~~~eA~~~ 23 (26)
T PF07721_consen 4 RLALARALLAQGDPDEAERL 23 (26)
T ss_pred HHHHHHHHHHcCCHHHHHHH
Confidence 44556899999999999864
No 51
>smart00028 TPR Tetratricopeptide repeats. Repeats present in 4 or more copies in proteins. Contain a minimum of 34 amino acids each and self-associate via a "knobs and holes" mechanism.
Probab=39.87 E-value=41 Score=15.29 Aligned_cols=19 Identities=26% Similarity=0.693 Sum_probs=15.1
Q ss_pred HHHHhhhccChHHHHHHHH
Q psy5990 63 ASKVYFHLGSFSDSLQYAL 81 (119)
Q Consensus 63 aSKVyyhLgey~~aL~yAL 81 (119)
...+|+++|++++|....-
T Consensus 7 ~a~~~~~~~~~~~a~~~~~ 25 (34)
T smart00028 7 LGNAYLKLGDYDEALEYYE 25 (34)
T ss_pred HHHHHHHHhhHHHHHHHHH
Confidence 3578999999999987653
No 52
>smart00145 PI3Ka Phosphoinositide 3-kinase family, accessory domain (PIK domain). PIK domain is conserved in all PI3 and PI4-kinases. Its role is unclear but it has been suggested to be involved in substrate presentation.
Probab=38.26 E-value=1.8e+02 Score=22.61 Aligned_cols=58 Identities=14% Similarity=0.255 Sum_probs=42.2
Q ss_pred HHHHHhcCC--CchHHHHHHHHHHhhhhhcchHHHHhhHHHHHHHhhCCCCCchhHHHHHHHH
Q psy5990 5 AGVISLLDD--PMIELKEFSLKKLNDIVDDFWPEVSEAIQKIEILHEDKGFPQYKLAALVASK 65 (119)
Q Consensus 5 ag~laLL~E--~d~~Lk~~AL~~L~~vVd~~W~EIsd~i~~IE~LyED~~F~~R~lAALvaSK 65 (119)
.-.|.||+. +++.++.||.+.|.+.=|+ |+...|+++=....-+.+....||-.+..+
T Consensus 77 ~~aL~LL~~~~~~~~Vr~yAV~~L~~~~d~---~l~~yLpQLVQaLr~E~~~~~~L~~fLl~r 136 (184)
T smart00145 77 EDALELLSPKFPDPFVRAYAVERLESASDE---ELLLYLLQLVQALKYEPYLDSALARFLLER 136 (184)
T ss_pred HHHHHHhCccCCCHHHHHHHHHHHHhCCHH---HHHHHHHHHHHHHHcccccccHHHHHHHHH
Confidence 445777775 5789999999999987766 788888888666566666666666655443
No 53
>PF13935 Ead_Ea22: Ead/Ea22-like protein
Probab=37.41 E-value=59 Score=23.94 Aligned_cols=61 Identities=15% Similarity=-0.013 Sum_probs=41.0
Q ss_pred HHHHHHhcCCCchH-HHHHHHHHH--hhhhhcchHHHHhhHHHHHHHhhCCCCCchhHHHHHHH
Q psy5990 4 VAGVISLLDDPMIE-LKEFSLKKL--NDIVDDFWPEVSEAIQKIEILHEDKGFPQYKLAALVAS 64 (119)
Q Consensus 4 aag~laLL~E~d~~-Lk~~AL~~L--~~vVd~~W~EIsd~i~~IE~LyED~~F~~R~lAALvaS 64 (119)
.+-+|+||+|-+.. =..-.+++. +.-+..-|.+.-..|+..+...+.+.+.++..+.-+..
T Consensus 66 P~tvLALLDElE~~~~~i~~~~~~~e~~~~a~~~~~l~~~Le~ae~~~~~~~~~~~~~~e~~~~ 129 (139)
T PF13935_consen 66 PATVLALLDELERAQQRIAELEQECENEDIALDVQKLRVELEAAEKRIAAELAEQAEAYEGEIA 129 (139)
T ss_pred chHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHH
Confidence 46789999997743 234455555 55566778887777877777776667776666555443
No 54
>PF14689 SPOB_a: Sensor_kinase_SpoOB-type, alpha-helical domain; PDB: 1F51_C 2FTK_B 1IXM_B.
Probab=37.19 E-value=1.1e+02 Score=19.62 Aligned_cols=40 Identities=20% Similarity=0.266 Sum_probs=30.0
Q ss_pred HHHHHHHhhhhhcchHHHHhhHHHHHHHhhCCCCCchhHHHHHHHHHhhhccChHHHHHH
Q psy5990 20 EFSLKKLNDIVDDFWPEVSEAIQKIEILHEDKGFPQYKLAALVASKVYFHLGSFSDSLQY 79 (119)
Q Consensus 20 ~~AL~~L~~vVd~~W~EIsd~i~~IE~LyED~~F~~R~lAALvaSKVyyhLgey~~aL~y 79 (119)
.-.++++...+....++..+++..|-- |-.+|++++|.+|
T Consensus 6 ~~~~~~~~~~lR~~RHD~~NhLqvI~g--------------------llqlg~~~~a~eY 45 (62)
T PF14689_consen 6 LEELEELIDSLRAQRHDFLNHLQVIYG--------------------LLQLGKYEEAKEY 45 (62)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHHHHH--------------------HHHTT-HHHHHHH
T ss_pred HHHHHHHHHHHHHHhHHHHHHHHHHHH--------------------HHHCCCHHHHHHH
Confidence 345677888888889999999997744 4568888888765
No 55
>PRK13800 putative oxidoreductase/HEAT repeat-containing protein; Provisional
Probab=36.79 E-value=1.4e+02 Score=28.21 Aligned_cols=42 Identities=19% Similarity=0.087 Sum_probs=19.1
Q ss_pred HHHhcCCCchHHHHHHHHHHhhhhhcchHHHHhhHHHHHHHhhCCC
Q psy5990 7 VISLLDDPMIELKEFSLKKLNDIVDDFWPEVSEAIQKIEILHEDKG 52 (119)
Q Consensus 7 ~laLL~E~d~~Lk~~AL~~L~~vVd~~W~EIsd~i~~IE~LyED~~ 52 (119)
++.+|.+++++++..|.+.|-.+ +.+-+..++.+..+..|+.
T Consensus 747 l~~~l~D~~~~VR~~aa~aL~~~----~~~~~~~~~~L~~ll~D~d 788 (897)
T PRK13800 747 VAGAATDENREVRIAVAKGLATL----GAGGAPAGDAVRALTGDPD 788 (897)
T ss_pred HHHHhcCCCHHHHHHHHHHHHHh----ccccchhHHHHHHHhcCCC
Confidence 44444444444444444444332 2222223455556666665
No 56
>PHA00510 transcriptional regulator
Probab=36.68 E-value=18 Score=27.29 Aligned_cols=34 Identities=18% Similarity=0.318 Sum_probs=28.2
Q ss_pred HHHHhcCCCc---hHHHHHHHHHHhhhhhcchHHHHh
Q psy5990 6 GVISLLDDPM---IELKEFSLKKLNDIVDDFWPEVSE 39 (119)
Q Consensus 6 g~laLL~E~d---~~Lk~~AL~~L~~vVd~~W~EIsd 39 (119)
|+.++|..++ .+.++|||++.+.--...|.+|+.
T Consensus 78 GFh~wlKGdnatWqE~hvyaLr~mtkp~tlnwsri~k 114 (125)
T PHA00510 78 GFHVWLKGDNATWQESHVYALRRMTKPKTLNWSRISK 114 (125)
T ss_pred ceeeEeeCCcchHHHHHHHHHHhhcCccccCHHHhcc
Confidence 6677777766 467899999999999999999974
No 57
>PRK09687 putative lyase; Provisional
Probab=36.51 E-value=99 Score=25.13 Aligned_cols=57 Identities=18% Similarity=0.063 Sum_probs=33.8
Q ss_pred cHHHHHHhcCCCchHHHHHHHHHHhhhhhcchHHHHhhHHHHHHHhhCCCCCchhHHHHHHHH
Q psy5990 3 TVAGVISLLDDPMIELKEFSLKKLNDIVDDFWPEVSEAIQKIEILHEDKGFPQYKLAALVASK 65 (119)
Q Consensus 3 Saag~laLL~E~d~~Lk~~AL~~L~~vVd~~W~EIsd~i~~IE~LyED~~F~~R~lAALvaSK 65 (119)
|...++.+|..++..++.-|+..|-.+=+ .+.++.+..|..|++-..|..|+-+.+.
T Consensus 24 ~~~~L~~~L~d~d~~vR~~A~~aL~~~~~------~~~~~~l~~ll~~~d~~vR~~A~~aLg~ 80 (280)
T PRK09687 24 NDDELFRLLDDHNSLKRISSIRVLQLRGG------QDVFRLAIELCSSKNPIERDIGADILSQ 80 (280)
T ss_pred cHHHHHHHHhCCCHHHHHHHHHHHHhcCc------chHHHHHHHHHhCCCHHHHHHHHHHHHh
Confidence 44566677777777777777666654432 3344455556666666666666544444
No 58
>PF10579 Rapsyn_N: Rapsyn N-terminal myristoylation and linker region; InterPro: IPR019568 Neuromuscular junction formation relies upon the clustering of acetylcholine receptors and other proteins in the muscle membrane. Rapsyn is a peripheral membrane protein that is selectively concentrated at the neuromuscular junction and is essential for the formation of synaptic acetylcholine receptor aggregates. Acetylcholine receptors fail to aggregate beneath nerve terminals in mice where rapsyn has been knocked out. The N-terminal six amino acids of rapsyn are its myristoylation site, and myristoylation is necessary for the targeting of the protein to the membrane []. ; GO: 0008270 zinc ion binding, 0033130 acetylcholine receptor binding, 0007268 synaptic transmission, 0005856 cytoskeleton, 0030054 cell junction, 0045211 postsynaptic membrane
Probab=36.32 E-value=26 Score=24.58 Aligned_cols=21 Identities=19% Similarity=0.379 Sum_probs=18.7
Q ss_pred HHHHHhhhccChHHHHHHHHh
Q psy5990 62 VASKVYFHLGSFSDSLQYALG 82 (119)
Q Consensus 62 vaSKVyyhLgey~~aL~yAL~ 82 (119)
-+..+|...|.|.++|+||+.
T Consensus 48 ~l~qA~~e~Gkyr~~L~fA~~ 68 (80)
T PF10579_consen 48 YLIQAHMEWGKYREMLAFALQ 68 (80)
T ss_pred HHHHHHHHHHHHHHHHHHHHH
Confidence 456899999999999999985
No 59
>TIGR02521 type_IV_pilW type IV pilus biogenesis/stability protein PilW. Members of this family are designated PilF in ref (PubMed:8973346) and PilW in ref (PubMed:15612916). This outer membrane protein is required both for pilus stability and for pilus function such as adherence to human cells. Members of this family contain copies of the TPR (tetratricopeptide repeat) domain.
Probab=35.45 E-value=88 Score=21.49 Aligned_cols=26 Identities=27% Similarity=0.247 Sum_probs=15.2
Q ss_pred HHHHHHHHHhhhccChHHHHHHHHhC
Q psy5990 58 LAALVASKVYFHLGSFSDSLQYALGA 83 (119)
Q Consensus 58 lAALvaSKVyyhLgey~~aL~yAL~A 83 (119)
.+....+.+|++.|++++|+++.-.+
T Consensus 66 ~~~~~la~~~~~~~~~~~A~~~~~~a 91 (234)
T TIGR02521 66 LAYLALALYYQQLGELEKAEDSFRRA 91 (234)
T ss_pred HHHHHHHHHHHHcCCHHHHHHHHHHH
Confidence 34445566677777777666654433
No 60
>TIGR03302 OM_YfiO outer membrane assembly lipoprotein YfiO. Members of this protein family include YfiO, a near-essential protein of the outer membrane, part of a complex involved in protein insertion into the bacterial outer membrane. Many proteins in this family are annotated as ComL, based on the involvement of this protein in natural transformation with exogenous DNA in Neisseria gonorrhoeae. This protein family shows sequence similarity to, but is distinct from, the tol-pal system protein YbgF (TIGR02795).
Probab=34.19 E-value=87 Score=23.16 Aligned_cols=34 Identities=21% Similarity=0.163 Sum_probs=19.8
Q ss_pred CchhHHHHHHHHHhhhccChHHHHHHHHhCCCCC
Q psy5990 54 PQYKLAALVASKVYFHLGSFSDSLQYALGAGDLF 87 (119)
Q Consensus 54 ~~R~lAALvaSKVyyhLgey~~aL~yAL~AG~lF 87 (119)
|...-|-.....+|.++|++++|..+.-.-+..|
T Consensus 200 ~~~~~a~~~l~~~~~~lg~~~~A~~~~~~l~~~~ 233 (235)
T TIGR03302 200 PATEEALARLVEAYLKLGLKDLAQDAAAVLGANY 233 (235)
T ss_pred cchHHHHHHHHHHHHHcCCHHHHHHHHHHHHhhC
Confidence 3344455566666777777777766655444433
No 61
>PF04826 Arm_2: Armadillo-like; InterPro: IPR006911 This entry consists of mammalian proteins of unknown function.
Probab=33.87 E-value=2.6e+02 Score=22.71 Aligned_cols=35 Identities=17% Similarity=0.199 Sum_probs=20.0
Q ss_pred CchHHHHHHHHHHhhh-hhcchHH-HHhhHHHHHHHh
Q psy5990 14 PMIELKEFSLKKLNDI-VDDFWPE-VSEAIQKIEILH 48 (119)
Q Consensus 14 ~d~~Lk~~AL~~L~~v-Vd~~W~E-Isd~i~~IE~Ly 48 (119)
.+.+++.-||+-|..+ |++.+++ ++.+++.+=.|.
T Consensus 107 lns~~Q~agLrlL~nLtv~~~~~~~l~~~i~~ll~LL 143 (254)
T PF04826_consen 107 LNSEVQLAGLRLLTNLTVTNDYHHMLANYIPDLLSLL 143 (254)
T ss_pred CCCHHHHHHHHHHHccCCCcchhhhHHhhHHHHHHHH
Confidence 3567777777777663 4444433 566666654433
No 62
>PF13513 HEAT_EZ: HEAT-like repeat; PDB: 2Z5J_A 2OT8_B 2Z5O_A 2H4M_A 2QMR_A 1QBK_B 2Z5M_A 2Z5K_A 2Z5N_A 1GCJ_B ....
Probab=32.75 E-value=72 Score=18.83 Aligned_cols=22 Identities=23% Similarity=0.238 Sum_probs=15.6
Q ss_pred HHHHhcCCCchHHHHHHHHHHh
Q psy5990 6 GVISLLDDPMIELKEFSLKKLN 27 (119)
Q Consensus 6 g~laLL~E~d~~Lk~~AL~~L~ 27 (119)
.++.+|.+++++++.-|...|-
T Consensus 32 ~L~~~L~d~~~~VR~~A~~aLg 53 (55)
T PF13513_consen 32 ALIPLLQDDDDSVRAAAAWALG 53 (55)
T ss_dssp HHHHHTTSSSHHHHHHHHHHHH
T ss_pred HHHHHHcCCCHHHHHHHHHHHh
Confidence 4667777777788777766653
No 63
>COG5096 Vesicle coat complex, various subunits [Intracellular trafficking and secretion]
Probab=32.73 E-value=1.5e+02 Score=28.45 Aligned_cols=71 Identities=27% Similarity=0.327 Sum_probs=54.3
Q ss_pred HHhcCCCchHHHHHHHHHHhhh-hhcchHHHHhhHHHHHHHhhCCCCCchhHHHHHHHHHh-----hhccC-hHHHHHHH
Q psy5990 8 ISLLDDPMIELKEFSLKKLNDI-VDDFWPEVSEAIQKIEILHEDKGFPQYKLAALVASKVY-----FHLGS-FSDSLQYA 80 (119)
Q Consensus 8 laLL~E~d~~Lk~~AL~~L~~v-Vd~~W~EIsd~i~~IE~LyED~~F~~R~lAALvaSKVy-----yhLge-y~~aL~yA 80 (119)
.-=|++|++.+|.+||+.|-.+ |...|..+-+ -|-.+.+|+.=--|+-||+-.-|.| ++.+. ..+.++..
T Consensus 98 ~kDl~d~N~~iR~~AlR~ls~l~~~el~~~~~~---~ik~~l~d~~ayVRk~Aalav~kly~ld~~l~~~~g~~~~l~~l 174 (757)
T COG5096 98 QKDLQDPNEEIRGFALRTLSLLRVKELLGNIID---PIKKLLTDPHAYVRKTAALAVAKLYRLDKDLYHELGLIDILKEL 174 (757)
T ss_pred HhhccCCCHHHHHHHHHHHHhcChHHHHHHHHH---HHHHHccCCcHHHHHHHHHHHHHHHhcCHhhhhcccHHHHHHHH
Confidence 3347899999999999999875 5577766654 4558899988889999999999998 44455 66666655
Q ss_pred H
Q psy5990 81 L 81 (119)
Q Consensus 81 L 81 (119)
+
T Consensus 175 ~ 175 (757)
T COG5096 175 V 175 (757)
T ss_pred h
Confidence 4
No 64
>PRK00736 hypothetical protein; Provisional
Probab=32.52 E-value=99 Score=20.45 Aligned_cols=32 Identities=22% Similarity=0.457 Sum_probs=25.1
Q ss_pred HHHHHHHHHHhhhhhcchHHHHhhHHHHHHHh
Q psy5990 17 ELKEFSLKKLNDIVDDFWPEVSEAIQKIEILH 48 (119)
Q Consensus 17 ~Lk~~AL~~L~~vVd~~W~EIsd~i~~IE~Ly 48 (119)
..+.-.++.||.+|-.-|.+|..--.++..|.
T Consensus 15 afqe~tie~Ln~~v~~Qq~~i~~L~~ql~~L~ 46 (68)
T PRK00736 15 AEQEKTIEELSDQLAEQWKTVEQMRKKLDALT 46 (68)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 45778899999999999999976655555554
No 65
>PF12719 Cnd3: Nuclear condensing complex subunits, C-term domain
Probab=32.38 E-value=2.1e+02 Score=22.97 Aligned_cols=103 Identities=12% Similarity=0.051 Sum_probs=68.1
Q ss_pred HHhcCCCchHHHHHHHHHHhhhhhcchHHHHhhHH-------------HHHHHhhCCCCCchhHHHHHHHHHhhhccCh-
Q psy5990 8 ISLLDDPMIELKEFSLKKLNDIVDDFWPEVSEAIQ-------------KIEILHEDKGFPQYKLAALVASKVYFHLGSF- 73 (119)
Q Consensus 8 laLL~E~d~~Lk~~AL~~L~~vVd~~W~EIsd~i~-------------~IE~LyED~~F~~R~lAALvaSKVyyhLgey- 73 (119)
+..++..++++|.-||+-+-+++-.|=.++-+.-+ .+....++++=.-|..|+--.+|...+=-=.
T Consensus 70 ~~~~~~~~~~v~~~al~~l~Dll~~~g~~~~~~~~~~~~~~~~~~l~~~l~~~l~~~~~~~~~~a~EGl~KLlL~~~i~~ 149 (298)
T PF12719_consen 70 LQALQKDDEEVKITALKALFDLLLTHGIDIFDSESDNDESVDSKSLLKILTKFLDSENPELQAIAVEGLCKLLLSGRISD 149 (298)
T ss_pred HHHHHhCCHHHHHHHHHHHHHHHHHcCchhccchhccCccchHhHHHHHHHHHHhcCCHHHHHHHHHHHHHHHhcCCCCc
Confidence 34456679999999999999987654333332222 2233334443235777888888987764444
Q ss_pred -HHHHHHHHhCCCCCCCCCCC-hhHHHhhhhhhhhHHHHHhhh
Q psy5990 74 -SDSLQYALGAGDLFDVRNDT-VYVKTIICKYFCISLSTYRYS 114 (119)
Q Consensus 74 -~~aL~yAL~AG~lFdv~~~s-eYvetiisk~~cID~Yi~~~~ 114 (119)
++.|.--+-. +||+...+ ++...+++. ++..|...+.
T Consensus 150 ~~~vL~~Lll~--yF~p~t~~~~~LrQ~L~~--Ffp~y~~s~~ 188 (298)
T PF12719_consen 150 PPKVLSRLLLL--YFNPSTEDNQRLRQCLSV--FFPVYASSSP 188 (298)
T ss_pred HHHHHHHHHHH--HcCcccCCcHHHHHHHHH--HHHHHHcCCH
Confidence 4666665665 89986544 889999999 9999987554
No 66
>KOG2019|consensus
Probab=31.23 E-value=43 Score=32.58 Aligned_cols=28 Identities=21% Similarity=0.339 Sum_probs=23.9
Q ss_pred HHHHHHHhhhhhcchHHHHhhHHHHHHH
Q psy5990 20 EFSLKKLNDIVDDFWPEVSEAIQKIEIL 47 (119)
Q Consensus 20 ~~AL~~L~~vVd~~W~EIsd~i~~IE~L 47 (119)
.-=|++|.+.||++|.+|++.++.|..-
T Consensus 732 l~fl~~L~~~~d~d~~~i~~kL~eIrk~ 759 (998)
T KOG2019|consen 732 LEFLHRLEEKVDNDWEPIVSKLTEIRKS 759 (998)
T ss_pred HHHHHHHHHHhhhhHHHHHHHHHHHHHH
Confidence 3458899999999999999999998543
No 67
>cd00189 TPR Tetratricopeptide repeat domain; typically contains 34 amino acids [WLF]-X(2)-[LIM]-[GAS]-X(2)-[YLF]-X(8)-[ASE]-X(3)-[FYL]-X(2)-[ASL]-X(4)-[PKE] is the consensus sequence; found in a variety of organisms including bacteria, cyanobacteria, yeast, fungi, plants, and humans in various subcellular locations; involved in a variety of functions including protein-protein interactions, but common features in the interaction partners have not been defined; involved in chaperone, cell-cycle, transciption, and protein transport complexes; the number of TPR motifs varies among proteins (1,3-11,13 15,16,19); 5-6 tandem repeats generate a right-handed helical structure with an amphipathic channel that is thought to accomodate an alpha-helix of a target protein; it has been proposed that TPR proteins preferably interact with WD-40 repeat proteins, but in many instances several TPR-proteins seem to aggregate to multi-protein complexes; examples of TPR-proteins include, Cdc16p, Cdc23p and C
Probab=29.42 E-value=1.1e+02 Score=16.97 Aligned_cols=26 Identities=23% Similarity=0.336 Sum_probs=17.0
Q ss_pred HHHHHHHHHhhhccChHHHHHHHHhC
Q psy5990 58 LAALVASKVYFHLGSFSDSLQYALGA 83 (119)
Q Consensus 58 lAALvaSKVyyhLgey~~aL~yAL~A 83 (119)
.+-...+.+|++.|++++|+++--.+
T Consensus 35 ~~~~~~~~~~~~~~~~~~a~~~~~~~ 60 (100)
T cd00189 35 DAYYNLAAAYYKLGKYEEALEDYEKA 60 (100)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 44445567777777777777765444
No 68
>PF01602 Adaptin_N: Adaptin N terminal region; InterPro: IPR002553 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. This traffic is bidirectional, to ensure that proteins required to form vesicles are recycled. Vesicles have specific coat proteins (such as clathrin or coatomer) that are important for cargo selection and direction of transfer []. Clathrin coats contain both clathrin 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 []. All AP complexes are heterotetramers composed of two large subunits (adaptins), a medium subunit (mu) and a small subunit (sigma). Each subunit has a specific function. Adaptin subunits recognise and bind to clathrin through their hinge region (clathrin box), and recruit accessory proteins that modulate AP function through their C-terminal appendage domains. By contrast, GGAs are monomers composed of four domains, which have functions similar to AP subunits: an N-terminal VHS (Vps27p/Hrs/Stam) domain, a GAT (GGA and Tom1) domain, a hinge region, and a C-terminal GAE (gamma-adaptin ear) domain. The GAE domain is similar to the AP gamma-adaptin ear domain, being responsible for the recruitment of accessory proteins that regulate clathrin-mediated endocytosis []. While clathrin mediates endocytic protein transport from ER to Golgi, coatomers (COPI, COPII) primarily mediate intra-Golgi transport, as well as the reverse Golgi to ER transport of dilysine-tagged proteins []. Coatomers reversibly associate with Golgi (non-clathrin-coated) vesicles to mediate protein transport and for budding from Golgi membranes []. Coatomer complexes are hetero-oligomers composed of at least an alpha, beta, beta', gamma, delta, epsilon and zeta subunits. This entry represents the N-terminal domain of various adaptins from different AP clathrin adaptor complexes (including AP1, AP2, AP3 and AP4), and from the beta and gamma subunits of various coatomer (COP) adaptors. This domain has a 2-layer alpha/alpha fold that forms a right-handed superhelix, and is a member of the ARM repeat superfamily []. The N-terminal region of the various AP adaptor proteins share strong sequence identity; by contrast, the C-terminal domains of different adaptins share similar structural folds, but have little sequence identity []. It has been proposed that the N-terminal domain interacts with another uniform component of the coated vesicles. More information about these proteins can be found at Protein of the Month: Clathrin [].; GO: 0006886 intracellular protein transport, 0016192 vesicle-mediated transport, 0030117 membrane coat; PDB: 1W63_C 2JKR_A 2JKT_A 2XA7_A 2VGL_B 3TJZ_E.
Probab=28.14 E-value=1.6e+02 Score=24.63 Aligned_cols=58 Identities=29% Similarity=0.348 Sum_probs=32.0
Q ss_pred HhcCCCchHHHHHHHHHHhhhhhcchHHHHh-hHHHHHHHhhCCCCCchhHHHHHHHHHhhh
Q psy5990 9 SLLDDPMIELKEFSLKKLNDIVDDFWPEVSE-AIQKIEILHEDKGFPQYKLAALVASKVYFH 69 (119)
Q Consensus 9 aLL~E~d~~Lk~~AL~~L~~vVd~~W~EIsd-~i~~IE~LyED~~F~~R~lAALvaSKVyyh 69 (119)
.=|..+++.++..||+.|-.+.+ +|+++ -++.|..+..|++=-=|.-|++-..|+|-.
T Consensus 86 kdl~~~n~~~~~lAL~~l~~i~~---~~~~~~l~~~v~~ll~~~~~~VRk~A~~~l~~i~~~ 144 (526)
T PF01602_consen 86 KDLNSPNPYIRGLALRTLSNIRT---PEMAEPLIPDVIKLLSDPSPYVRKKAALALLKIYRK 144 (526)
T ss_dssp HHHCSSSHHHHHHHHHHHHHH-S---HHHHHHHHHHHHHHHHSSSHHHHHHHHHHHHHHHHH
T ss_pred HhhcCCCHHHHHHHHhhhhhhcc---cchhhHHHHHHHHHhcCCchHHHHHHHHHHHHHhcc
Confidence 33556666667777776666553 22222 234445555555555666666666666643
No 69
>PF13133 DUF3949: Protein of unknown function (DUF3949)
Probab=28.12 E-value=55 Score=22.16 Aligned_cols=23 Identities=43% Similarity=0.597 Sum_probs=14.9
Q ss_pred HHHhhCCCCCchhH------------HHHHHHHHh
Q psy5990 45 EILHEDKGFPQYKL------------AALVASKVY 67 (119)
Q Consensus 45 E~LyED~~F~~R~l------------AALvaSKVy 67 (119)
++||++-+|.+.+| |++|||-+|
T Consensus 24 ~e~Y~nMsfeEeqLHy~~Qgn~f~~pa~~vAs~iy 58 (62)
T PF13133_consen 24 EELYDNMSFEEEQLHYNVQGNPFFIPAAFVASIIY 58 (62)
T ss_pred HHHHHhcchhHHHHHHhhcCCcccchHHHHHHHHH
Confidence 56777777765543 666666554
No 70
>PF10363 DUF2435: Protein of unknown function (DUF2435)
Probab=27.95 E-value=66 Score=22.32 Aligned_cols=38 Identities=26% Similarity=0.349 Sum_probs=27.8
Q ss_pred HHHHhcCCCchHHHHHHHHHHhhhhhcchHHHHhhHHHH
Q psy5990 6 GVISLLDDPMIELKEFSLKKLNDIVDDFWPEVSEAIQKI 44 (119)
Q Consensus 6 g~laLL~E~d~~Lk~~AL~~L~~vVd~~W~EIsd~i~~I 44 (119)
-.+..|.+|.+-+|.+||..|..+|..-= +....++.|
T Consensus 7 ~al~~L~dp~~PvRa~gL~~L~~Li~~~~-~~~~~~~~i 44 (92)
T PF10363_consen 7 EALSDLNDPLPPVRAHGLVLLRKLIESKS-EPVIDIPKI 44 (92)
T ss_pred HHHHHccCCCcchHHHHHHHHHHHHHcCC-cchhhHHHH
Confidence 35778899999999999999999887543 223334444
No 71
>PRK09687 putative lyase; Provisional
Probab=27.77 E-value=1.7e+02 Score=23.71 Aligned_cols=58 Identities=19% Similarity=0.160 Sum_probs=36.5
Q ss_pred HHHHHHhcCCCchHHHHHHHHHHhhhhhcchHHHHhhHHHHHHHhhCCCCCchhHHHHHHHH
Q psy5990 4 VAGVISLLDDPMIELKEFSLKKLNDIVDDFWPEVSEAIQKIEILHEDKGFPQYKLAALVASK 65 (119)
Q Consensus 4 aag~laLL~E~d~~Lk~~AL~~L~~vVd~~W~EIsd~i~~IE~LyED~~F~~R~lAALvaSK 65 (119)
...++.+|+.+++.++..|...|..+=.. -.+.++.+..+..|+...-|.-|+.-..+
T Consensus 161 i~~L~~~L~d~~~~VR~~A~~aLg~~~~~----~~~~~~~L~~~L~D~~~~VR~~A~~aLg~ 218 (280)
T PRK09687 161 IPLLINLLKDPNGDVRNWAAFALNSNKYD----NPDIREAFVAMLQDKNEEIRIEAIIGLAL 218 (280)
T ss_pred HHHHHHHhcCCCHHHHHHHHHHHhcCCCC----CHHHHHHHHHHhcCCChHHHHHHHHHHHc
Confidence 45677777777788887777777766111 12445556666677777666666655544
No 72
>PF13428 TPR_14: Tetratricopeptide repeat
Probab=27.65 E-value=79 Score=18.06 Aligned_cols=18 Identities=17% Similarity=0.311 Sum_probs=15.1
Q ss_pred HHHHhhhccChHHHHHHH
Q psy5990 63 ASKVYFHLGSFSDSLQYA 80 (119)
Q Consensus 63 aSKVyyhLgey~~aL~yA 80 (119)
..++|..+|++++|.+..
T Consensus 7 la~~~~~~G~~~~A~~~~ 24 (44)
T PF13428_consen 7 LARAYRRLGQPDEAERLL 24 (44)
T ss_pred HHHHHHHcCCHHHHHHHH
Confidence 458999999999998754
No 73
>PF05464 Phi-29_GP4: Phi-29-like late genes activator (early protein GP4); InterPro: IPR008771 This family consists of phi-29-like late genes activator (or early protein GP4). This protein is thought to be a positive regulator of late transcription and may function as a sigma-like component of the host RNA polymerase [].; GO: 0003899 DNA-directed RNA polymerase activity, 0016987 sigma factor activity, 0006355 regulation of transcription, DNA-dependent; PDB: 2FIP_B 2FIO_A.
Probab=27.36 E-value=11 Score=28.46 Aligned_cols=34 Identities=18% Similarity=0.339 Sum_probs=22.1
Q ss_pred HHHHhcCCCc---hHHHHHHHHHHhhhhhcchHHHHh
Q psy5990 6 GVISLLDDPM---IELKEFSLKKLNDIVDDFWPEVSE 39 (119)
Q Consensus 6 g~laLL~E~d---~~Lk~~AL~~L~~vVd~~W~EIsd 39 (119)
|++++|..++ .+.+++||+..+.=-.+.|.+|+.
T Consensus 78 GF~~~~KGd~~TWqE~~~~~Lr~~~k~~tln~s~i~k 114 (125)
T PF05464_consen 78 GFHAWLKGDNMTWQESHVYALRRMTKPKTLNWSRISK 114 (125)
T ss_dssp ---EEETTEEE-HHHHHHHHHHHTTSSS----EEES-
T ss_pred hhhheecCCcchHHHHHHHHHHhhcCccccCHHHhcc
Confidence 7778888766 577899999999988899998863
No 74
>PF13429 TPR_15: Tetratricopeptide repeat; PDB: 2VQ2_A 2PL2_B.
Probab=27.09 E-value=1.2e+02 Score=23.31 Aligned_cols=48 Identities=23% Similarity=0.243 Sum_probs=30.4
Q ss_pred cchHHHHhhHHHHHHHhhCCCCCchhHHHHHHHHHhhhccChHHHHHHHHh
Q psy5990 32 DFWPEVSEAIQKIEILHEDKGFPQYKLAALVASKVYFHLGSFSDSLQYALG 82 (119)
Q Consensus 32 ~~W~EIsd~i~~IE~LyED~~F~~R~lAALvaSKVyyhLgey~~aL~yAL~ 82 (119)
.-|.++.+.|..++ +...++.....=...+.+|...|+.++|++.--.
T Consensus 124 ~~~~~~~~~l~~~~---~~~~~~~~~~~~~~~a~~~~~~G~~~~A~~~~~~ 171 (280)
T PF13429_consen 124 GDYDEAEELLEKLE---ELPAAPDSARFWLALAEIYEQLGDPDKALRDYRK 171 (280)
T ss_dssp T-HHHHHHHHHHHH---H-T---T-HHHHHHHHHHHHHCCHHHHHHHHHHH
T ss_pred hHHHHHHHHHHHHH---hccCCCCCHHHHHHHHHHHHHcCCHHHHHHHHHH
Confidence 45777777766655 4555665555556678999999999999876533
No 75
>PF04102 SlyX: SlyX; InterPro: IPR007236 The SlyX protein has no known function. It is short, less than 80 amino acids, and its gene is found close to the slyD gene. The SlyX protein has a conserved PPH(Y/W) motif at its C terminus. The protein may be a coiled-coil structure.; PDB: 3EFG_A.
Probab=26.77 E-value=1.5e+02 Score=19.39 Aligned_cols=33 Identities=21% Similarity=0.452 Sum_probs=26.6
Q ss_pred HHHHHHHHHHhhhhhcchHHHHhhHHHHHHHhh
Q psy5990 17 ELKEFSLKKLNDIVDDFWPEVSEAIQKIEILHE 49 (119)
Q Consensus 17 ~Lk~~AL~~L~~vVd~~W~EIsd~i~~IE~LyE 49 (119)
..+...++.||.+|-.-|.+|..-=..+..|.+
T Consensus 14 a~qe~~ie~Ln~~v~~Qq~~I~~L~~~l~~L~~ 46 (69)
T PF04102_consen 14 AFQEDTIEELNDVVTEQQRQIDRLQRQLRLLRE 46 (69)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 346788999999999999999877777766654
No 76
>PF00613 PI3Ka: Phosphoinositide 3-kinase family, accessory domain (PIK domain); InterPro: IPR001263 Phosphatidylinositol 3-kinase (PI3-kinase) (2.7.1.137 from EC) is an enzyme that phosphorylates phosphoinositides on the 3-hydroxyl group of the inositol ring. The role of the accessory domain of phosphoinositide 3-kinase (PI3-kinase) is unclear. It may be involved in substrate presentation [].; GO: 0004428 inositol or phosphatidylinositol kinase activity; PDB: 1E8W_A 1E8X_A 1E7V_A 1E90_A 1E7U_A 2WXL_A 4AJW_B 2WXQ_A 2WXP_A 2WXM_A ....
Probab=26.30 E-value=3e+02 Score=21.12 Aligned_cols=58 Identities=14% Similarity=0.279 Sum_probs=35.5
Q ss_pred cHHHHHHhcCC--CchHHHHHHHHHHhhhhhcchHHHHhhHHHHHHHhhCCCCCchhHHHHHH
Q psy5990 3 TVAGVISLLDD--PMIELKEFSLKKLNDIVDDFWPEVSEAIQKIEILHEDKGFPQYKLAALVA 63 (119)
Q Consensus 3 Saag~laLL~E--~d~~Lk~~AL~~L~~vVd~~W~EIsd~i~~IE~LyED~~F~~R~lAALva 63 (119)
+..-.|.||+. +++.++.||.+.|++.=|+ |+...|+++=....-+.+....||-.+.
T Consensus 76 ~p~~AL~LL~~~f~~~~VR~yAv~~L~~~~d~---~l~~yLpQLVQaLr~e~~~~s~L~~fLl 135 (184)
T PF00613_consen 76 SPEDALELLSPNFPDPFVRQYAVRRLESLSDE---ELLFYLPQLVQALRYEPYHDSPLARFLL 135 (184)
T ss_dssp THHHHHHCTSTT---HHHHHHHHHHHCTS-HH---HHHHHHHHHHHHGGGSSSSS-HHHHHHH
T ss_pred CHHHHHHHHHhhccHHHHHHHHHHHHHHcCch---HHHHHHHHHHHHheeccccccHHHHHHH
Confidence 34456888888 4799999999999874432 4566666655443344455566665543
No 77
>PRK02119 hypothetical protein; Provisional
Probab=25.90 E-value=1.5e+02 Score=19.92 Aligned_cols=32 Identities=13% Similarity=0.133 Sum_probs=25.1
Q ss_pred HHHHHHHHHHhhhhhcchHHHHhhHHHHHHHh
Q psy5990 17 ELKEFSLKKLNDIVDDFWPEVSEAIQKIEILH 48 (119)
Q Consensus 17 ~Lk~~AL~~L~~vVd~~W~EIsd~i~~IE~Ly 48 (119)
..+.-.++.||.+|-.-|.+|..--..+..|.
T Consensus 19 a~QE~tie~LN~~v~~Qq~~id~L~~ql~~L~ 50 (73)
T PRK02119 19 AFQENLLEELNQALIEQQFVIDKMQVQLRYMA 50 (73)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 35778899999999999999976655555554
No 78
>PF09295 ChAPs: ChAPs (Chs5p-Arf1p-binding proteins); InterPro: IPR015374 ChAPs (Chs5p-Arf1p-binding proteins) are required for the export of specialised cargo from the Golgi. They physically interact with Chs3, Chs5 and the small GTPase Arf1, and they also form interactions with each other [].
Probab=25.64 E-value=66 Score=27.96 Aligned_cols=36 Identities=22% Similarity=0.450 Sum_probs=28.4
Q ss_pred HHHhhhccChHHHHHHHHhCCCCCCCCCCChhHHHhhhh
Q psy5990 64 SKVYFHLGSFSDSLQYALGAGDLFDVRNDTVYVKTIICK 102 (119)
Q Consensus 64 SKVyyhLgey~~aL~yAL~AG~lFdv~~~seYvetiisk 102 (119)
.++|-.+|+|++|| .||.+=|++...+ .|+.+++..
T Consensus 275 a~~Yi~~~d~e~AL-laLNs~Pm~~~~~--k~~~~~~~p 310 (395)
T PF09295_consen 275 AECYIQLGDFENAL-LALNSCPMLTYKD--KYKLKRPVP 310 (395)
T ss_pred HHHHHhcCCHHHHH-HHHhcCcCCCCcc--chhhhcCCC
Confidence 57899999999999 9999999996555 366665553
No 79
>PRK00295 hypothetical protein; Provisional
Probab=25.05 E-value=1.6e+02 Score=19.44 Aligned_cols=32 Identities=13% Similarity=0.212 Sum_probs=25.2
Q ss_pred HHHHHHHHHHhhhhhcchHHHHhhHHHHHHHh
Q psy5990 17 ELKEFSLKKLNDIVDDFWPEVSEAIQKIEILH 48 (119)
Q Consensus 17 ~Lk~~AL~~L~~vVd~~W~EIsd~i~~IE~Ly 48 (119)
..+.-.++.||.+|-+-|.+|..--..+..|.
T Consensus 15 a~qE~tie~Ln~~v~~Qq~~I~~L~~ql~~L~ 46 (68)
T PRK00295 15 AFQDDTIQALNDVLVEQQRVIERLQLQMAALI 46 (68)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 35677899999999999999977666666554
No 80
>PF11817 Foie-gras_1: Foie gras liver health family 1; InterPro: IPR021773 Mutating the gene foie gras in zebrafish has been shown to affect development; the mutants develop large, lipid-filled hepatocytes in the liver, resembling those in individuals with fatty liver disease []. Foie-gras protein is long and has several well-defined domains though none of them has a known function. We have annotated this one as the first []. THe C terminus of this region contains TPR repeats.
Probab=24.61 E-value=83 Score=24.76 Aligned_cols=25 Identities=24% Similarity=0.530 Sum_probs=19.6
Q ss_pred HHHHhhhccChHHHHHHHHhCCCCC
Q psy5990 63 ASKVYFHLGSFSDSLQYALGAGDLF 87 (119)
Q Consensus 63 aSKVyyhLgey~~aL~yAL~AG~lF 87 (119)
..+-||++|+|++|+++--.+...|
T Consensus 184 ~A~ey~~~g~~~~A~~~l~~~~~~y 208 (247)
T PF11817_consen 184 MAEEYFRLGDYDKALKLLEPAASSY 208 (247)
T ss_pred HHHHHHHCCCHHHHHHHHHHHHHHH
Confidence 3477999999999999977664333
No 81
>PF10020 DUF2262: Uncharacterized protein conserved in bacteria (DUF2262); InterPro: IPR019260 This entry consists of various hypothetical bacterial proteins with no known function.
Probab=24.11 E-value=57 Score=23.89 Aligned_cols=34 Identities=26% Similarity=0.525 Sum_probs=27.5
Q ss_pred HHHHHhcCCCchHHHHHHHHHHhhhhhcchHHHHh
Q psy5990 5 AGVISLLDDPMIELKEFSLKKLNDIVDDFWPEVSE 39 (119)
Q Consensus 5 ag~laLL~E~d~~Lk~~AL~~L~~vVd~~W~EIsd 39 (119)
.-++.-.++.+..+|.+|.++|..+..+ |.+=.+
T Consensus 53 ~~l~~~~e~~~~~i~~~aae~ll~laNd-W~~~~e 86 (150)
T PF10020_consen 53 EKLLKNIEEWDKKIKDFAAEKLLDLAND-WREDDE 86 (150)
T ss_pred HHHHHhHHHHHHHHHHHHHHHHHHHHHH-Hhhccc
Confidence 3456667788999999999999999999 988543
No 82
>KOG1130|consensus
Probab=22.83 E-value=39 Score=31.23 Aligned_cols=15 Identities=33% Similarity=0.824 Sum_probs=13.6
Q ss_pred HHhhhccChHHHHHH
Q psy5990 65 KVYFHLGSFSDSLQY 79 (119)
Q Consensus 65 KVyyhLgey~~aL~y 79 (119)
..||+|++|+.||+|
T Consensus 63 NAyfyL~DY~kAl~y 77 (639)
T KOG1130|consen 63 NAYFYLKDYEKALKY 77 (639)
T ss_pred chhhhHhhHHHHHhh
Confidence 459999999999998
No 83
>COG2909 MalT ATP-dependent transcriptional regulator [Transcription]
Probab=22.82 E-value=3.4e+02 Score=26.75 Aligned_cols=75 Identities=31% Similarity=0.421 Sum_probs=51.9
Q ss_pred hcCCCchHHHHHHHHHHhhhhhcchHHHHhhHHHH-------HHHh---------hCCC--C------------------
Q psy5990 10 LLDDPMIELKEFSLKKLNDIVDDFWPEVSEAIQKI-------EILH---------EDKG--F------------------ 53 (119)
Q Consensus 10 LL~E~d~~Lk~~AL~~L~~vVd~~W~EIsd~i~~I-------E~Ly---------ED~~--F------------------ 53 (119)
+|+.-++++|.|.++. +|.++|=.|..+.|.-+ |.|- +|+. |
T Consensus 265 Vld~Lp~~l~~FLl~~--svl~~f~~eL~~~Ltg~~ng~amLe~L~~~gLFl~~Ldd~~~WfryH~LFaeFL~~r~~~~~ 342 (894)
T COG2909 265 VLDRLPPELRDFLLQT--SVLSRFNDELCNALTGEENGQAMLEELERRGLFLQRLDDEGQWFRYHHLFAEFLRQRLQREL 342 (894)
T ss_pred HHhcCCHHHHHHHHHH--HhHHHhhHHHHHHHhcCCcHHHHHHHHHhCCCceeeecCCCceeehhHHHHHHHHhhhcccc
Confidence 6777889999988874 78888888877776654 4442 1221 1
Q ss_pred Cch-hHHHHHHHHHhhhccChHHHHHHHHhCCCC
Q psy5990 54 PQY-KLAALVASKVYFHLGSFSDSLQYALGAGDL 86 (119)
Q Consensus 54 ~~R-~lAALvaSKVyyhLgey~~aL~yAL~AG~l 86 (119)
+.+ .-==+=|++-+=.-|...+|+++||.||+.
T Consensus 343 ~~~~~~lH~~Aa~w~~~~g~~~eAI~hAlaA~d~ 376 (894)
T COG2909 343 AARLKELHRAAAEWFAEHGLPSEAIDHALAAGDP 376 (894)
T ss_pred CCchhHHHHHHHHHHHhCCChHHHHHHHHhCCCH
Confidence 111 111234678899999999999999999973
No 84
>PRK02793 phi X174 lysis protein; Provisional
Probab=22.75 E-value=1.2e+02 Score=20.25 Aligned_cols=32 Identities=19% Similarity=0.319 Sum_probs=25.0
Q ss_pred HHHHHHHHHHhhhhhcchHHHHhhHHHHHHHh
Q psy5990 17 ELKEFSLKKLNDIVDDFWPEVSEAIQKIEILH 48 (119)
Q Consensus 17 ~Lk~~AL~~L~~vVd~~W~EIsd~i~~IE~Ly 48 (119)
..+...++.||++|-+-|.+|..--..+..|.
T Consensus 18 afQe~tIe~Ln~~v~~Qq~~I~~L~~~l~~L~ 49 (72)
T PRK02793 18 AFQEITIEELNVTVTAHEMEMAKLRDHLRLLT 49 (72)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 45778999999999999999976655555554
No 85
>PF05004 IFRD: Interferon-related developmental regulator (IFRD); InterPro: IPR007701 Interferon-related developmental regulator (IFRD1) is the human homologue of the Rattus norvegicus early response protein PC4 and its murine homologue TIS7 []. The exact function of IFRD1 is unknown but it has been shown that PC4 is necessary for muscle differentiation and that it might have a role in signal transduction. This entry also contains IFRD2 and its murine equivalent SKMc15, which are highly expressed soon after gastrulation and in the hepatic primordium, suggesting an involvement in early hematopoiesis [].
Probab=22.70 E-value=2.8e+02 Score=22.98 Aligned_cols=67 Identities=16% Similarity=0.104 Sum_probs=47.4
Q ss_pred HHHHHhcCCCchHHHHHHHHHHhhhhhcc------hHHHHhhHHHHHHHhhCCCCCchhHHHHHHHHHhhhcc
Q psy5990 5 AGVISLLDDPMIELKEFSLKKLNDIVDDF------WPEVSEAIQKIEILHEDKGFPQYKLAALVASKVYFHLG 71 (119)
Q Consensus 5 ag~laLL~E~d~~Lk~~AL~~L~~vVd~~------W~EIsd~i~~IE~LyED~~F~~R~lAALvaSKVyyhLg 71 (119)
.+.|..|.|+..+-|.-||+.|...+-.. +.....-++.++....-.+=.++.+|+.++.=..-.||
T Consensus 46 ~~~Id~l~eK~~~~Re~aL~~l~~~l~~~~~~d~v~~~~~tL~~~~~k~lkkg~~~E~~lA~~~l~Ll~ltlg 118 (309)
T PF05004_consen 46 KEAIDLLTEKSSSTREAALEALIRALSSRYLPDFVEDRRETLLDALLKSLKKGKSEEQALAARALALLALTLG 118 (309)
T ss_pred HHHHHHHHhcCHHHHHHHHHHHHHHHHhcccHHHHHHHHHHHHHHHHHHhccCCHHHHHHHHHHHHHHhhhcC
Confidence 36788899999999999999999865322 22233344555555543332678899999999999988
No 86
>PRK04406 hypothetical protein; Provisional
Probab=22.04 E-value=1.2e+02 Score=20.45 Aligned_cols=32 Identities=13% Similarity=0.253 Sum_probs=25.1
Q ss_pred HHHHHHHHHHhhhhhcchHHHHhhHHHHHHHh
Q psy5990 17 ELKEFSLKKLNDIVDDFWPEVSEAIQKIEILH 48 (119)
Q Consensus 17 ~Lk~~AL~~L~~vVd~~W~EIsd~i~~IE~Ly 48 (119)
..+...++.||.+|-.-|.+|..--..+..|.
T Consensus 21 AfQE~tIe~LN~~v~~Qq~~I~~L~~ql~~L~ 52 (75)
T PRK04406 21 AFQEQTIEELNDALSQQQLLITKMQDQMKYVV 52 (75)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 45778899999999999999976666555553
No 87
>TIGR03302 OM_YfiO outer membrane assembly lipoprotein YfiO. Members of this protein family include YfiO, a near-essential protein of the outer membrane, part of a complex involved in protein insertion into the bacterial outer membrane. Many proteins in this family are annotated as ComL, based on the involvement of this protein in natural transformation with exogenous DNA in Neisseria gonorrhoeae. This protein family shows sequence similarity to, but is distinct from, the tol-pal system protein YbgF (TIGR02795).
Probab=21.85 E-value=3.3e+02 Score=20.01 Aligned_cols=58 Identities=16% Similarity=0.108 Sum_probs=35.3
Q ss_pred cchHHHHhhHHHHHHHhhCCCCCchhHHHHHHHHHhhhccChHHHHHHHHhCCCCCCCCC
Q psy5990 32 DFWPEVSEAIQKIEILHEDKGFPQYKLAALVASKVYFHLGSFSDSLQYALGAGDLFDVRN 91 (119)
Q Consensus 32 ~~W~EIsd~i~~IE~LyED~~F~~R~lAALvaSKVyyhLgey~~aL~yAL~AG~lFdv~~ 91 (119)
.-|.+-...+..+-.+ ++.-|...-|.+-...+|+..|++++|+...-.+=+.+.-+.
T Consensus 47 ~~~~~A~~~~~~~~~~--~p~~~~~~~a~~~la~~~~~~~~~~~A~~~~~~~l~~~p~~~ 104 (235)
T TIGR03302 47 GDYTEAIKYFEALESR--YPFSPYAEQAQLDLAYAYYKSGDYAEAIAAADRFIRLHPNHP 104 (235)
T ss_pred CCHHHHHHHHHHHHHh--CCCchhHHHHHHHHHHHHHhcCCHHHHHHHHHHHHHHCcCCC
Confidence 3455444444333222 333344555666777899999999999988776655554333
No 88
>PF03368 Dicer_dimer: Dicer dimerisation domain; InterPro: IPR005034 This domain is found in members of the Dicer protein family of dsRNA nucleases. This entry represents a dsRNA-binding domain. RNA interference (RNAi) is an ancient gene-silencing process that plays a fundamental role in diverse eukaryotic functions including viral defence, chromatin remodelling, genome rearrangement, developmental timing, brain morphogenesis, and stem cell maintenance. All RNAi pathways require the multidomain ribonuclease Dicer, which initiates RNAi by cleaving double-stranded RNA (dsRNA) substrates into small fragments ~25 nuleotides in length. A typical eukaryotic Dicer consists of a helicase domain (PDOC51192 from PROSITEDOC), a domain of unknown function, and a PAZ domain (PDOC50821 from PROSITEDOC) at the amino (N)-terminus as well as two ribonuclease III domains (PDOC00448 from PROSITEDOC) and a dsRNA-binding domain (dsRBD) (PDOC50137 from PROSITEDOC) at the carboxy (C)-terminus. The domain of unknown function of ~100 amino acids is predicted to adopt the canonical alpha-beta-beta-beta-alpha-fold found in all dsRBDs [, , , ].; GO: 0016891 endoribonuclease activity, producing 5'-phosphomonoesters; PDB: 2KOU_A.
Probab=21.77 E-value=61 Score=22.10 Aligned_cols=23 Identities=30% Similarity=0.351 Sum_probs=18.3
Q ss_pred chhHHHHHHHHHhhhccChHHHH
Q psy5990 55 QYKLAALVASKVYFHLGSFSDSL 77 (119)
Q Consensus 55 ~R~lAALvaSKVyyhLgey~~aL 77 (119)
.+.-||+-|.+.-|.+|+.||-|
T Consensus 59 AK~sAAf~Ac~~L~~~g~ldd~L 81 (90)
T PF03368_consen 59 AKRSAAFEACKKLHEAGELDDHL 81 (90)
T ss_dssp HHHHHHHHHHHHHHHH-S-TTTS
T ss_pred HHHHHHHHHHHHHHHcCCCcccc
Confidence 46789999999999999999855
No 89
>PRK00846 hypothetical protein; Provisional
Probab=21.30 E-value=2e+02 Score=19.88 Aligned_cols=33 Identities=21% Similarity=0.228 Sum_probs=26.2
Q ss_pred HHHHHHHHHHhhhhhcchHHHHhhHHHHHHHhh
Q psy5990 17 ELKEFSLKKLNDIVDDFWPEVSEAIQKIEILHE 49 (119)
Q Consensus 17 ~Lk~~AL~~L~~vVd~~W~EIsd~i~~IE~LyE 49 (119)
..+...++.||.+|-.-|.+|..--.++..|-+
T Consensus 23 AfQe~tIe~LN~~v~~qq~~I~~L~~ql~~L~~ 55 (77)
T PRK00846 23 SFQEQALTELSEALADARLTGARNAELIRHLLE 55 (77)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 457788999999999999999877666665543
No 90
>PF05757 PsbQ: Oxygen evolving enhancer protein 3 (PsbQ); InterPro: IPR008797 Oxygenic photosynthesis uses two multi-subunit photosystems (I and II) located in the cell membranes of cyanobacteria and in the thylakoid membranes of chloroplasts in plants and algae. Photosystem II (PSII) has a P680 reaction centre containing chlorophyll 'a' that uses light energy to carry out the oxidation (splitting) of water molecules, and to produce ATP via a proton pump. Photosystem I (PSI) has a P700 reaction centre containing chlorophyll that takes the electron and associated hydrogen donated from PSII to reduce NADP+ to NADPH. Both ATP and NADPH are subsequently used in the light-independent reactions to convert carbon dioxide to glucose using the hydrogen atom extracted from water by PSII, releasing oxygen as a by-product. PSII is a multisubunit protein-pigment complex containing polypeptides both intrinsic and extrinsic to the photosynthetic membrane [, ]. Within the core of the complex, the chlorophyll and beta-carotene pigments are mainly bound to the antenna proteins CP43 (PsbC) and CP47 (PsbB), which pass the excitation energy on to the reaction centre proteins D1 (Qb, PsbA) and D2 (Qa, PsbD) that bind all the redox-active cofactors involved in the energy conversion process. The PSII oxygen-evolving complex (OEC) oxidises water to provide protons for use by PSI, and consists of OEE1 (PsbO), OEE2 (PsbP) and OEE3 (PsbQ). The remaining subunits in PSII are of low molecular weight (less than 10 kDa), and are involved in PSII assembly, stabilisation, dimerisation, and photo-protection []. In PSII, the oxygen-evolving complex (OEC) is responsible for catalysing the splitting of water to O(2) and 4H+. The OEC is composed of a cluster of manganese, calcium and chloride ions bound to extrinsic proteins. In cyanobacteria there are five extrinsic proteins in OEC (PsbO, PsbP-like, PsbQ-like, PsbU and PsbV), while in plants there are only three (PsbO, PsbP and PsbQ), PsbU and PsbV having been lost during the evolution of green plants []. This family represents the PSII OEC protein PsbQ. Both PsbQ and PsbP (IPR002683 from INTERPRO) are regulators that are necessary for the biogenesis of optically active PSII. The crystal structure of PsbQ from spinach revealed a 4-helical bundle polypeptide. The distribution of positive and negative charges on the protein surface might explain the ability of PsbQ to increase the binding of chloride and calcium ions and make them available to PSII [].; GO: 0005509 calcium ion binding, 0015979 photosynthesis, 0009523 photosystem II, 0009654 oxygen evolving complex, 0019898 extrinsic to membrane; PDB: 1VYK_A 1NZE_A 3LS1_A 3LS0_A.
Probab=21.17 E-value=1.1e+02 Score=24.60 Aligned_cols=56 Identities=20% Similarity=0.337 Sum_probs=38.0
Q ss_pred HHHHhhhhh-cchHHHHhhHHH--------HHHHhhCCCCCchhHHHHHHHHHhhhccChHHHHH
Q psy5990 23 LKKLNDIVD-DFWPEVSEAIQK--------IEILHEDKGFPQYKLAALVASKVYFHLGSFSDSLQ 78 (119)
Q Consensus 23 L~~L~~vVd-~~W~EIsd~i~~--------IE~LyED~~F~~R~lAALvaSKVyyhLgey~~aL~ 78 (119)
|..|.++|| ..|+++-..|-. +-.+.....=.+|+-+--++.|.|.+++++|.|.+
T Consensus 112 L~~lk~lIdk~sW~~v~~~LRlka~~Lr~DL~~liss~p~~~kk~l~~La~~lf~~ie~LD~Aar 176 (202)
T PF05757_consen 112 LLSLKELIDKKSWPYVRNYLRLKAGYLRYDLNTLISSKPKDEKKALTDLANKLFDNIEELDYAAR 176 (202)
T ss_dssp HCCCHHHHHTT-HHHHHHHHHCCCCCHHHHHHHHHCCS-HHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHhhccHHHHHHHHHHHHhHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 445556666 789999988753 34444454423566667888999999999887764
No 91
>cd00633 Secretoglobin Secretoglobins are relatively small, secreted, disulphide-bridged dimeric proteins with encoding genes sharing substantial sequence similarity. Their family subunits may be grouped into five subfamilies, A-E. Uteroglobin (subfamily A), which is identical to Clara cell protein (CC10), forms a globular shaped homodimer with a large hydrophobic pocket located between the two dimers. The uteroglobin monomer structure is composed of four alpha helices that do not form a canonical four helix-bundle motif but rather a boomerang-shaped structure in which helices H1, H3, and H4 are able to bind a homodimeric partner. The hydrophobic pocket binds steroids, particularly progesterone, with high specificity. However, the true biological function of uteroglobin is poorly understood. In mammals, uteroglobin has immunosuppressive and anti-inflammatory properties through the inhibition of phospholipase A2. The other four main subfamilies of secretoglobins are found in heterodimeri
Probab=21.17 E-value=1.8e+02 Score=18.60 Aligned_cols=34 Identities=21% Similarity=0.265 Sum_probs=29.1
Q ss_pred HHHHhhHHHHHHHhhCCCCCchhHHHHHHHHHhh
Q psy5990 35 PEVSEAIQKIEILHEDKGFPQYKLAALVASKVYF 68 (119)
Q Consensus 35 ~EIsd~i~~IE~LyED~~F~~R~lAALvaSKVyy 68 (119)
|++.++..+|..+++..+...|.....+.-+|+.
T Consensus 30 ~~~~~A~~~lK~C~d~~~~e~k~~~~~~m~~I~~ 63 (67)
T cd00633 30 PEAVEAKEKLKQCVDEQSLETKENIAKLLEKILA 63 (67)
T ss_pred HHHHHHHHHHHHHHhcCCHhHHHHHHHHHHHHHc
Confidence 6778889999999999999999998888877764
No 92
>PF12688 TPR_5: Tetratrico peptide repeat
Probab=21.16 E-value=1.5e+02 Score=21.36 Aligned_cols=28 Identities=14% Similarity=0.211 Sum_probs=14.6
Q ss_pred CCchhHHHHHHHHHhhhccChHHHHHHH
Q psy5990 53 FPQYKLAALVASKVYFHLGSFSDSLQYA 80 (119)
Q Consensus 53 F~~R~lAALvaSKVyyhLgey~~aL~yA 80 (119)
-+.|.-|-+..+-.|-+||++++|+..-
T Consensus 34 ~~~~~~a~i~lastlr~LG~~deA~~~L 61 (120)
T PF12688_consen 34 GADRRRALIQLASTLRNLGRYDEALALL 61 (120)
T ss_pred chHHHHHHHHHHHHHHHcCCHHHHHHHH
Confidence 3344445555555555555555555443
No 93
>PRK04325 hypothetical protein; Provisional
Probab=20.42 E-value=2.2e+02 Score=19.08 Aligned_cols=31 Identities=16% Similarity=0.158 Sum_probs=23.6
Q ss_pred HHHHHHHHHHhhhhhcchHHHHhhHHHHHHH
Q psy5990 17 ELKEFSLKKLNDIVDDFWPEVSEAIQKIEIL 47 (119)
Q Consensus 17 ~Lk~~AL~~L~~vVd~~W~EIsd~i~~IE~L 47 (119)
..+...++.||++|-+-|.+|..-=..+..|
T Consensus 19 AfQE~tIe~LN~vv~~Qq~~I~~L~~ql~~L 49 (74)
T PRK04325 19 AFQEDLIDGLNATVARQQQTLDLLQAQLRLL 49 (74)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 4577889999999999999886655444444
No 94
>PF12862 Apc5: Anaphase-promoting complex subunit 5
Probab=20.25 E-value=2.7e+02 Score=18.52 Aligned_cols=28 Identities=21% Similarity=0.243 Sum_probs=21.3
Q ss_pred hhHHHHHHHHHhhhccChHHHHHHHHhC
Q psy5990 56 YKLAALVASKVYFHLGSFSDSLQYALGA 83 (119)
Q Consensus 56 R~lAALvaSKVyyhLgey~~aL~yAL~A 83 (119)
...|.+-...+.+.+|.+++|++..-.|
T Consensus 40 ~~~all~lA~~~~~~G~~~~A~~~l~eA 67 (94)
T PF12862_consen 40 LAYALLNLAELHRRFGHYEEALQALEEA 67 (94)
T ss_pred HHHHHHHHHHHHHHhCCHHHHHHHHHHH
Confidence 4566666788999999999988765444
Done!