Query psy13474
Match_columns 105
No_of_seqs 68 out of 70
Neff 5.1
Searched_HMMs 46136
Date Fri Aug 16 20:19:34 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy13474.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/13474hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 cd02661 Peptidase_C19E A subfa 99.1 2.2E-10 4.8E-15 86.8 6.2 93 2-97 51-147 (304)
2 PF00443 UCH: Ubiquitin carbox 98.6 4E-08 8.8E-13 71.2 3.6 91 1-94 55-151 (269)
3 cd02657 Peptidase_C19A A subfa 98.6 1.7E-07 3.7E-12 72.1 6.8 94 1-101 49-147 (305)
4 cd02660 Peptidase_C19D A subfa 98.6 1.2E-07 2.7E-12 73.4 5.9 94 1-97 51-146 (328)
5 cd02663 Peptidase_C19G A subfa 98.4 3.1E-07 6.8E-12 71.3 5.3 93 1-96 27-131 (300)
6 cd02668 Peptidase_C19L A subfa 98.4 5.2E-07 1.1E-11 70.7 5.1 84 1-96 57-140 (324)
7 cd02659 peptidase_C19C A subfa 98.2 1.8E-06 3.9E-11 67.1 3.6 88 1-98 50-137 (334)
8 cd02658 Peptidase_C19B A subfa 97.9 1.6E-05 3.5E-10 61.4 4.9 71 13-94 76-146 (311)
9 KOG1887|consensus 97.9 3.1E-06 6.8E-11 75.3 0.5 87 19-105 528-627 (806)
10 cd02664 Peptidase_C19H A subfa 97.8 3E-05 6.6E-10 61.2 5.2 75 1-96 46-121 (327)
11 cd02666 Peptidase_C19J A subfa 97.6 8.4E-05 1.8E-09 60.2 4.7 81 1-92 70-156 (343)
12 cd02671 Peptidase_C19O A subfa 97.6 0.00013 2.7E-09 58.6 5.6 67 11-96 79-145 (332)
13 cd02667 Peptidase_C19K A subfa 97.6 0.00011 2.3E-09 56.7 4.8 61 17-96 31-91 (279)
14 cd02669 Peptidase_C19M A subfa 97.5 0.00029 6.2E-09 58.3 6.1 83 3-92 170-254 (440)
15 cd02257 Peptidase_C19 Peptidas 97.4 0.00013 2.9E-09 51.6 2.5 57 39-95 21-78 (255)
16 cd02673 Peptidase_C19Q A subfa 96.9 0.00081 1.8E-08 52.0 3.4 76 21-96 14-92 (245)
17 cd02674 Peptidase_C19R A subfa 96.6 0.0018 3.9E-08 47.4 2.8 43 39-97 21-63 (230)
18 cd02662 Peptidase_C19F A subfa 94.3 0.066 1.4E-06 40.5 3.9 42 39-96 33-74 (240)
19 KOG1865|consensus 92.8 0.25 5.5E-06 43.1 5.4 84 11-97 167-251 (545)
20 PF13423 UCH_1: Ubiquitin carb 88.8 0.88 1.9E-05 35.2 4.7 91 3-96 47-144 (295)
21 KOG2026|consensus 87.7 1.1 2.5E-05 38.1 5.0 59 13-79 194-252 (442)
22 PF13405 EF-hand_6: EF-hand do 85.6 0.49 1.1E-05 25.1 1.2 27 1-27 2-28 (31)
23 smart00054 EFh EF-hand, calciu 81.5 1.8 3.8E-05 20.2 2.2 27 1-27 2-28 (29)
24 PF08715 Viral_protease: Papai 80.8 0.77 1.7E-05 37.6 1.1 29 32-60 155-183 (320)
25 KOG1867|consensus 80.2 3.3 7.1E-05 35.6 4.7 91 2-95 212-307 (492)
26 cd00051 EFh EF-hand, calcium b 78.4 7.4 0.00016 21.2 4.5 28 1-28 2-29 (63)
27 PF13499 EF-hand_7: EF-hand do 77.6 2.5 5.4E-05 25.2 2.4 30 1-30 2-31 (66)
28 PF00036 EF-hand_1: EF hand; 77.5 1.4 3.1E-05 23.5 1.2 28 1-28 2-29 (29)
29 KOG0037|consensus 71.4 4.1 8.8E-05 32.0 2.7 27 2-28 127-153 (221)
30 cd02665 Peptidase_C19I A subfa 70.9 4.1 9E-05 31.4 2.7 61 39-101 21-83 (228)
31 cd00052 EH Eps15 homology doma 59.8 13 0.00028 21.6 2.9 26 2-27 2-27 (67)
32 PF00515 TPR_1: Tetratricopept 59.5 5.3 0.00011 20.7 1.0 21 33-53 10-30 (34)
33 cd05027 S-100B S-100B: S-100B 59.1 20 0.00043 23.5 3.9 49 1-54 10-60 (88)
34 PF13174 TPR_6: Tetratricopept 58.6 4.4 9.5E-05 20.4 0.5 19 35-53 11-29 (33)
35 KOG4849|consensus 57.4 15 0.00032 31.5 3.7 43 11-60 367-409 (498)
36 COG3109 ProQ Activator of osmo 57.2 11 0.00024 29.1 2.7 44 2-46 36-81 (208)
37 PF13176 TPR_7: Tetratricopept 56.8 9.7 0.00021 20.5 1.8 23 33-56 8-30 (36)
38 PF13428 TPR_14: Tetratricopep 55.9 15 0.00032 20.4 2.5 27 22-53 4-30 (44)
39 KOG0027|consensus 55.3 25 0.00054 24.5 4.2 33 1-33 87-119 (151)
40 PF07719 TPR_2: Tetratricopept 54.3 7.3 0.00016 19.8 1.0 21 32-52 9-29 (34)
41 PF02748 PyrI_C: Aspartate car 53.9 5.1 0.00011 24.5 0.4 28 66-93 8-43 (52)
42 cd05022 S-100A13 S-100A13: S-1 52.8 33 0.00072 22.6 4.2 28 1-28 10-38 (89)
43 PF13202 EF-hand_5: EF hand; P 52.6 8.4 0.00018 19.7 1.0 23 1-23 1-23 (25)
44 cd02064 FAD_synthetase_N FAD s 51.2 8 0.00017 28.2 1.1 27 12-48 142-168 (180)
45 PF06667 PspB: Phage shock pro 46.4 36 0.00078 22.4 3.5 37 11-53 31-67 (75)
46 PF03130 HEAT_PBS: PBS lyase H 44.4 45 0.00097 17.1 3.1 19 35-54 7-25 (27)
47 KOG1872|consensus 44.4 28 0.0006 30.3 3.4 59 2-62 158-219 (473)
48 PF14803 Nudix_N_2: Nudix N-te 42.5 9 0.0002 21.5 0.2 13 81-93 18-30 (34)
49 smart00027 EH Eps15 homology d 42.3 22 0.00048 23.0 2.1 27 1-27 12-38 (96)
50 smart00764 Citrate_ly_lig Citr 41.9 13 0.00029 27.6 1.0 27 12-48 149-175 (182)
51 COG3423 Nlp Predicted transcri 40.6 13 0.00029 25.0 0.8 24 11-34 28-51 (82)
52 KOG1868|consensus 38.8 40 0.00086 30.3 3.6 83 11-96 365-475 (653)
53 PRK15359 type III secretion sy 38.7 36 0.00078 23.6 2.8 42 12-53 7-53 (144)
54 PRK10220 hypothetical protein; 38.5 15 0.00032 26.1 0.8 22 78-99 13-34 (111)
55 cd02169 Citrate_lyase_ligase C 37.7 17 0.00037 29.2 1.1 27 11-47 263-289 (297)
56 cd05026 S-100Z S-100Z: S-100Z 37.4 71 0.0015 20.8 3.9 28 1-28 12-41 (93)
57 KOG1863|consensus 36.7 42 0.0009 31.6 3.6 83 1-95 219-301 (1093)
58 cd00213 S-100 S-100: S-100 dom 36.3 46 0.001 20.9 2.8 28 1-28 10-39 (88)
59 PRK07143 hypothetical protein; 35.8 21 0.00046 28.5 1.4 27 12-48 146-172 (279)
60 PF13181 TPR_8: Tetratricopept 35.0 24 0.00051 17.9 1.1 19 34-52 11-29 (34)
61 COG4871 Uncharacterized protei 34.8 12 0.00027 28.6 -0.1 21 40-60 92-112 (193)
62 PF08274 PhnA_Zn_Ribbon: PhnA 34.4 8.7 0.00019 21.1 -0.7 13 83-95 17-29 (30)
63 TIGR00686 phnA alkylphosphonat 34.2 17 0.00037 25.7 0.5 22 78-99 12-33 (109)
64 PF01535 PPR: PPR repeat; Int 33.2 22 0.00048 17.3 0.8 18 35-52 11-28 (31)
65 PRK00893 aspartate carbamoyltr 32.9 18 0.00038 26.9 0.5 29 66-94 107-143 (152)
66 PRK05627 bifunctional riboflav 32.8 32 0.00069 27.7 1.9 28 11-48 156-183 (305)
67 PF13041 PPR_2: PPR repeat fam 31.7 27 0.00058 19.7 1.0 19 35-53 14-32 (50)
68 PF12854 PPR_1: PPR repeat 31.6 20 0.00044 19.2 0.5 14 36-49 19-32 (34)
69 PRK10292 hypothetical protein; 31.6 21 0.00045 23.4 0.6 32 17-48 37-68 (69)
70 cd05029 S-100A6 S-100A6: S-100 31.5 1.3E+02 0.0028 19.5 4.4 25 3-27 14-40 (88)
71 TIGR00083 ribF riboflavin kina 30.2 31 0.00068 27.6 1.5 26 14-49 142-167 (288)
72 cd05025 S-100A1 S-100A1: S-100 29.7 46 0.001 21.3 2.0 27 1-27 11-39 (92)
73 PF12688 TPR_5: Tetratrico pep 29.5 67 0.0015 22.3 2.9 37 14-52 30-66 (120)
74 PF13432 TPR_16: Tetratricopep 28.1 35 0.00076 19.7 1.1 21 33-53 40-60 (65)
75 KOG0027|consensus 27.9 1.4E+02 0.0031 20.6 4.4 31 1-31 10-40 (151)
76 PRK13376 pyrB bifunctional asp 27.7 22 0.00048 31.0 0.3 30 66-95 480-517 (525)
77 PF09279 EF-hand_like: Phospho 27.6 95 0.0021 19.3 3.2 27 1-28 2-28 (83)
78 PF12387 Peptidase_C74: Pestiv 27.4 30 0.00064 26.7 0.9 34 66-99 156-189 (200)
79 cd05031 S-100A10_like S-100A10 27.4 58 0.0013 20.9 2.2 27 1-27 10-38 (94)
80 PF09976 TPR_21: Tetratricopep 27.3 47 0.001 22.7 1.8 23 31-53 55-77 (145)
81 PF01599 Ribosomal_S27: Riboso 27.3 28 0.00061 21.0 0.6 29 65-94 19-47 (47)
82 PF05741 zf-nanos: Nanos RNA b 26.3 24 0.00053 22.0 0.2 14 83-96 31-44 (55)
83 PTZ00183 centrin; Provisional 26.0 73 0.0016 21.3 2.6 28 1-28 19-46 (158)
84 PF10825 DUF2752: Protein of u 25.1 27 0.00059 21.0 0.3 17 72-94 2-18 (52)
85 PF12994 DUF3878: Domain of un 25.0 28 0.00061 28.6 0.4 11 39-49 32-42 (299)
86 TIGR00756 PPR pentatricopeptid 24.8 47 0.001 16.2 1.1 18 35-52 11-28 (35)
87 PF13371 TPR_9: Tetratricopept 23.6 43 0.00093 19.6 0.9 21 33-53 38-58 (73)
88 PF14169 YdjO: Cold-inducible 23.5 49 0.0011 20.9 1.2 31 64-94 18-48 (59)
89 PF09538 FYDLN_acid: Protein o 23.4 51 0.0011 22.9 1.4 19 80-99 22-40 (108)
90 PF13414 TPR_11: TPR repeat; P 23.3 60 0.0013 18.8 1.5 23 31-53 10-32 (69)
91 PF12895 Apc3: Anaphase-promot 23.0 38 0.00082 20.8 0.6 19 31-49 65-83 (84)
92 PRK11788 tetratricopeptide rep 22.6 1.1E+02 0.0024 23.5 3.3 20 34-53 292-311 (389)
93 TIGR00240 ATCase_reg aspartate 21.8 36 0.00077 25.3 0.4 29 66-94 105-141 (150)
94 PF13374 TPR_10: Tetratricopep 21.6 1E+02 0.0022 15.7 2.1 25 34-58 12-36 (42)
95 PF14559 TPR_19: Tetratricopep 21.1 49 0.0011 19.1 0.9 19 35-53 2-20 (68)
96 PF09723 Zn-ribbon_8: Zinc rib 20.9 32 0.0007 19.6 -0.0 8 86-93 27-34 (42)
97 PF03604 DNA_RNApol_7kD: DNA d 20.9 47 0.001 18.4 0.6 11 86-96 1-11 (32)
98 PF06957 COPI_C: Coatomer (COP 20.4 65 0.0014 27.5 1.7 31 31-61 211-241 (422)
99 smart00834 CxxC_CXXC_SSSS Puta 20.3 49 0.0011 17.9 0.7 13 83-95 24-36 (41)
100 COG5207 UBP14 Isopeptidase T [ 20.2 1.4E+02 0.0031 27.0 3.7 74 15-99 372-445 (749)
No 1
>cd02661 Peptidase_C19E A subfamily of Peptidase C19. Peptidase C19 contains ubiquitinyl hydrolases. They are intracellular peptidases that remove ubiquitin molecules from polyubiquinated peptides by cleavage of isopeptide bonds. They hydrolyze bonds involving the carboxyl group of the C-terminal Gly residue of ubiquitin. The purpose of the de-ubiquitination is thought to be editing of the ubiquitin conjugates, which could rescue them from degradation, as well as recycling of the ubiquitin. The ubiquitin/proteasome system is responsible for most protein turnover in the mammalian cell, and with over 50 members, family C19 is one of the largest families of peptidases in the human genome.
Probab=99.09 E-value=2.2e-10 Score=86.76 Aligned_cols=93 Identities=17% Similarity=0.247 Sum_probs=77.3
Q ss_pred HHHhhhhhhcCCCCCChHHHHHHHHhhchhhhhhcccccCcHHHHHHHHHHHhhhccCCchhh----hccCCCCchhhhh
Q psy13474 2 QELFSQLQSSHESALPPDALRRALAEAFFDQQRFQLGFMDDAAECFENMLLRIHYHIASEEAE----DMCGAKHCIPHEK 77 (105)
Q Consensus 2 ~~iF~~~~~s~~~~l~p~~LR~ALa~~~~~~~~Fq~G~M~DA~E~fe~IL~~lH~~~~~~~~~----d~c~~~~Ci~H~~ 77 (105)
+.+|.+...++.+.++|..++++|... ...|+.|.+.||.|.|..+|+.||.+....... .......++.+++
T Consensus 51 ~~~~~~~~~~~~~~~~p~~~~~~l~~~---~~~f~~~~qqDa~Efl~~ll~~l~~~~~~~~~~~~~~~~~~~~~~~i~~~ 127 (304)
T cd02661 51 EAHVERALASSGPGSAPRIFSSNLKQI---SKHFRIGRQEDAHEFLRYLLDAMQKACLDRFKKLKAVDPSSQETTLVQQI 127 (304)
T ss_pred HHHHHHHHhCCCCccChHHHHHHHHHH---HHhhcCcchhhHHHHHHHHHHHHHHHHhhhcccccccCccccCCChhhhc
Confidence 467777788889999999999999875 457999999999999999999999875442211 2344567899999
Q ss_pred hcceehhhhccCCcCCCCCC
Q psy13474 78 FAMTLVEQSVCGACGATSEP 97 (105)
Q Consensus 78 F~m~l~Eq~vC~~Cg~~S~p 97 (105)
|+..+..+.+|.+|+..+..
T Consensus 128 F~g~~~~~~~C~~C~~~s~~ 147 (304)
T cd02661 128 FGGYLRSQVKCLNCKHVSNT 147 (304)
T ss_pred CCcEEeeeEEeCCCCCCcCc
Confidence 99999999999999998874
No 2
>PF00443 UCH: Ubiquitin carboxyl-terminal hydrolase; InterPro: IPR001394 In the MEROPS database peptidases and peptidase homologues are grouped into clans and families. Clans are groups of families for which there is evidence of common ancestry based on a common structural fold: Each clan is identified with two letters, the first representing the catalytic type of the families included in the clan (with the letter 'P' being used for a clan containing families of more than one of the catalytic types serine, threonine and cysteine). Some families cannot yet be assigned to clans, and when a formal assignment is required, such a family is described as belonging to clan A-, C-, M-, N-, S-, T- or U-, according to the catalytic type. Some clans are divided into subclans because there is evidence of a very ancient divergence within the clan, for example MA(E), the gluzincins, and MA(M), the metzincins. Peptidase families are grouped by their catalytic type, the first character representing the catalytic type: A, aspartic; C, cysteine; G, glutamic acid; M, metallo; N, asparagine; S, serine; T, threonine; and U, unknown. The serine, threonine and cysteine peptidases utilise the amino acid as a nucleophile and form an acyl intermediate - these peptidases can also readily act as transferases. In the case of aspartic, glutamic and metallopeptidases, the nucleophile is an activated water molecule. In the case of the asparagine endopeptidases, the nucleophile is asparagine and all are self-processing endopeptidases. In many instances the structural protein fold that characterises the clan or family may have lost its catalytic activity, yet retain its function in protein recognition and binding. Cysteine peptidases have characteristic molecular topologies, which can be seen not only in their three-dimensional structures, but commonly also in the two-dimensional structures. These are peptidases in which the nucleophile is the sulphydryl group of a cysteine residue. Cysteine proteases are divided into clans (proteins which are evolutionary related), and further sub-divided into families, on the basis of the architecture of their catalytic dyad or triad []. This group of cysteine peptidases belong to the MEROPS peptidase family C19 (ubiquitin-specific protease family, clan CA). Families within the CA clan are loosely termed papain-like as protein fold of the peptidase unit resembles that of papain, the type example for clan CA. Predicted active site residues for members of this family and family C1 occur in the same order in the sequence: N/Q, C, H. The type example is human ubiquitin-specific protease 14. Ubiquitin is highly conserved, commonly found conjugated to proteins in eukaryotic cells, where it may act as a marker for rapid degradation, or it may have a chaperone function in protein assembly []. The ubiquitin is released by cleavage from the bound protein by a protease []. A number of deubiquitinising proteases are known: all are activated by thiol compounds [, ], and inhibited by thiol-blocking agents and ubiquitin aldehyde [, ], and as such have the properties of cysteine proteases []. The deubiquitinsing proteases can be split into 2 size ranges (20-30 kDa, IPR001578 from INTERPRO, and 100-200 kDa) []: this family are the 100-200 kDa peptides which includes the Ubp1 ubiquitin peptidase from yeast. Only one conserved cysteine can be identified, along with two conserved histidines. The spacing between the cysteine and the second histidine is thought to be more representative of the cysteine/histidine spacing of a cysteine protease catalytic dyad [].; GO: 0004221 ubiquitin thiolesterase activity, 0006511 ubiquitin-dependent protein catabolic process; PDB: 2LBC_A 3MHH_A 3MHS_A 3M99_A 2Y6E_D 2VHF_A 2HD5_A 3NHE_A 2IBI_A 1NBF_B ....
Probab=98.59 E-value=4e-08 Score=71.19 Aligned_cols=91 Identities=22% Similarity=0.319 Sum_probs=76.9
Q ss_pred CHHHhhhhhhc--CCCCCChHHHHHHHHhhchhhhhhcccccCcHHHHHHHHHHHhhhccCCchh----hhccCCCCchh
Q psy13474 1 MQELFSQLQSS--HESALPPDALRRALAEAFFDQQRFQLGFMDDAAECFENMLLRIHYHIASEEA----EDMCGAKHCIP 74 (105)
Q Consensus 1 l~~iF~~~~~s--~~~~l~p~~LR~ALa~~~~~~~~Fq~G~M~DA~E~fe~IL~~lH~~~~~~~~----~d~c~~~~Ci~ 74 (105)
|+.||..+..+ ....+.|..+..+|...++. |..|.+.||.|.|..||+.|+..+..... ...-....++.
T Consensus 55 l~~l~~~~~~~~~~~~~i~~~~~~~~l~~~~~~---~~~~~qqDa~E~l~~ll~~l~~~~~~~~~~~~~~~~~~~~~~~~ 131 (269)
T PF00443_consen 55 LQNLFRSLWSSNSSDSSISPSDFINALSSINPS---FSNGEQQDAHEFLSFLLDWLDEEFNSSFKRKSWKNTNSSEDSLI 131 (269)
T ss_dssp HHHHHHHHHSSCSSSSEEHCHHHHHHHHHHCGG---GGSSSTEEHHHHHHHHHHHHHHHHTSCSSHHHHHHHHCCEESHH
T ss_pred hhhhhhhhhhhcccccceeeccccccccccccc---cccccccchhhhhcccccccchhhcccccccccccccccccccc
Confidence 46788888877 88999999999999986444 99999999999999999999998877432 34556677899
Q ss_pred hhhhcceehhhhccCCcCCC
Q psy13474 75 HEKFAMTLVEQSVCGACGAT 94 (105)
Q Consensus 75 H~~F~m~l~Eq~vC~~Cg~~ 94 (105)
+.+|+..+.+...|..|+..
T Consensus 132 ~~~f~~~~~~~~~c~~c~~~ 151 (269)
T PF00443_consen 132 SDLFGGQFESSIKCSSCKNS 151 (269)
T ss_dssp HHHH-EEEEEEEEETTTTCE
T ss_pred cccccccccccccccccccc
Confidence 99999999999999999875
No 3
>cd02657 Peptidase_C19A A subfamily of Peptidase C19. Peptidase C19 contains ubiquitinyl hydrolases. They are intracellular peptidases that remove ubiquitin molecules from polyubiquinated peptides by cleavage of isopeptide bonds. They hydrolyse bonds involving the carboxyl group of the C-terminal Gly residue of ubiquitin. The purpose of the de-ubiquitination is thought to be editing of the ubiquitin conjugates, which could rescue them from degradation, as well as recycling of the ubiquitin. The ubiquitin/proteasome system is responsible for most protein turnover in the mammalian cell, and with over 50 members, family C19 is one of the largest families of peptidases in the human genome.
Probab=98.57 E-value=1.7e-07 Score=72.06 Aligned_cols=94 Identities=19% Similarity=0.305 Sum_probs=72.4
Q ss_pred CHHHhhhhhhcCCCCCChHHHHHHHHhhchhhhhh---cccccCcHHHHHHHHHHHhhhccCCchhhhccCCCCchhhhh
Q psy13474 1 MQELFSQLQSSHESALPPDALRRALAEAFFDQQRF---QLGFMDDAAECFENMLLRIHYHIASEEAEDMCGAKHCIPHEK 77 (105)
Q Consensus 1 l~~iF~~~~~s~~~~l~p~~LR~ALa~~~~~~~~F---q~G~M~DA~E~fe~IL~~lH~~~~~~~~~d~c~~~~Ci~H~~ 77 (105)
|+.||.+++.+.+ ++.|..+..+|.+.++.=.-. ..++-.||.|.|..+|+.||..+.. .....++.+.+
T Consensus 49 l~~L~~~l~~~~~-~i~p~~~~~~l~~~~~~f~~~~~~~~~~QqDA~EFl~~lld~L~~~~~~------~~~~~~~i~~~ 121 (305)
T cd02657 49 LRDLFDTMDKKQE-PVPPIEFLQLLRMAFPQFAEKQNQGGYAQQDAEECWSQLLSVLSQKLPG------AGSKGSFIDQL 121 (305)
T ss_pred HHHHHHHHHhCCC-cCCcHHHHHHHHHHCcCcccccCCCCccccCHHHHHHHHHHHHHHHhcc------cCCCCcHHHHh
Confidence 4678888887654 899999999999865432112 4458899999999999999998764 22457799999
Q ss_pred hcceehhhhccCCcC-CCC-CCCCCc
Q psy13474 78 FAMTLVEQSVCGACG-ATS-EPLPFT 101 (105)
Q Consensus 78 F~m~l~Eq~vC~~Cg-~~S-~p~~~t 101 (105)
|+..+..+.+|..|+ .++ ...||.
T Consensus 122 F~g~~~~~~~C~~C~~~~~~~~e~f~ 147 (305)
T cd02657 122 FGIELETKMKCTESPDEEEVSTESEY 147 (305)
T ss_pred hceEEEEEEEcCCCCCCCccccccce
Confidence 999999999999999 333 344444
No 4
>cd02660 Peptidase_C19D A subfamily of Peptidase C19. Peptidase C19 contains ubiquitinyl hydrolases. They are intracellular peptidases that remove ubiquitin molecules from polyubiquinated peptides by cleavage of isopeptide bonds. They hydrolyze bonds involving the carboxyl group of the C-terminal Gly residue of ubiquitin. The purpose of the de-ubiquitination is thought to be editing of the ubiquitin conjugates, which could rescue them from degradation, as well as recycling of the ubiquitin. The ubiquitin/proteasome system is responsible for most protein turnover in the mammalian cell, and with over 50 members, family C19 is one of the largest families of peptidases in the human genome.
Probab=98.57 E-value=1.2e-07 Score=73.39 Aligned_cols=94 Identities=24% Similarity=0.359 Sum_probs=73.2
Q ss_pred CHHHhhhhhh-cCCCCCChHHHHHHHHhhchhhhhhcccccCcHHHHHHHHHHHhhhccCCchhhh-ccCCCCchhhhhh
Q psy13474 1 MQELFSQLQS-SHESALPPDALRRALAEAFFDQQRFQLGFMDDAAECFENMLLRIHYHIASEEAED-MCGAKHCIPHEKF 78 (105)
Q Consensus 1 l~~iF~~~~~-s~~~~l~p~~LR~ALa~~~~~~~~Fq~G~M~DA~E~fe~IL~~lH~~~~~~~~~d-~c~~~~Ci~H~~F 78 (105)
|..||..+.. .....++|..+.+++... ...|..+.+.||.|.|..||++||.......... .=....+|.+++|
T Consensus 51 l~~l~~~l~~~~~~~~~~~~~~l~~~~~~---~~~f~~~~QqDa~Efl~~ll~~l~~~~~~~~~~~~~~~~~~~~i~~~F 127 (328)
T cd02660 51 MDEIFQEFYYSGDRSPYGPINLLYLSWKH---SRNLAGYSQQDAHEFFQFLLDQLHTHYGGDKNEANDESHCNCIIHQTF 127 (328)
T ss_pred HHHHHHHHhcCCCCCCcCHHHHHHHHHhh---chhhcccccccHHHHHHHHHHHHHHHhhcccccccccccCCceeEEec
Confidence 4578998844 456788999998888764 3479999999999999999999998765432110 0012257899999
Q ss_pred cceehhhhccCCcCCCCCC
Q psy13474 79 AMTLVEQSVCGACGATSEP 97 (105)
Q Consensus 79 ~m~l~Eq~vC~~Cg~~S~p 97 (105)
+..+.....|..|+..+..
T Consensus 128 ~g~~~~~~~C~~C~~~s~~ 146 (328)
T cd02660 128 SGSLQSSVTCQRCGGVSTT 146 (328)
T ss_pred ccEEEeeeEcCCCCCccce
Confidence 9999999999999988764
No 5
>cd02663 Peptidase_C19G A subfamily of Peptidase C19. Peptidase C19 contains ubiquitinyl hydrolases. They are intracellular peptidases that remove ubiquitin molecules from polyubiquinated peptides by cleavage of isopeptide bonds. They hydrolyze bonds involving the carboxyl group of the C-terminal Gly residue of ubiquitin. The purpose of the de-ubiquitination is thought to be editing of the ubiquitin conjugates, which could rescue them from degradation, as well as recycling of the ubiquitin. The ubiquitin/proteasome system is responsible for most protein turnover in the mammalian cell, and with over 50 members, family C19 is one of the largest families of peptidases in the human genome.
Probab=98.45 E-value=3.1e-07 Score=71.26 Aligned_cols=93 Identities=19% Similarity=0.332 Sum_probs=74.4
Q ss_pred CHHHhhhhhhc--CCCCCChHHHHHHHHhhchhhhhhcccccCcHHHHHHHHHHHhhhccCCchh----------hhccC
Q psy13474 1 MQELFSQLQSS--HESALPPDALRRALAEAFFDQQRFQLGFMDDAAECFENMLLRIHYHIASEEA----------EDMCG 68 (105)
Q Consensus 1 l~~iF~~~~~s--~~~~l~p~~LR~ALa~~~~~~~~Fq~G~M~DA~E~fe~IL~~lH~~~~~~~~----------~d~c~ 68 (105)
|+.||.+++.+ ...+++|..+.+||... ...|..+...||.|.|..+|+.||..+..... .....
T Consensus 27 L~~lf~~l~~~~~~~~~isP~~f~~~l~~~---~~~f~~~~QqDA~EFl~~lLd~l~~~l~~~~~~~~~~~~~~~~~~~~ 103 (300)
T cd02663 27 LKDLFESISEQKKRTGVISPKKFITRLKRE---NELFDNYMHQDAHEFLNFLLNEIAEILDAERKAEKANRKLNNNNNAE 103 (300)
T ss_pred HHHHHHHHHhCCCCCeeECHHHHHHHHHhh---cCCCCCCccccHHHHHHHHHHHHHHHHHHHhhcccccccccccccCC
Confidence 57889988775 45689999999999864 34799999999999999999999998753211 11223
Q ss_pred CCCchhhhhhcceehhhhccCCcCCCCC
Q psy13474 69 AKHCIPHEKFAMTLVEQSVCGACGATSE 96 (105)
Q Consensus 69 ~~~Ci~H~~F~m~l~Eq~vC~~Cg~~S~ 96 (105)
....+.+.+|+-.+.....|.+|+..|.
T Consensus 104 ~~~~~i~~~F~G~~~~~~~C~~C~~~s~ 131 (300)
T cd02663 104 PQPTWVHEIFQGILTNETRCLTCETVSS 131 (300)
T ss_pred cCCCChhhhCceEEEeeEEeCCCCCCcc
Confidence 3467789999999999999999998764
No 6
>cd02668 Peptidase_C19L A subfamily of Peptidase C19. Peptidase C19 contains ubiquitinyl hydrolases. They are intracellular peptidases that remove ubiquitin molecules from polyubiquinated peptides by cleavage of isopeptide bonds. They hydrolyze bonds involving the carboxyl group of the C-terminal Gly residue of ubiquitin. The purpose of the de-ubiquitination is thought to be editing of the ubiquitin conjugates, which could rescue them from degradation, as well as recycling of the ubiquitin. The ubiquitin/proteasome system is responsible for most protein turnover in the mammalian cell, and with over 50 members, family C19 is one of the largest families of peptidases in the human genome.
Probab=98.38 E-value=5.2e-07 Score=70.74 Aligned_cols=84 Identities=24% Similarity=0.359 Sum_probs=69.9
Q ss_pred CHHHhhhhhhcCCCCCChHHHHHHHHhhchhhhhhcccccCcHHHHHHHHHHHhhhccCCchhhhccCCCCchhhhhhcc
Q psy13474 1 MQELFSQLQSSHESALPPDALRRALAEAFFDQQRFQLGFMDDAAECFENMLLRIHYHIASEEAEDMCGAKHCIPHEKFAM 80 (105)
Q Consensus 1 l~~iF~~~~~s~~~~l~p~~LR~ALa~~~~~~~~Fq~G~M~DA~E~fe~IL~~lH~~~~~~~~~d~c~~~~Ci~H~~F~m 80 (105)
|+.||.+.+.++..+++|..|.++|. |..|...||.|.|..||+.||..+..... .....+.+..|+.
T Consensus 57 L~~lf~~l~~~~~~~i~p~~f~~~l~--------~~~~~QqDa~EFl~~lLd~L~~~l~~~~~----~~~~~~i~~~F~G 124 (324)
T cd02668 57 LQLIFAQLQFGNRSVVDPSGFVKALG--------LDTGQQQDAQEFSKLFLSLLEAKLSKSKN----PDLKNIVQDLFRG 124 (324)
T ss_pred HHHHHHHHHhCCCceEChHHHHHHhC--------CCCccccCHHHHHHHHHHHHHHHHhhccC----Ccccchhhhhcce
Confidence 46789999989999999999999984 66788999999999999999987653211 1124688999999
Q ss_pred eehhhhccCCcCCCCC
Q psy13474 81 TLVEQSVCGACGATSE 96 (105)
Q Consensus 81 ~l~Eq~vC~~Cg~~S~ 96 (105)
.+..+..|..||.++.
T Consensus 125 ~~~~~~~C~~C~~~s~ 140 (324)
T cd02668 125 EYSYVTQCSKCGRESS 140 (324)
T ss_pred EEEEEEEeCCCCCccc
Confidence 9999999999998753
No 7
>cd02659 peptidase_C19C A subfamily of Peptidase C19. Peptidase C19 contains ubiquitinyl hydrolases. They are intracellular peptidases that remove ubiquitin molecules from polyubiquinated peptides by cleavage of isopeptide bonds. They hydrolyze bonds involving the carboxyl group of the C-terminal Gly residue of ubiquitin. The purpose of the de-ubiquitination is thought to be editing of the ubiquitin conjugates, which could rescue them from degradation, as well as recycling of the ubiquitin. The ubiquitin/proteasome system is responsible for most protein turnover in the mammalian cell, and with over 50 members, family C19 is one of the largest families of peptidases in the human genome.
Probab=98.16 E-value=1.8e-06 Score=67.07 Aligned_cols=88 Identities=19% Similarity=0.260 Sum_probs=69.5
Q ss_pred CHHHhhhhhhcCCCCCChHHHHHHHHhhchhhhhhcccccCcHHHHHHHHHHHhhhccCCchhhhccCCCCchhhhhhcc
Q psy13474 1 MQELFSQLQSSHESALPPDALRRALAEAFFDQQRFQLGFMDDAAECFENMLLRIHYHIASEEAEDMCGAKHCIPHEKFAM 80 (105)
Q Consensus 1 l~~iF~~~~~s~~~~l~p~~LR~ALa~~~~~~~~Fq~G~M~DA~E~fe~IL~~lH~~~~~~~~~d~c~~~~Ci~H~~F~m 80 (105)
|+.||..++.++...++|+.++ +...+ ....|..|...||.|.|..||+.||...... ....+...+|+.
T Consensus 50 l~~lf~~~~~~~~~~~~~~~~~--~~~~~-~~~~~~~~~QqDa~Efl~~ll~~l~~~~~~~-------~~~~~i~~lF~g 119 (334)
T cd02659 50 LQRLFLFLQLSESPVKTTELTD--KTRSF-GWDSLNTFEQHDVQEFFRVLFDKLEEKLKGT-------GQEGLIKNLFGG 119 (334)
T ss_pred HHHHHHHHHhCCccccCcchhh--eeccC-CCCCCCcccchhHHHHHHHHHHHHHHHhccC-------cccchhhhhCce
Confidence 4678888888888888887776 22222 2356899999999999999999999877542 234688899999
Q ss_pred eehhhhccCCcCCCCCCC
Q psy13474 81 TLVEQSVCGACGATSEPL 98 (105)
Q Consensus 81 ~l~Eq~vC~~Cg~~S~p~ 98 (105)
.+.....|..|+..|...
T Consensus 120 ~~~~~~~C~~C~~~s~~~ 137 (334)
T cd02659 120 KLVNYIICKECPHESERE 137 (334)
T ss_pred EEEeEEEecCCCceeccc
Confidence 999999999998776543
No 8
>cd02658 Peptidase_C19B A subfamily of Peptidase C19. Peptidase C19 contains ubiquitinyl hydrolases. They are intracellular peptidases that remove ubiquitin molecules from polyubiquinated peptides by cleavage of isopeptide bonds. They hydrolyze bonds involving the carboxyl group of the C-terminal Gly residue of ubiquitin. The purpose of the de-ubiquitination is thought to be editing of the ubiquitin conjugates, which could rescue them from degradation, as well as recycling of the ubiquitin. The ubiquitin/proteasome system is responsible for most protein turnover in the mammalian cell, and with over 50 members, family C19 is one of the largest families of peptidases in the human genome.
Probab=97.92 E-value=1.6e-05 Score=61.38 Aligned_cols=71 Identities=13% Similarity=0.279 Sum_probs=58.1
Q ss_pred CCCCChHHHHHHHHhhchhhhhhcccccCcHHHHHHHHHHHhhhccCCchhhhccCCCCchhhhhhcceehhhhccCCcC
Q psy13474 13 ESALPPDALRRALAEAFFDQQRFQLGFMDDAAECFENMLLRIHYHIASEEAEDMCGAKHCIPHEKFAMTLVEQSVCGACG 92 (105)
Q Consensus 13 ~~~l~p~~LR~ALa~~~~~~~~Fq~G~M~DA~E~fe~IL~~lH~~~~~~~~~d~c~~~~Ci~H~~F~m~l~Eq~vC~~Cg 92 (105)
..++.|..++.+|... ...|..|.+.||.|.|..+|+.||....... .-.+.++|+..+.....|.+|+
T Consensus 76 ~~~i~p~~~~~~l~~~---~~~f~~~~QqDa~Efl~~ll~~l~~~~~~~~--------~~~~~~~f~~~~~~~i~C~~C~ 144 (311)
T cd02658 76 QVGIKPSMFKALIGKG---HPEFSTMRQQDALEFLLHLIDKLDRESFKNL--------GLNPNDLFKFMIEDRLECLSCK 144 (311)
T ss_pred ccccCcHHHHHHHhcc---ChhhcccccccHHHHHHHHHHHHHHhhcccc--------cCCchhheEEEeeEEEEcCCCC
Confidence 4579999999999864 4569999999999999999999998764211 1135689999999999999999
Q ss_pred CC
Q psy13474 93 AT 94 (105)
Q Consensus 93 ~~ 94 (105)
..
T Consensus 145 ~~ 146 (311)
T cd02658 145 KV 146 (311)
T ss_pred CE
Confidence 63
No 9
>KOG1887|consensus
Probab=97.89 E-value=3.1e-06 Score=75.33 Aligned_cols=87 Identities=13% Similarity=0.089 Sum_probs=76.8
Q ss_pred HHHHHHHHhhchhhhhhcccccCcHHHHHHHHHHHhhhccCCchh-------------hhccCCCCchhhhhhcceehhh
Q psy13474 19 DALRRALAEAFFDQQRFQLGFMDDAAECFENMLLRIHYHIASEEA-------------EDMCGAKHCIPHEKFAMTLVEQ 85 (105)
Q Consensus 19 ~~LR~ALa~~~~~~~~Fq~G~M~DA~E~fe~IL~~lH~~~~~~~~-------------~d~c~~~~Ci~H~~F~m~l~Eq 85 (105)
..++.||...|++.-.++...|++|++.|-++|.+|+...+..+. .|.+...-||+|.+|||...|+
T Consensus 528 ~~vp~al~~~~~~s~~~~~~~~~~~S~lL~~ll~~l~~~~~~ss~~~~v~~aile~~~~Wk~~er~~l~~~lf~l~~~e~ 607 (806)
T KOG1887|consen 528 LQVPIALQNFFPASVSESIKHEGVYSELLSDLLLSLEEVHNASSSAADVVVAILEFWQCWKNPERESLVNRLFTLEEKER 607 (806)
T ss_pred ccCcchhhhcCCcchHHHHHhhhhHHHHHHHHHhhhHHHhhhcchhhHHHHHHHhcccccccHHHHHHHHhhhhhhhhhh
Confidence 478899999999999999999999999999999999987765422 2566677899999999999999
Q ss_pred hccCCcCCCCCCCCCccCCC
Q psy13474 86 SVCGACGATSEPLPFTQEGK 105 (105)
Q Consensus 86 ~vC~~Cg~~S~p~~~t~~~~ 105 (105)
+.|.+|+..+....+|++|.
T Consensus 608 ~Sc~~cr~~~n~peqsS~~~ 627 (806)
T KOG1887|consen 608 MSCSKCRRDLNYPEQSSYGI 627 (806)
T ss_pred ccccccccCCCCcchhhhhh
Confidence 99999999999888888763
No 10
>cd02664 Peptidase_C19H A subfamily of Peptidase C19. Peptidase C19 contains ubiquitinyl hydrolases. They are intracellular peptidases that remove ubiquitin molecules from polyubiquinated peptides by cleavage of isopeptide bonds. They hydrolyze bonds involving the carboxyl group of the C-terminal Gly residue of ubiquitin. The purpose of the de-ubiquitination is thought to be editing of the ubiquitin conjugates, which could rescue them from degradation, as well as recycling of the ubiquitin. The ubiquitin/proteasome system is responsible for most protein turnover in the mammalian cell, and with over 50 members, family C19 is one of the largest families of peptidases in the human genome.
Probab=97.83 E-value=3e-05 Score=61.18 Aligned_cols=75 Identities=25% Similarity=0.355 Sum_probs=60.5
Q ss_pred CHHHhhhhhhcCCCCCChHH-HHHHHHhhchhhhhhcccccCcHHHHHHHHHHHhhhccCCchhhhccCCCCchhhhhhc
Q psy13474 1 MQELFSQLQSSHESALPPDA-LRRALAEAFFDQQRFQLGFMDDAAECFENMLLRIHYHIASEEAEDMCGAKHCIPHEKFA 79 (105)
Q Consensus 1 l~~iF~~~~~s~~~~l~p~~-LR~ALa~~~~~~~~Fq~G~M~DA~E~fe~IL~~lH~~~~~~~~~d~c~~~~Ci~H~~F~ 79 (105)
|+.+|..+..++..+++|.. +-.++ ....|..|...||.|.|..+|+.|| .+..++|+
T Consensus 46 L~~lf~~l~~~~~~~~~~~~~~l~~~-----~~~~f~~~~QqDa~EFl~~lLd~l~----------------~~i~~~F~ 104 (327)
T cd02664 46 LQLLQAHLMHTQRRAEAPPDYFLEAS-----RPPWFTPGSQQDCSEYLRYLLDRLH----------------TLIEKMFG 104 (327)
T ss_pred HHHHHHHHhhcCCcccCCHHHHHHHh-----cccccCCCCcCCHHHHHHHHHHHHH----------------HHHHhhCc
Confidence 46788888888777777765 22222 2356999999999999999999999 37889999
Q ss_pred ceehhhhccCCcCCCCC
Q psy13474 80 MTLVEQSVCGACGATSE 96 (105)
Q Consensus 80 m~l~Eq~vC~~Cg~~S~ 96 (105)
..+..+..|..|+..|.
T Consensus 105 G~~~~~i~C~~C~~~s~ 121 (327)
T cd02664 105 GKLSTTIRCLNCNSTSA 121 (327)
T ss_pred EEeEeEEEcCCCCCEec
Confidence 99999999999997765
No 11
>cd02666 Peptidase_C19J A subfamily of Peptidase C19. Peptidase C19 contains ubiquitinyl hydrolases. They are intracellular peptidases that remove ubiquitin molecules from polyubiquinated peptides by cleavage of isopeptide bonds. They hydrolyze bonds involving the carboxyl group of the C-terminal Gly residue of ubiquitin. The purpose of the de-ubiquitination is thought to be editing of the ubiquitin conjugates, which could rescue them from degradation, as well as recycling of the ubiquitin. The ubiquitin/proteasome system is responsible for most protein turnover in the mammalian cell, and with over 50 members, family C19 is one of the largest families of peptidases in the human genome.
Probab=97.61 E-value=8.4e-05 Score=60.25 Aligned_cols=81 Identities=20% Similarity=0.278 Sum_probs=64.5
Q ss_pred CHHHhhhhhhcCCCCCChHHHHHHHHhhchhhhhhcccccCcHHHHHHHHHHHhhhccCCchhh------hccCCCCchh
Q psy13474 1 MQELFSQLQSSHESALPPDALRRALAEAFFDQQRFQLGFMDDAAECFENMLLRIHYHIASEEAE------DMCGAKHCIP 74 (105)
Q Consensus 1 l~~iF~~~~~s~~~~l~p~~LR~ALa~~~~~~~~Fq~G~M~DA~E~fe~IL~~lH~~~~~~~~~------d~c~~~~Ci~ 74 (105)
|+.||...+.+....+.|...=..|+. .-.||.|++..+|+.||..+...... +.=....++.
T Consensus 70 L~~LF~~l~~s~~~~v~P~~~l~~l~~-----------~QQDa~Ef~~~lld~Le~~lk~~~~~~~~~~~~~~~~~~~~I 138 (343)
T cd02666 70 LRSLFNDLIHSNTRSVTPSKELAYLAL-----------RQQDVTECIDNVLFQLEVALEPISNAFAGPDTEDDKEQSDLI 138 (343)
T ss_pred HHHHHHHHHhCCCCccCcHHHHHhccc-----------cccchHHHHHHHHHHHHHHhcCccccccCcccccccchhhhh
Confidence 578999999999899988876555552 67899999999999999998654321 1112447899
Q ss_pred hhhhcceehhhhccCCcC
Q psy13474 75 HEKFAMTLVEQSVCGACG 92 (105)
Q Consensus 75 H~~F~m~l~Eq~vC~~Cg 92 (105)
+++|+-.+-...+|..|+
T Consensus 139 ~~lF~G~~~~~i~c~~~~ 156 (343)
T cd02666 139 KRLFSGKTKQQLVPESMG 156 (343)
T ss_pred hHhceeeEEEEEEecccC
Confidence 999999988888898886
No 12
>cd02671 Peptidase_C19O A subfamily of Peptidase C19. Peptidase C19 contains ubiquitinyl hydrolases. They are intracellular peptidases that remove ubiquitin molecules from polyubiquinated peptides by cleavage of isopeptide bonds. They hydrolyze bonds involving the carboxyl group of the C-terminal Gly residue of ubiquitin. The purpose of the de-ubiquitination is thought to be editing of the ubiquitin conjugates, which could rescue them from degradation, as well as recycling of the ubiquitin. The ubiquitin/proteasome system is responsible for most protein turnover in the mammalian cell, and with over 50 members, family C19 is one of the largest families of peptidases in the human genome.
Probab=97.60 E-value=0.00013 Score=58.58 Aligned_cols=67 Identities=24% Similarity=0.324 Sum_probs=57.8
Q ss_pred cCCCCCChHHHHHHHHhhchhhhhhcccccCcHHHHHHHHHHHhhhccCCchhhhccCCCCchhhhhhcceehhhhccCC
Q psy13474 11 SHESALPPDALRRALAEAFFDQQRFQLGFMDDAAECFENMLLRIHYHIASEEAEDMCGAKHCIPHEKFAMTLVEQSVCGA 90 (105)
Q Consensus 11 s~~~~l~p~~LR~ALa~~~~~~~~Fq~G~M~DA~E~fe~IL~~lH~~~~~~~~~d~c~~~~Ci~H~~F~m~l~Eq~vC~~ 90 (105)
+...+.+|..|..++.+. ...|..+.-.||.|.|..+|+.|| .+.+..|+-.+..+..|.+
T Consensus 79 ~~~~~~~P~~~~~~l~~~---~~~f~~~~QQDA~EFl~~LLd~L~----------------~~i~~~F~g~~~~~~~C~~ 139 (332)
T cd02671 79 DELANQAPRRLLNALREV---NPMYEGYLQHDAQEVLQCILGNIQ----------------ELVEKDFQGQLVLRTRCLE 139 (332)
T ss_pred hcccccCHHHHHHHHHHh---ccccCCccccCHHHHHHHHHHHHH----------------HHHHhhhceEEEEEEEeCC
Confidence 344566799999999864 356889999999999999999998 2678899999999999999
Q ss_pred cCCCCC
Q psy13474 91 CGATSE 96 (105)
Q Consensus 91 Cg~~S~ 96 (105)
||..|.
T Consensus 140 C~~~s~ 145 (332)
T cd02671 140 CETFTE 145 (332)
T ss_pred CCCeec
Confidence 998876
No 13
>cd02667 Peptidase_C19K A subfamily of Peptidase C19. Peptidase C19 contains ubiquitinyl hydrolases. They are intracellular peptidases that remove ubiquitin molecules from polyubiquinated peptides by cleavage of isopeptide bonds. They hydrolyze bonds involving the carboxyl group of the C-terminal Gly residue of ubiquitin. The purpose of the de-ubiquitination is thought to be editing of the ubiquitin conjugates, which could rescue them from degradation, as well as recycling of the ubiquitin. The ubiquitin/proteasome system is responsible for most protein turnover in the mammalian cell, and with over 50 members, family C19 is one of the largest families of peptidases in the human genome.
Probab=97.59 E-value=0.00011 Score=56.71 Aligned_cols=61 Identities=20% Similarity=0.317 Sum_probs=54.3
Q ss_pred ChHHHHHHHHhhchhhhhhcccccCcHHHHHHHHHHHhhhccCCchhhhccCCCCchhhhhhcceehhhhccCCcCCCCC
Q psy13474 17 PPDALRRALAEAFFDQQRFQLGFMDDAAECFENMLLRIHYHIASEEAEDMCGAKHCIPHEKFAMTLVEQSVCGACGATSE 96 (105)
Q Consensus 17 ~p~~LR~ALa~~~~~~~~Fq~G~M~DA~E~fe~IL~~lH~~~~~~~~~d~c~~~~Ci~H~~F~m~l~Eq~vC~~Cg~~S~ 96 (105)
.|..|..+|.+ ....|..|.+.||.|-|..+|+.|| .+.+.+|+..+.....|.+|+..|.
T Consensus 31 ~P~~~~~~l~~---~~~~f~~~~QqDA~Efl~~lld~l~----------------~~i~~~F~G~~~~~i~C~~C~~~s~ 91 (279)
T cd02667 31 TPKELFSQVCR---KAPQFKGYQQQDSHELLRYLLDGLR----------------TFIDSIFGGELTSTIMCESCGTVSL 91 (279)
T ss_pred CHHHHHHHHHH---hhHhhcCCchhhHHHHHHHHHHHHH----------------HhhhhhcceEEEEEEEcCCCCCEeC
Confidence 78888888875 4567999999999999999999999 3778899999999999999998876
No 14
>cd02669 Peptidase_C19M A subfamily of Peptidase C19. Peptidase C19 contains ubiquitinyl hydrolases. They are intracellular peptidases that remove ubiquitin molecules from polyubiquinated peptides by cleavage of isopeptide bonds. They hydrolyze bonds involving the carboxyl group of the C-terminal Gly residue of ubiquitin. The purpose of the de-ubiquitination is thought to be editing of the ubiquitin conjugates, which could rescue them from degradation, as well as recycling of the ubiquitin. The ubiquitin/proteasome system is responsible for most protein turnover in the mammalian cell, and with over 50 members, family C19 is one of the largest families of peptidases in the human genome.
Probab=97.46 E-value=0.00029 Score=58.33 Aligned_cols=83 Identities=16% Similarity=0.257 Sum_probs=62.8
Q ss_pred HHhhhhhhcC--CCCCChHHHHHHHHhhchhhhhhcccccCcHHHHHHHHHHHhhhccCCchhhhccCCCCchhhhhhcc
Q psy13474 3 ELFSQLQSSH--ESALPPDALRRALAEAFFDQQRFQLGFMDDAAECFENMLLRIHYHIASEEAEDMCGAKHCIPHEKFAM 80 (105)
Q Consensus 3 ~iF~~~~~s~--~~~l~p~~LR~ALa~~~~~~~~Fq~G~M~DA~E~fe~IL~~lH~~~~~~~~~d~c~~~~Ci~H~~F~m 80 (105)
.+|..+...+ ..+++|..+-++|... ..+.|..+.-.||.|.|.-+|+.||..+.... ....||.|+.|+-
T Consensus 170 ~l~~kl~~~~~~~~~isP~~fl~~l~~~--~~~~f~~~~QqDA~EFl~~LLd~L~~~l~~~~-----~~~~~ii~~~F~G 242 (440)
T cd02669 170 ELIRKIWNPRNFKGHVSPHELLQAVSKV--SKKKFSITEQSDPVEFLSWLLNTLHKDLGGSK-----KPNSSIIHDCFQG 242 (440)
T ss_pred HHHHHHhccccCCCccCHHHHHHHHHhh--cccccCCcccCCHHHHHHHHHHHHHHHhccCC-----CCCCCcceeccCc
Confidence 4455443222 5789999999999865 45779999999999999999999999876431 2347899999998
Q ss_pred eehhhhccCCcC
Q psy13474 81 TLVEQSVCGACG 92 (105)
Q Consensus 81 ~l~Eq~vC~~Cg 92 (105)
.+.-...|..|.
T Consensus 243 ~l~~~~~c~~~~ 254 (440)
T cd02669 243 KVQIETQKIKPH 254 (440)
T ss_pred eEEEEEEeeccc
Confidence 876666665444
No 15
>cd02257 Peptidase_C19 Peptidase C19 contains ubiquitinyl hydrolases. They are intracellular peptidases that remove ubiquitin molecules from polyubiquinated peptides by cleavage of isopeptide bonds. They hydrolyse bonds involving the carboxyl group of the C-terminal Gly residue of ubiquitin The purpose of the de-ubiquitination is thought to be editing of the ubiquitin conjugates, which could rescue them from degradation, as well as recycling of the ubiquitin. The ubiquitin/proteasome system is responsible for most protein turnover in the mammalian cell, and with over 50 members, family C19 is one of the largest families of peptidases in the human genome.
Probab=97.36 E-value=0.00013 Score=51.57 Aligned_cols=57 Identities=23% Similarity=0.321 Sum_probs=47.2
Q ss_pred ccCcHHHHHHHHHHHhhhccCCchh-hhccCCCCchhhhhhcceehhhhccCCcCCCC
Q psy13474 39 FMDDAAECFENMLLRIHYHIASEEA-EDMCGAKHCIPHEKFAMTLVEQSVCGACGATS 95 (105)
Q Consensus 39 ~M~DA~E~fe~IL~~lH~~~~~~~~-~d~c~~~~Ci~H~~F~m~l~Eq~vC~~Cg~~S 95 (105)
.+.||.|+|..||+.||..+..... ...+.....+.+++|++.+.++.+|..|+..+
T Consensus 21 ~q~Da~E~l~~ll~~l~~~~~~~~~~~~~~~~~~~~i~~~F~~~~~~~~~c~~c~~~~ 78 (255)
T cd02257 21 EQQDAHEFLLFLLDKLHEELKKSSKRTSDSSSLKSLIHDLFGGKLESTIVCLECGHES 78 (255)
T ss_pred HHHHHHHHHHHHHHHHHHHHHhhcccccccccCCchhhhhcccEEeeEEECCCCCCCc
Confidence 8899999999999999998766332 23445556799999999999999999998543
No 16
>cd02673 Peptidase_C19Q A subfamily of Peptidase C19. Peptidase C19 contains ubiquitinyl hydrolases. They are intracellular peptidases that remove ubiquitin molecules from polyubiquinated peptides by cleavage of isopeptide bonds. They hydrolyze bonds involving the carboxyl group of the C-terminal Gly residue of ubiquitin. The purpose of the de-ubiquitination is thought to be editing of the ubiquitin conjugates, which could rescue them from degradation, as well as recycling of the ubiquitin. The ubiquitin/proteasome system is responsible for most protein turnover in the mammalian cell, and with over 50 members, family C19 is one of the largest families of peptidases in the human genome.
Probab=96.95 E-value=0.00081 Score=51.97 Aligned_cols=76 Identities=21% Similarity=0.187 Sum_probs=57.6
Q ss_pred HHHHHHhhchhhhhhcccccCcHHHHHHHHHHHhhhccCCch--hh-hccCCCCchhhhhhcceehhhhccCCcCCCCC
Q psy13474 21 LRRALAEAFFDQQRFQLGFMDDAAECFENMLLRIHYHIASEE--AE-DMCGAKHCIPHEKFAMTLVEQSVCGACGATSE 96 (105)
Q Consensus 21 LR~ALa~~~~~~~~Fq~G~M~DA~E~fe~IL~~lH~~~~~~~--~~-d~c~~~~Ci~H~~F~m~l~Eq~vC~~Cg~~S~ 96 (105)
--.||+..-.....|.-|...||-|-|--+|+.||....... .. ..=...++.++..|+..+.....|.+||..|.
T Consensus 14 ~~~~~~~i~~~~~~F~~~~QQDAhEFL~~LLd~l~~~~~~~~~~~~~~~~~~~~~~~~~~F~~~l~s~i~C~~C~~~s~ 92 (245)
T cd02673 14 TMQALSSIGKINTEFDNDDQQDAHEFLLTLLEAIDDIMQVNRTNVPPSNIEIKRLNPLEAFKYTIESSYVCIGCSFEEN 92 (245)
T ss_pred HHHHHHHHhhhhhhcCCCchhhHHHHHHHHHHHHHHHHHhhcccCCCCcccccccCHhHheeeEEEeEEEecCCCCeee
Confidence 346888887888999999999999999999999997432210 00 00012345678999999999999999998863
No 17
>cd02674 Peptidase_C19R A subfamily of peptidase C19. Peptidase C19 contains ubiquitinyl hydrolases. They are intracellular peptidases that remove ubiquitin molecules from polyubiquinated peptides by cleavage of isopeptide bonds. They hydrolyze bonds involving the carboxyl group of the C-terminal Gly residue of ubiquitin. The purpose of the de-ubiquitination is thought to be editing of the ubiquitin conjugates, which could rescue them from degradation, as well as recycling of the ubiquitin. The ubiquitin/proteasome system is responsible for most protein turnover in the mammalian cell, and with over 50 members, family C19 is one of the largest families of peptidases in the human genome.
Probab=96.58 E-value=0.0018 Score=47.41 Aligned_cols=43 Identities=30% Similarity=0.367 Sum_probs=39.2
Q ss_pred ccCcHHHHHHHHHHHhhhccCCchhhhccCCCCchhhhhhcceehhhhccCCcCCCCCC
Q psy13474 39 FMDDAAECFENMLLRIHYHIASEEAEDMCGAKHCIPHEKFAMTLVEQSVCGACGATSEP 97 (105)
Q Consensus 39 ~M~DA~E~fe~IL~~lH~~~~~~~~~d~c~~~~Ci~H~~F~m~l~Eq~vC~~Cg~~S~p 97 (105)
.+.||.|.|..||+.|| .+...+|+..+..+..|.+||..+..
T Consensus 21 ~QqDa~Ef~~~ll~~l~----------------~~i~~~F~~~~~~~~~C~~C~~~~~~ 63 (230)
T cd02674 21 DQQDAQEFLLFLLDGLH----------------SIIVDLFQGQLKSRLTCLTCGKTSTT 63 (230)
T ss_pred hhhhHHHHHHHHHHHHh----------------hhHHheeCCEEeCcEEcCCCcCCcce
Confidence 79999999999999999 26778999999999999999999863
No 18
>cd02662 Peptidase_C19F A subfamily of Peptidase C19. Peptidase C19 contains ubiquitinyl hydrolases. They are intracellular peptidases that remove ubiquitin molecules from polyubiquinated peptides by cleavage of isopeptide bonds. They hydrolyze bonds involving the carboxyl group of the C-terminal Gly residue of ubiquitin. The purpose of the de-ubiquitination is thought to be editing of the ubiquitin conjugates, which could rescue them from degradation, as well as recycling of the ubiquitin. The ubiquitin/proteasome system is responsible for most protein turnover in the mammalian cell, and with over 50 members, family C19 is one of the largest families of peptidases in the human genome.
Probab=94.26 E-value=0.066 Score=40.50 Aligned_cols=42 Identities=29% Similarity=0.414 Sum_probs=37.7
Q ss_pred ccCcHHHHHHHHHHHhhhccCCchhhhccCCCCchhhhhhcceehhhhccCCcCCCCC
Q psy13474 39 FMDDAAECFENMLLRIHYHIASEEAEDMCGAKHCIPHEKFAMTLVEQSVCGACGATSE 96 (105)
Q Consensus 39 ~M~DA~E~fe~IL~~lH~~~~~~~~~d~c~~~~Ci~H~~F~m~l~Eq~vC~~Cg~~S~ 96 (105)
...||.|-|..+|+.||. +....|...+.....|..||..|.
T Consensus 33 ~QqDa~EFl~~ll~~l~~----------------~i~~~F~g~~~~~i~C~~C~~~s~ 74 (240)
T cd02662 33 EQQDAHELFQVLLETLEQ----------------LLKFPFDGLLASRIVCLQCGESSK 74 (240)
T ss_pred hhcCHHHHHHHHHHHHHH----------------hccCccccEEEEEEEeCCCCCccC
Confidence 889999999999999991 466789999999999999999865
No 19
>KOG1865|consensus
Probab=92.75 E-value=0.25 Score=43.12 Aligned_cols=84 Identities=18% Similarity=0.215 Sum_probs=65.1
Q ss_pred cCCCCCChHHHHHHHHhhchhhhhhcccccCcHHHHHHHHHHHhhhccCCchh-hhccCCCCchhhhhhcceehhhhccC
Q psy13474 11 SHESALPPDALRRALAEAFFDQQRFQLGFMDDAAECFENMLLRIHYHIASEEA-EDMCGAKHCIPHEKFAMTLVEQSVCG 89 (105)
Q Consensus 11 s~~~~l~p~~LR~ALa~~~~~~~~Fq~G~M~DA~E~fe~IL~~lH~~~~~~~~-~d~c~~~~Ci~H~~F~m~l~Eq~vC~ 89 (105)
+.+.+|.|..+..-|-. =+..|.-|.=+||=|-|..+++.|+...-+... .+.=....=|+|++||=.|.-|.-|.
T Consensus 167 ~~g~pisP~~i~s~L~~---I~~~f~~grQEDAHEFLr~~vd~mqk~cL~g~~~~~~~sq~ttlv~~iFGG~LrS~vkC~ 243 (545)
T KOG1865|consen 167 NPGHPISPSQILSNLRN---ISAHFGRGRQEDAHEFLRFTVDAMQKACLPGHKQVDPRSQDTTLVHQIFGGYLRSQIKCL 243 (545)
T ss_pred CCCCccChHHHHHhhhh---hcccccCCchhhHHHHHHHHHHHHHHhhcCCCccCCcccccceehhhhhccchhhceecc
Confidence 34448999988777765 467799999999999999999999986532211 12222334599999999999999999
Q ss_pred CcCCCCCC
Q psy13474 90 ACGATSEP 97 (105)
Q Consensus 90 ~Cg~~S~p 97 (105)
.|...|+-
T Consensus 244 ~C~~vS~t 251 (545)
T KOG1865|consen 244 HCKGVSDT 251 (545)
T ss_pred cCCCcccc
Confidence 99998873
No 20
>PF13423 UCH_1: Ubiquitin carboxyl-terminal hydrolase
Probab=88.85 E-value=0.88 Score=35.25 Aligned_cols=91 Identities=18% Similarity=0.234 Sum_probs=69.0
Q ss_pred HHhhhhh-hcCCCCCChHHHHHHHHhhchhhhhhcccccCcHHHHHHHHHHHhhhccCCchh------hhccCCCCchhh
Q psy13474 3 ELFSQLQ-SSHESALPPDALRRALAEAFFDQQRFQLGFMDDAAECFENMLLRIHYHIASEEA------EDMCGAKHCIPH 75 (105)
Q Consensus 3 ~iF~~~~-~s~~~~l~p~~LR~ALa~~~~~~~~Fq~G~M~DA~E~fe~IL~~lH~~~~~~~~------~d~c~~~~Ci~H 75 (105)
=||..+. .+++....+..+=+||+... +-..+|.-.|..+.+.-||++||.-+..... ........=...
T Consensus 47 fLf~ml~~~~~g~~cq~sNflr~l~~~~---~a~~l~~~~~iq~~~~Fll~~l~~~~~~~~~~~~~~~~~~~~~~~~~i~ 123 (295)
T PF13423_consen 47 FLFDMLDSKAKGINCQASNFLRALSWIP---EAAALGLQQDIQSLNRFLLEQLSMELLTFKPDIFHTSENSSSSPESSIS 123 (295)
T ss_pred HHHHHhhhhcCCCcChHHHHHHHHhcCH---HHHhcchhHHHHHHHHHHHHHHhHHHHhcCcccccccccccCCCcchHH
Confidence 3788888 78888888877777998763 4456788999999999999999997644331 112233334567
Q ss_pred hhhcceehhhhccCCcCCCCC
Q psy13474 76 EKFAMTLVEQSVCGACGATSE 96 (105)
Q Consensus 76 ~~F~m~l~Eq~vC~~Cg~~S~ 96 (105)
++||+.......|.+||.++.
T Consensus 124 ~~f~~~~~~~~~c~~c~~~~~ 144 (295)
T PF13423_consen 124 QLFGTSFETTIRCTSCGHESV 144 (295)
T ss_pred HHhCcceeeeecccccCCeEE
Confidence 899999999999999999874
No 21
>KOG2026|consensus
Probab=87.74 E-value=1.1 Score=38.08 Aligned_cols=59 Identities=20% Similarity=0.424 Sum_probs=51.3
Q ss_pred CCCCChHHHHHHHHhhchhhhhhcccccCcHHHHHHHHHHHhhhccCCchhhhccCCCCchhhhhhc
Q psy13474 13 ESALPPDALRRALAEAFFDQQRFQLGFMDDAAECFENMLLRIHYHIASEEAEDMCGAKHCIPHEKFA 79 (105)
Q Consensus 13 ~~~l~p~~LR~ALa~~~~~~~~Fq~G~M~DA~E~fe~IL~~lH~~~~~~~~~d~c~~~~Ci~H~~F~ 79 (105)
..-|+|-.+-.|.+.+ ..++|+.|+=.|+.|-+.-+|+.||..+.+.. ++..|.|--|.
T Consensus 194 k~hvSphe~lqaV~~~--s~k~f~i~~q~DpveFlswllntlhs~l~~~k------~~~SIi~~~fq 252 (442)
T KOG2026|consen 194 KGHVSPHEFLQAVMKL--SKKRFRIGQQSDPVEFLSWLLNTLHSDLRGSK------KASSIIHKSFQ 252 (442)
T ss_pred cccCCHHHHHHHHHHH--hhhheecCCCCCHHHHHHHHHHHHHHHhCCCC------CchhHhhHhhc
Confidence 3568899999999987 88999999999999999999999999987754 56679998885
No 22
>PF13405 EF-hand_6: EF-hand domain; PDB: 2AMI_A 3QRX_A 1W7J_B 1OE9_B 1W7I_B 1KFU_S 1KFX_S 2BL0_B 1Y1X_B 3MSE_B ....
Probab=85.57 E-value=0.49 Score=25.07 Aligned_cols=27 Identities=19% Similarity=0.354 Sum_probs=23.9
Q ss_pred CHHHhhhhhhcCCCCCChHHHHHHHHh
Q psy13474 1 MQELFSQLQSSHESALPPDALRRALAE 27 (105)
Q Consensus 1 l~~iF~~~~~s~~~~l~p~~LR~ALa~ 27 (105)
|+.+|..|+.....-|..+.|+.+|.+
T Consensus 2 l~~~F~~~D~d~dG~I~~~el~~~l~~ 28 (31)
T PF13405_consen 2 LREAFKMFDKDGDGFIDFEELRAILRK 28 (31)
T ss_dssp HHHHHHHH-TTSSSEEEHHHHHHHHHH
T ss_pred HHHHHHHHCCCCCCcCcHHHHHHHHHH
Confidence 478999999999999999999999984
No 23
>smart00054 EFh EF-hand, calcium binding motif. EF-hands are calcium-binding motifs that occur at least in pairs. Links between disease states and genes encoding EF-hands, particularly the S100 subclass, are emerging. Each motif consists of a 12 residue loop flanked on either side by a 12 residue alpha-helix. EF-hands undergo a conformational change unpon binding calcium ions.
Probab=81.51 E-value=1.8 Score=20.24 Aligned_cols=27 Identities=11% Similarity=0.304 Sum_probs=22.6
Q ss_pred CHHHhhhhhhcCCCCCChHHHHHHHHh
Q psy13474 1 MQELFSQLQSSHESALPPDALRRALAE 27 (105)
Q Consensus 1 l~~iF~~~~~s~~~~l~p~~LR~ALa~ 27 (105)
++.+|..++......|+.+.++..+..
T Consensus 2 ~~~~f~~~d~~~~g~i~~~e~~~~~~~ 28 (29)
T smart00054 2 LKEAFRLFDKDGDGKIDFEEFKDLLKA 28 (29)
T ss_pred HHHHHHHHCCCCCCcEeHHHHHHHHHh
Confidence 467899998888889999999988764
No 24
>PF08715 Viral_protease: Papain like viral protease; InterPro: IPR014827 This family of viral proteases are similar to the papain protease and are required for proteolytic processing of the replicase polyprotein. The structure of this protein has shown it adopts a fold similar to that of de-ubiquitinating enzymes []. ; GO: 0004197 cysteine-type endopeptidase activity, 0008242 omega peptidase activity, 0016740 transferase activity; PDB: 3MP2_A 3EWP_B 3EWO_B 2FE8_A 3MJ5_B 3EKE_A 3EJF_A 3JZT_H 3ETI_E 3E9S_A.
Probab=80.80 E-value=0.77 Score=37.56 Aligned_cols=29 Identities=14% Similarity=0.101 Sum_probs=17.8
Q ss_pred hhhhcccccCcHHHHHHHHHHHhhhccCC
Q psy13474 32 QQRFQLGFMDDAAECFENMLLRIHYHIAS 60 (105)
Q Consensus 32 ~~~Fq~G~M~DA~E~fe~IL~~lH~~~~~ 60 (105)
...+..|+|+||.++|+.+|+.++-..+.
T Consensus 155 ~~~~~~G~~gDa~~~L~~ll~~~~~~~~~ 183 (320)
T PF08715_consen 155 STNAKKGDPGDAEYVLSKLLKDADLDYSV 183 (320)
T ss_dssp HTT--TTS---HHHHHHHHHTTB-TTT-E
T ss_pred HcCCCCCCCcCHHHHHHHHHHhccccceE
Confidence 34578999999999999999987765443
No 25
>KOG1867|consensus
Probab=80.19 E-value=3.3 Score=35.65 Aligned_cols=91 Identities=25% Similarity=0.319 Sum_probs=67.8
Q ss_pred HHHhhhhhhcC-CCCCChHHHHHHHHhhchhhhhhcccccCcHHHHHHHHHHHhhhccCCchhhhccCCC----Cchhhh
Q psy13474 2 QELFSQLQSSH-ESALPPDALRRALAEAFFDQQRFQLGFMDDAAECFENMLLRIHYHIASEEAEDMCGAK----HCIPHE 76 (105)
Q Consensus 2 ~~iF~~~~~s~-~~~l~p~~LR~ALa~~~~~~~~Fq~G~M~DA~E~fe~IL~~lH~~~~~~~~~d~c~~~----~Ci~H~ 76 (105)
.++|....... ...+.|-.+....-+.-+ .|+-=.=-||-|-+..+++.+|.+...+.....|... .||.|.
T Consensus 212 ~~~~~~~~s~~~~~~~sp~~~l~~~~k~~~---~~~g~~Qqda~eF~~~~~~~~~~~~~~~~k~~~~~~~~~~c~~iv~~ 288 (492)
T KOG1867|consen 212 DRLFQALYSGHNRTPYSPFELLNLVWKHSP---NLAGYEQQDAHEFLIALLDRLHREKDDCGKSLIASQSNKQCPCIVHT 288 (492)
T ss_pred hhhhhHhhcCCCCCCcChHHHHHHHHHhCc---ccccccccchHHHHHHhcccccccccccccccccccCCcccccccce
Confidence 45566665555 788888888777776433 3444555799999999999999999333333333332 699999
Q ss_pred hhcceehhhhccCCcCCCC
Q psy13474 77 KFAMTLVEQSVCGACGATS 95 (105)
Q Consensus 77 ~F~m~l~Eq~vC~~Cg~~S 95 (105)
.|.=.+--+.+|..|+..|
T Consensus 289 ~F~G~L~~~v~c~~c~~~S 307 (492)
T KOG1867|consen 289 IFSGTLQSDVTCQTCGSKS 307 (492)
T ss_pred eecceeccceeehhhccee
Confidence 9999999999999999988
No 26
>cd00051 EFh EF-hand, calcium binding motif; A diverse superfamily of calcium sensors and calcium signal modulators; most examples in this alignment model have 2 active canonical EF hands. Ca2+ binding induces a conformational change in the EF-hand motif, leading to the activation or inactivation of target proteins. EF-hands tend to occur in pairs or higher copy numbers.
Probab=78.42 E-value=7.4 Score=21.16 Aligned_cols=28 Identities=21% Similarity=0.442 Sum_probs=24.4
Q ss_pred CHHHhhhhhhcCCCCCChHHHHHHHHhh
Q psy13474 1 MQELFSQLQSSHESALPPDALRRALAEA 28 (105)
Q Consensus 1 l~~iF~~~~~s~~~~l~p~~LR~ALa~~ 28 (105)
++.+|..|+......|+...++.+|...
T Consensus 2 ~~~~f~~~d~~~~g~l~~~e~~~~l~~~ 29 (63)
T cd00051 2 LREAFRLFDKDGDGTISADELKAALKSL 29 (63)
T ss_pred HHHHHHHhCCCCCCcCcHHHHHHHHHHh
Confidence 4678999988888899999999999875
No 27
>PF13499 EF-hand_7: EF-hand domain pair; PDB: 1TCF_A 2TN4_A 1TN4_A 1A2X_A 2CT9_B 2OTG_B 2OS8_B 1SNL_A 3O4Y_A 3J04_E ....
Probab=77.58 E-value=2.5 Score=25.16 Aligned_cols=30 Identities=23% Similarity=0.377 Sum_probs=27.1
Q ss_pred CHHHhhhhhhcCCCCCChHHHHHHHHhhch
Q psy13474 1 MQELFSQLQSSHESALPPDALRRALAEAFF 30 (105)
Q Consensus 1 l~~iF~~~~~s~~~~l~p~~LR~ALa~~~~ 30 (105)
|+.+|..|+......|....|+.++.....
T Consensus 2 l~~~F~~~D~d~~G~i~~~el~~~~~~~~~ 31 (66)
T PF13499_consen 2 LKEAFKKFDKDGDGYISKEELRRALKHLGR 31 (66)
T ss_dssp HHHHHHHHSTTSSSEEEHHHHHHHHHHTTS
T ss_pred HHHHHHHHcCCccCCCCHHHHHHHHHHhcc
Confidence 578999999999999999999999998743
No 28
>PF00036 EF-hand_1: EF hand; InterPro: IPR018248 Many calcium-binding proteins belong to the same evolutionary family and share a type of calcium-binding domain known as the EF-hand. This type of domain consists of a twelve residue loop flanked on both sides by a twelve residue alpha-helical domain. In an EF-hand loop the calcium ion is coordinated in a pentagonal bipyramidal configuration. The six residues involved in the binding are in positions 1, 3, 5, 7, 9 and 12; these residues are denoted by X, Y, Z, -Y, -X and -Z. The invariant Glu or Asp at position 12 provides two oxygens for liganding Ca (bidentate ligand).; PDB: 1BJF_A 1XFW_R 1XFV_O 2K0J_A 2F3Z_A 3BYA_A 1XFU_Q 2R28_B 1ZOT_B 3G43_D ....
Probab=77.54 E-value=1.4 Score=23.53 Aligned_cols=28 Identities=7% Similarity=0.332 Sum_probs=24.9
Q ss_pred CHHHhhhhhhcCCCCCChHHHHHHHHhh
Q psy13474 1 MQELFSQLQSSHESALPPDALRRALAEA 28 (105)
Q Consensus 1 l~~iF~~~~~s~~~~l~p~~LR~ALa~~ 28 (105)
++.+|..|+.....-|..+.++.++.++
T Consensus 2 ~~~~F~~~D~d~dG~I~~~Ef~~~~~~L 29 (29)
T PF00036_consen 2 LKEAFREFDKDGDGKIDFEEFKEMMKKL 29 (29)
T ss_dssp HHHHHHHHSTTSSSEEEHHHHHHHHHHT
T ss_pred HHHHHHHHCCCCCCcCCHHHHHHHHHhC
Confidence 4789999999999999999999998753
No 29
>KOG0037|consensus
Probab=71.36 E-value=4.1 Score=32.05 Aligned_cols=27 Identities=19% Similarity=0.430 Sum_probs=25.1
Q ss_pred HHHhhhhhhcCCCCCChHHHHHHHHhh
Q psy13474 2 QELFSQLQSSHESALPPDALRRALAEA 28 (105)
Q Consensus 2 ~~iF~~~~~s~~~~l~p~~LR~ALa~~ 28 (105)
+.||.+|+..++..|.+..||.||...
T Consensus 127 r~vF~~~D~D~SG~I~~sEL~~Al~~~ 153 (221)
T KOG0037|consen 127 RNVFRTYDRDRSGTIDSSELRQALTQL 153 (221)
T ss_pred HHHHHhcccCCCCcccHHHHHHHHHHc
Confidence 679999999999999999999999875
No 30
>cd02665 Peptidase_C19I A subfamily of Peptidase C19. Peptidase C19 contains ubiquitinyl hydrolases. They are intracellular peptidases that remove ubiquitin molecules from polyubiquinated peptides by cleavage of isopeptide bonds. They hydrolyze bonds involving the carboxyl group of the C-terminal Gly residue of ubiquitin. The purpose of the de-ubiquitination is thought to be editing of the ubiquitin conjugates, which could rescue them from degradation, as well as recycling of the ubiquitin. The ubiquitin/proteasome system is responsible for most protein turnover in the mammalian cell, and with over 50 members, family C19 is one of the largest families of peptidases in the human genome.
Probab=70.93 E-value=4.1 Score=31.45 Aligned_cols=61 Identities=13% Similarity=0.020 Sum_probs=40.3
Q ss_pred ccCcHHHHHHHHHHHhhhccCCchhh-hccCCCCchhhhhhcceehhhhccCCcCCCC-CCCCCc
Q psy13474 39 FMDDAAECFENMLLRIHYHIASEEAE-DMCGAKHCIPHEKFAMTLVEQSVCGACGATS-EPLPFT 101 (105)
Q Consensus 39 ~M~DA~E~fe~IL~~lH~~~~~~~~~-d~c~~~~Ci~H~~F~m~l~Eq~vC~~Cg~~S-~p~~~t 101 (105)
...||.|++-.||+.|+..+...... ..-.+..-+..++|+-.+...++| ||..| +..+|.
T Consensus 21 ~QQDa~Ef~~~Lld~Le~~l~~~~~~~~~~~~~~~~i~~lF~G~~~~~~~~--~~~~s~~~E~F~ 83 (228)
T cd02665 21 QQQDVSEFTHLLLDWLEDAFQAAAEAISPGEKSKNPMVQLFYGTFLTEGVL--EGKPFCNCETFG 83 (228)
T ss_pred HHHHHHHHHHHHHHHHHHHhccccccccccccccchHhhceEEEEEEEEEE--CCCcccccCccE
Confidence 56899999999999999987542210 112234557889998777766777 44433 344443
No 31
>cd00052 EH Eps15 homology domain; found in proteins implicated in endocytosis, vesicle transport, and signal transduction. The alignment contains a pair of EF-hand motifs, typically one of them is canonical and binds to Ca2+, while the other may not bind to Ca2+. A hydrophobic binding pocket is formed by residues from both EF-hand motifs. The EH domain binds to proteins containing NPF (class I), [WF]W or SWG (class II), or H[TS]F (class III) sequence motifs.
Probab=59.84 E-value=13 Score=21.57 Aligned_cols=26 Identities=19% Similarity=0.399 Sum_probs=23.6
Q ss_pred HHHhhhhhhcCCCCCChHHHHHHHHh
Q psy13474 2 QELFSQLQSSHESALPPDALRRALAE 27 (105)
Q Consensus 2 ~~iF~~~~~s~~~~l~p~~LR~ALa~ 27 (105)
+.+|..|+......|+.+.|+.+|..
T Consensus 2 ~~~F~~~D~~~~G~i~~~el~~~l~~ 27 (67)
T cd00052 2 DQIFRSLDPDGDGLISGDEARPFLGK 27 (67)
T ss_pred hHHHHHhCCCCCCcCcHHHHHHHHHH
Confidence 67899999999999999999999975
No 32
>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=59.47 E-value=5.3 Score=20.65 Aligned_cols=21 Identities=33% Similarity=0.456 Sum_probs=16.9
Q ss_pred hhhcccccCcHHHHHHHHHHH
Q psy13474 33 QRFQLGFMDDAAECFENMLLR 53 (105)
Q Consensus 33 ~~Fq~G~M~DA~E~fe~IL~~ 53 (105)
--++.|++++|.++|+..|+.
T Consensus 10 ~~~~~~~~~~A~~~~~~al~~ 30 (34)
T PF00515_consen 10 AYFQLGDYEEALEYYQRALEL 30 (34)
T ss_dssp HHHHTT-HHHHHHHHHHHHHH
T ss_pred HHHHhCCchHHHHHHHHHHHH
Confidence 457899999999999998864
No 33
>cd05027 S-100B S-100B: S-100B domain found in proteins similar to S100B. S100B is a calcium-binding protein belonging to a large S100 vertebrate-specific protein family within the EF-hand superfamily of calcium-binding proteins. Note that the S-100 hierarchy, to which this S-100B group belongs, contains only S-100 EF-hand domains, other EF-hands have been modeled separately. S100B is most abundant in glial cells of the central nervous system, predominately in astrocytes. S100B is involved in signal transduction via the inhibition of protein phoshorylation, regulation of enzyme activity and by affecting the calcium homeostasis. Upon calcium binding the S100B homodimer changes conformation to expose a hydrophobic cleft, which represents the interaction site of S100B with its more than 20 known target proteins. These target proteins include several cellular architecture proteins such as tubulin and GFAP; S100B can inhibit polymerization of these oligomeric molecules. Furthermore, S100B i
Probab=59.05 E-value=20 Score=23.47 Aligned_cols=49 Identities=10% Similarity=0.249 Sum_probs=32.1
Q ss_pred CHHHhhhhh-hcCCC-CCChHHHHHHHHhhchhhhhhcccccCcHHHHHHHHHHHh
Q psy13474 1 MQELFSQLQ-SSHES-ALPPDALRRALAEAFFDQQRFQLGFMDDAAECFENMLLRI 54 (105)
Q Consensus 1 l~~iF~~~~-~s~~~-~l~p~~LR~ALa~~~~~~~~Fq~G~M~DA~E~fe~IL~~l 54 (105)
|+++|..|+ ..... .|+.+.||..|...+|+- +|...+..+ .+.++..+
T Consensus 10 l~~aF~~fD~~dgdG~~I~~~eL~~ll~~~~~~~----lg~~~~~~~-v~~~i~~~ 60 (88)
T cd05027 10 LIDVFHQYSGREGDKHKLKKSELKELINNELSHF----LEEIKEQEV-VDKVMETL 60 (88)
T ss_pred HHHHHHHhcccCCCcCEECHHHHHHHHHHHhHHH----hcCCCCHHH-HHHHHHHh
Confidence 468899997 45556 699999999999865533 555444333 34444433
No 34
>PF13174 TPR_6: Tetratricopeptide repeat; PDB: 3QKY_A 2XEV_A 3URZ_B 2Q7F_A.
Probab=58.56 E-value=4.4 Score=20.42 Aligned_cols=19 Identities=37% Similarity=0.733 Sum_probs=16.4
Q ss_pred hcccccCcHHHHHHHHHHH
Q psy13474 35 FQLGFMDDAAECFENMLLR 53 (105)
Q Consensus 35 Fq~G~M~DA~E~fe~IL~~ 53 (105)
++.|+.+.|.+.|+.+++.
T Consensus 11 ~~~g~~~~A~~~~~~~~~~ 29 (33)
T PF13174_consen 11 YKLGDYDEAIEYFQRLIKR 29 (33)
T ss_dssp HHHCHHHHHHHHHHHHHHH
T ss_pred HHccCHHHHHHHHHHHHHH
Confidence 5679999999999999874
No 35
>KOG4849|consensus
Probab=57.40 E-value=15 Score=31.46 Aligned_cols=43 Identities=21% Similarity=0.268 Sum_probs=37.6
Q ss_pred cCCCCCChHHHHHHHHhhchhhhhhcccccCcHHHHHHHHHHHhhhccCC
Q psy13474 11 SHESALPPDALRRALAEAFFDQQRFQLGFMDDAAECFENMLLRIHYHIAS 60 (105)
Q Consensus 11 s~~~~l~p~~LR~ALa~~~~~~~~Fq~G~M~DA~E~fe~IL~~lH~~~~~ 60 (105)
.++.+|++.++-+|.+.. ..|+..+|+|++.+.+..|.++-..
T Consensus 367 ~RNraiSSSAIsrAvsdA-------SaGDy~~AiETllTAI~lIKqSrv~ 409 (498)
T KOG4849|consen 367 TRNRAISSSAISRAVSDA-------SAGDYKGAIETLLTAIQLIKQSRVG 409 (498)
T ss_pred hhcchhhHHHHHHHhccc-------ccccchhHHHHHHHHHHHHHhhccc
Confidence 689999999999999864 5899999999999999998887544
No 36
>COG3109 ProQ Activator of osmoprotectant transporter ProP [Signal transduction mechanisms]
Probab=57.17 E-value=11 Score=29.12 Aligned_cols=44 Identities=20% Similarity=0.397 Sum_probs=36.5
Q ss_pred HHHhhhhhh--cCCCCCChHHHHHHHHhhchhhhhhcccccCcHHHH
Q psy13474 2 QELFSQLQS--SHESALPPDALRRALAEAFFDQQRFQLGFMDDAAEC 46 (105)
Q Consensus 2 ~~iF~~~~~--s~~~~l~p~~LR~ALa~~~~~~~~Fq~G~M~DA~E~ 46 (105)
.+||.+++. ...+-|+.+.||.||. +|-.+-|+-.|.-.+|..+
T Consensus 36 iGifQDl~e~lq~d~~vSktQLrqAlr-~yts~wRYl~g~k~gA~Rv 81 (208)
T COG3109 36 IGIFQDLAERLQDDENVSKTQLRQALR-LYTSSWRYLYGVKEGATRV 81 (208)
T ss_pred hhHHHHHHHHHhccccccHHHHHHHHH-HHhcccceeeeccCCCcee
Confidence 378988876 5777799999999998 5788899999999888653
No 37
>PF13176 TPR_7: Tetratricopeptide repeat; PDB: 3SF4_C 3RO3_A 3RO2_A.
Probab=56.84 E-value=9.7 Score=20.51 Aligned_cols=23 Identities=26% Similarity=0.238 Sum_probs=17.1
Q ss_pred hhhcccccCcHHHHHHHHHHHhhh
Q psy13474 33 QRFQLGFMDDAAECFENMLLRIHY 56 (105)
Q Consensus 33 ~~Fq~G~M~DA~E~fe~IL~~lH~ 56 (105)
--++.|+.+.|.++|+..| .|+.
T Consensus 8 ~~~~~g~~~~Ai~~y~~aL-~l~~ 30 (36)
T PF13176_consen 8 IYRQQGDYEKAIEYYEQAL-ALAR 30 (36)
T ss_dssp HHHHCT-HHHHHHHHHHHH-HHHH
T ss_pred HHHHcCCHHHHHHHHHHHH-Hhcc
Confidence 3467899999999999977 4443
No 38
>PF13428 TPR_14: Tetratricopeptide repeat
Probab=55.91 E-value=15 Score=20.45 Aligned_cols=27 Identities=33% Similarity=0.348 Sum_probs=20.3
Q ss_pred HHHHHhhchhhhhhcccccCcHHHHHHHHHHH
Q psy13474 22 RRALAEAFFDQQRFQLGFMDDAAECFENMLLR 53 (105)
Q Consensus 22 R~ALa~~~~~~~~Fq~G~M~DA~E~fe~IL~~ 53 (105)
...|+..| .+.|+.++|.++|+.++..
T Consensus 4 ~~~la~~~-----~~~G~~~~A~~~~~~~l~~ 30 (44)
T PF13428_consen 4 WLALARAY-----RRLGQPDEAERLLRRALAL 30 (44)
T ss_pred HHHHHHHH-----HHcCCHHHHHHHHHHHHHH
Confidence 34455543 4579999999999999874
No 39
>KOG0027|consensus
Probab=55.34 E-value=25 Score=24.53 Aligned_cols=33 Identities=12% Similarity=0.222 Sum_probs=28.5
Q ss_pred CHHHhhhhhhcCCCCCChHHHHHHHHhhchhhh
Q psy13474 1 MQELFSQLQSSHESALPPDALRRALAEAFFDQQ 33 (105)
Q Consensus 1 l~~iF~~~~~s~~~~l~p~~LR~ALa~~~~~~~ 33 (105)
|++.|.-|+.....-|++..||+.|.++.....
T Consensus 87 l~eaF~~fD~d~~G~Is~~el~~~l~~lg~~~~ 119 (151)
T KOG0027|consen 87 LKEAFRVFDKDGDGFISASELKKVLTSLGEKLT 119 (151)
T ss_pred HHHHHHHHccCCCCcCcHHHHHHHHHHhCCcCC
Confidence 468899999999999999999999999855544
No 40
>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=54.31 E-value=7.3 Score=19.76 Aligned_cols=21 Identities=43% Similarity=0.601 Sum_probs=16.6
Q ss_pred hhhhcccccCcHHHHHHHHHH
Q psy13474 32 QQRFQLGFMDDAAECFENMLL 52 (105)
Q Consensus 32 ~~~Fq~G~M~DA~E~fe~IL~ 52 (105)
.--|+.|+.++|.++|+..+.
T Consensus 9 ~~~~~~~~~~~A~~~~~~al~ 29 (34)
T PF07719_consen 9 QAYYQLGNYEEAIEYFEKALE 29 (34)
T ss_dssp HHHHHTT-HHHHHHHHHHHHH
T ss_pred HHHHHhCCHHHHHHHHHHHHH
Confidence 345789999999999998875
No 41
>PF02748 PyrI_C: Aspartate carbamoyltransferase regulatory chain, metal binding domain; InterPro: IPR020542 Aspartate carbamoyltransferase (aspartate transcarbamylase, ATCase) 2.1.3.2 from EC is an allosteric enzyme that plays a central role in the regulation of the pyrimidine pathway in bacteria. The holoenzyme is a dodecamer composed of six catalytic chains, each with an active site, and six regulatory chains lacking catalytic activity []. The catalytic subunits exist as a dimer of catalytic trimers, (c3)2, while the regulatory subunits exist as a trimer of regulatory dimers, (r2)3, therefore the complete holoenzyme can be represented as (c3)2(r2)3. The association of the catalytic subunits c3 with the regulatory subunits r2 is responsible for the establishment of positive co-operativity between catalytic sites for the binding of aspartate and it dictates the pattern of allosteric response toward nucleotide effectors. ATCase from Escherichia coli is the most extensively studied allosteric enzyme []. The crystal structure of the T-state, the T-state with CTP bound, the R-state with N-phosphonacetyl-L-aspartate (PALA) bound, and the R-state with phosphonoacetamide plus malonate bound have been used in interpreting kinetic and mutational studies. A high-resolution structure of E. coli ATCase in the presence of PALA (a bisubstrate analog) allows a detailed description of the binding at the active site of the enzyme and allows a detailed model of the tetrahedral intermediate to be constructed. The entire regulatory chain has been traced showing that the N-terminal regions of the regulatory chains R1 and R6 are located in close proximity to each other and to the regulatory site. This portion of the molecule may be involved in the observed asymmetry between the regulatory binding sites as well as in the heterotropic response of the enzyme []. The C-terminal domain of the regulatory chains have a rubredoxin-like zinc-bound fold. ATCase from Enterobacter agglomerans (Erwinia herbicola) (Pantoea agglomerans) differs from the other investigated enterobacterial ATCases by its absence of homotropic co-operativity toward the substrate aspartate and its lack of response to ATP which is an allosteric effector (activator) of this family of enzymes. Nevertheless, the E. herbicola ATCase has the same quaternary structure, two trimers of catalytic chains with three dimers of regulatory chains, (c3)2(r2)3, as other enterobacterial ATCases and shows extensive primary structure conservation []. This entry represents the C-terminal domain.; PDB: 2YWW_B 1SKU_D 1Q95_L 8ATC_B 3AT1_D 1RAI_D 4E2F_D 1NBE_B 6AT1_B 2FZC_D ....
Probab=53.94 E-value=5.1 Score=24.49 Aligned_cols=28 Identities=21% Similarity=0.492 Sum_probs=16.6
Q ss_pred ccCCCCchhh------hhhcceeh--hhhccCCcCC
Q psy13474 66 MCGAKHCIPH------EKFAMTLV--EQSVCGACGA 93 (105)
Q Consensus 66 ~c~~~~Ci~H------~~F~m~l~--Eq~vC~~Cg~ 93 (105)
.|.+|.||+| ++|...-- -...|..|+.
T Consensus 8 ~C~Np~CITn~~E~v~~~F~v~~~~~~~~rC~YCe~ 43 (52)
T PF02748_consen 8 KCPNPNCITNSNEPVESRFYVIDKEPIKLRCHYCER 43 (52)
T ss_dssp E-SSTTBTTT-TSSS--EEEEEETTTCEEEETTT--
T ss_pred EcCCCCcccCCCCCCCceEEEEeCCCCEEEeeCCCC
Confidence 5999999999 56655111 3467888875
No 42
>cd05022 S-100A13 S-100A13: S-100A13 domain found in proteins similar to S100A13. S100A13 is a calcium-binding protein belonging to a large S100 vertebrate-specific protein family within the EF-hand superfamily of calcium-binding proteins. Note that the S-100 hierarchy, to which this S-100A13 group belongs, contains only S-100 EF-hand domains, other EF-hands have been modeled separately. S100A13 is involved in the cellular export of interleukin-1 (IL-1) and of fibroblast growth factor-1 (FGF-1), which plays an important role in angiogenesis and tissue regeneration. Export is based on the CuII-dependent formation of multiprotein complexes containing the S100A13 protein. Assembly of these complexes occurs near the inner surface of the plasma membrane. Binding of two Ca(II) ions per monomer triggers key conformational changes leading to the creation of two identical and symmetrical Cu(II)-binding sites on the surface of the protein, close to the interface between the two monomers. These Cu
Probab=52.81 E-value=33 Score=22.65 Aligned_cols=28 Identities=11% Similarity=0.240 Sum_probs=24.3
Q ss_pred CHHHhhhhhh-cCCCCCChHHHHHHHHhh
Q psy13474 1 MQELFSQLQS-SHESALPPDALRRALAEA 28 (105)
Q Consensus 1 l~~iF~~~~~-s~~~~l~p~~LR~ALa~~ 28 (105)
|..+|..|+. .....|+.+.||..|.+.
T Consensus 10 l~~~F~~fd~~~~~g~i~~~ELk~ll~~e 38 (89)
T cd05022 10 LVSNFHKASVKGGKESLTASEFQELLTQQ 38 (89)
T ss_pred HHHHHHHHhCCCCCCeECHHHHHHHHHHH
Confidence 4578999988 788899999999999984
No 43
>PF13202 EF-hand_5: EF hand; PDB: 3DD4_A 2Q4U_A 2BE4_A 1UHJ_B 1UHI_A 1UHH_B 1EJ3_B 1UHK_A 2ZFD_A 1UHN_A ....
Probab=52.57 E-value=8.4 Score=19.72 Aligned_cols=23 Identities=13% Similarity=0.468 Sum_probs=20.2
Q ss_pred CHHHhhhhhhcCCCCCChHHHHH
Q psy13474 1 MQELFSQLQSSHESALPPDALRR 23 (105)
Q Consensus 1 l~~iF~~~~~s~~~~l~p~~LR~ 23 (105)
|+.+|.+++......|+...+++
T Consensus 1 l~~~F~~~D~d~DG~is~~E~~~ 23 (25)
T PF13202_consen 1 LKDAFQQFDTDGDGKISFEEFQR 23 (25)
T ss_dssp HHHHHHHHTTTSSSEEEHHHHHH
T ss_pred CHHHHHHHcCCCCCcCCHHHHHH
Confidence 57889999999999999988876
No 44
>cd02064 FAD_synthetase_N FAD synthetase, N-terminal domain of the bifunctional enzyme. FAD synthetase_N. N-terminal domain of the bifunctional riboflavin biosynthesis protein riboflavin kinase/FAD synthetase. These enzymes have both ATP:riboflavin 5'-phosphotransferase and ATP:FMN-adenylyltransferase activities. The N-terminal domain is believed to play a role in the adenylylation reaction of FAD synthetases. The C-terminal domain is thought to have kinase activity. FAD synthetase is present among all kingdoms of life. However, the bifunctional enzyme is not found in mammals, which use separate enzymes for FMN and FAD formation.
Probab=51.19 E-value=8 Score=28.18 Aligned_cols=27 Identities=26% Similarity=0.284 Sum_probs=22.9
Q ss_pred CCCCCChHHHHHHHHhhchhhhhhcccccCcHHHHHH
Q psy13474 12 HESALPPDALRRALAEAFFDQQRFQLGFMDDAAECFE 48 (105)
Q Consensus 12 ~~~~l~p~~LR~ALa~~~~~~~~Fq~G~M~DA~E~fe 48 (105)
.++.++++.+|++|+ .|+|++|.+.|.
T Consensus 142 ~~~~iSST~IR~~i~----------~G~i~~an~lLg 168 (180)
T cd02064 142 DGERVSSTRIREALA----------EGDVELANELLG 168 (180)
T ss_pred CCcEEcHHHHHHHHH----------hCCHHHHHHHcC
Confidence 467899999999998 699999987653
No 45
>PF06667 PspB: Phage shock protein B; InterPro: IPR009554 This family consists of several bacterial phage shock protein B (PspB) sequences. The phage shock protein (psp) operon is induced in response to heat, ethanol, osmotic shock and infection by filamentous bacteriophages []. Expression of the operon requires the alternative sigma factor sigma54 and the transcriptional activator PspF. In addition, PspA plays a negative regulatory role, and the integral-membrane proteins PspB and PspC play a positive one [].; GO: 0006355 regulation of transcription, DNA-dependent, 0009271 phage shock
Probab=46.38 E-value=36 Score=22.39 Aligned_cols=37 Identities=19% Similarity=0.287 Sum_probs=27.2
Q ss_pred cCCCCCChHHHHHHHHhhchhhhhhcccccCcHHHHHHHHHHH
Q psy13474 11 SHESALPPDALRRALAEAFFDQQRFQLGFMDDAAECFENMLLR 53 (105)
Q Consensus 11 s~~~~l~p~~LR~ALa~~~~~~~~Fq~G~M~DA~E~fe~IL~~ 53 (105)
..++.|+.+. ++-|.+++... ..|.|-.|++|.||+.
T Consensus 31 ~~~~gLs~~d-~~~L~~L~~~a-----~rm~eRI~tLE~ILda 67 (75)
T PF06667_consen 31 KSSQGLSEED-EQRLQELYEQA-----ERMEERIETLERILDA 67 (75)
T ss_pred ccCCCCCHHH-HHHHHHHHHHH-----HHHHHHHHHHHHHHcC
Confidence 3556677655 66677776554 4699999999999974
No 46
>PF03130 HEAT_PBS: PBS lyase HEAT-like repeat; InterPro: IPR004155 These proteins contain a short bi-helical repeat that is related to HEAT. Cyanobacteria and red algae harvest light energy using macromolecular complexes known as phycobilisomes (PBS), peripherally attached to the photosynthetic membrane. The major components of PBS are the phycobiliproteins. These heterodimeric proteins are covalently attached to phycobilins: open-chain tetrapyrrole chromophores, which function as the photosynthetic light-harvesting pigments. Phycobiliproteins differ in sequence and in the nature and number of attached phycobilins to each of their subunits. These proteins include the lyase enzymes that specifically attach particular phycobilins to apophycobiliprotein subunits. The most comprehensively studied of these is the CpcE/Flyase P31967 from SWISSPROT, P31968 from SWISSPROT, which attaches phycocyanobilin (PCB) to the alpha subunit of apophycocyanin []. Similarly, MpeU/V attaches phycoerythrobilin to phycoerythrin II, while CpeY/Z is thought to be involved in phycoerythrobilin (PEB) attachment to phycoerythrin (PE) I (PEs I and II differ in sequence and in the number of attached molecules of PEB: PE I has five, PE II has six) []. All the reactions of the above lyases involve an apoprotein cysteine SH addition to a terminal delta 3,3'-double bond. Such a reaction is not possible in the case of phycoviolobilin (PVB), the phycobilin of alpha-phycoerythrocyanin (alpha-PEC). It is thought that in this case, PCB, not PVB, is first added to apo-alpha-PEC, and is then isomerized to PVB. The addition reaction has been shown to occur in the presence of either of the components of alpha-PEC-PVB lyase PecE or PecF (or both). The isomerisation reaction occurs only when both PecE and PecF components are present, i.e. the PecE/F phycobiliprotein lyase is also a phycobilin isomerase []. Another member of this family is the NblB protein, whose similarity to the phycobiliprotein lyases was previously noted []. This constitutively expressed protein is not known to have any lyase activity. It is thought to be involved in the coordination of PBS degradation with environmental nutrient limitation. It has been suggested that the similarity of NblB to the phycobiliprotein lyases is due to the ability to bind tetrapyrrole phycobilins via the common repeated motif [].; PDB: 1TE4_A.
Probab=44.40 E-value=45 Score=17.09 Aligned_cols=19 Identities=16% Similarity=0.323 Sum_probs=10.8
Q ss_pred hcccccCcHHHHHHHHHHHh
Q psy13474 35 FQLGFMDDAAECFENMLLRI 54 (105)
Q Consensus 35 Fq~G~M~DA~E~fe~IL~~l 54 (105)
+-+|+++| .++...+++.|
T Consensus 7 ~aLg~igd-~~ai~~L~~~L 25 (27)
T PF03130_consen 7 RALGQIGD-PRAIPALIEAL 25 (27)
T ss_dssp HHHGGG-S-HHHHHHHHHHH
T ss_pred HHHHHcCC-HHHHHHHHHHh
Confidence 34888888 45555555543
No 47
>KOG1872|consensus
Probab=44.36 E-value=28 Score=30.27 Aligned_cols=59 Identities=20% Similarity=0.305 Sum_probs=47.4
Q ss_pred HHHhhhhhhcCCCCCChHHHHHHHHhhchhhhh-hccccc--CcHHHHHHHHHHHhhhccCCch
Q psy13474 2 QELFSQLQSSHESALPPDALRRALAEAFFDQQR-FQLGFM--DDAAECFENMLLRIHYHIASEE 62 (105)
Q Consensus 2 ~~iF~~~~~s~~~~l~p~~LR~ALa~~~~~~~~-Fq~G~M--~DA~E~fe~IL~~lH~~~~~~~ 62 (105)
+.+|.+++.+ +.++|-.|-..|++.||.-.+ =+.|.. -||.||+-.++-.+|.......
T Consensus 158 R~~f~~~~~~--~~v~pi~llqtl~~~~Pqfa~~~~~g~~~qqda~ec~~~~m~~l~~~~~~~~ 219 (473)
T KOG1872|consen 158 RTCFRPLCEK--GAVAPINLLQTLSSQYPQFAEWVEYGIYMQQDAAECWMEEPGMLTEALTVAT 219 (473)
T ss_pred HHHHHhhhcc--CCcchHHHHHHHHHHhHHHHHHhhhhhHHHHHHhHhHHHhhhheeccccccc
Confidence 5678888877 999999999999999998744 234433 4899999999999999886643
No 48
>PF14803 Nudix_N_2: Nudix N-terminal; PDB: 3CNG_C.
Probab=42.51 E-value=9 Score=21.53 Aligned_cols=13 Identities=46% Similarity=0.731 Sum_probs=8.9
Q ss_pred eehhhhccCCcCC
Q psy13474 81 TLVEQSVCGACGA 93 (105)
Q Consensus 81 ~l~Eq~vC~~Cg~ 93 (105)
.=.|+.||.+||.
T Consensus 18 d~r~R~vC~~Cg~ 30 (34)
T PF14803_consen 18 DDRERLVCPACGF 30 (34)
T ss_dssp -SS-EEEETTTTE
T ss_pred CCccceECCCCCC
Confidence 3468899999984
No 49
>smart00027 EH Eps15 homology domain. Pair of EF hand motifs that recognise proteins containing Asn-Pro-Phe (NPF) sequences.
Probab=42.25 E-value=22 Score=22.97 Aligned_cols=27 Identities=11% Similarity=0.340 Sum_probs=23.9
Q ss_pred CHHHhhhhhhcCCCCCChHHHHHHHHh
Q psy13474 1 MQELFSQLQSSHESALPPDALRRALAE 27 (105)
Q Consensus 1 l~~iF~~~~~s~~~~l~p~~LR~ALa~ 27 (105)
++.+|..|+......|+...|+.+|..
T Consensus 12 l~~~F~~~D~d~~G~Is~~el~~~l~~ 38 (96)
T smart00027 12 YEQIFRSLDKNQDGTVTGAQAKPILLK 38 (96)
T ss_pred HHHHHHHhCCCCCCeEeHHHHHHHHHH
Confidence 467899999889999999999999976
No 50
>smart00764 Citrate_ly_lig Citrate lyase ligase C-terminal domain. Proteins of this family contain the C-terminal domain of citrate lyase ligase EC:6.2.1.22.
Probab=41.89 E-value=13 Score=27.61 Aligned_cols=27 Identities=15% Similarity=0.329 Sum_probs=22.1
Q ss_pred CCCCCChHHHHHHHHhhchhhhhhcccccCcHHHHHH
Q psy13474 12 HESALPPDALRRALAEAFFDQQRFQLGFMDDAAECFE 48 (105)
Q Consensus 12 ~~~~l~p~~LR~ALa~~~~~~~~Fq~G~M~DA~E~fe 48 (105)
.++.++++.+|++|+ .|.+++|.+.+=
T Consensus 149 ~g~~iSST~IR~~L~----------~G~v~~a~~lLP 175 (182)
T smart00764 149 NGQPISASTVRKLLK----------EGNLEELAKLVP 175 (182)
T ss_pred CCcEECHHHHHHHHH----------cCCHHHHHHhCC
Confidence 577899999999997 578888887653
No 51
>COG3423 Nlp Predicted transcriptional regulator [Transcription]
Probab=40.62 E-value=13 Score=25.01 Aligned_cols=24 Identities=29% Similarity=0.419 Sum_probs=21.4
Q ss_pred cCCCCCChHHHHHHHHhhchhhhh
Q psy13474 11 SHESALPPDALRRALAEAFFDQQR 34 (105)
Q Consensus 11 s~~~~l~p~~LR~ALa~~~~~~~~ 34 (105)
|.+..|+|++|+++|..-|+...+
T Consensus 28 S~~agls~~tL~n~L~rp~pkgEr 51 (82)
T COG3423 28 SREAGLSSSTLANALDRPWPKGER 51 (82)
T ss_pred HHHcCCCHHHHHHHHcCCCchHHH
Confidence 678889999999999999998755
No 52
>KOG1868|consensus
Probab=38.80 E-value=40 Score=30.34 Aligned_cols=83 Identities=23% Similarity=0.188 Sum_probs=56.1
Q ss_pred cCCCCCChHHHHHHHHhhchhhhhhcccccCcHHHHHHHHHHHhhhccCCchh------------------------hhc
Q psy13474 11 SHESALPPDALRRALAEAFFDQQRFQLGFMDDAAECFENMLLRIHYHIASEEA------------------------EDM 66 (105)
Q Consensus 11 s~~~~l~p~~LR~ALa~~~~~~~~Fq~G~M~DA~E~fe~IL~~lH~~~~~~~~------------------------~d~ 66 (105)
.....+.|..+++.+.+. ...|..+.--||.|.+.-.|+.||.++..... ...
T Consensus 365 ~~~~s~~P~~f~~~~~~y---~~~~~~~~Qqd~qEfl~~lld~Lhe~ln~~~~~~~~~p~~~~~~~~~~~~~~s~~s~~~ 441 (653)
T KOG1868|consen 365 HGQFSVLPRRFIRVLKRY---SPNFSGYSQQDAQEFLIFLLDRLHEELNENTRPLKLSPLMGSYLLSELELSDSKKSLAE 441 (653)
T ss_pred CCceecCcHHHHHHHhhc---ccccccccccchHHHHHHHHHhhhHhhhccCCCCccCccccccccccccccccchhHHH
Confidence 356668888999999875 33455555589999999999999999866421 114
Q ss_pred cCCCCchhhhh----hcceehhhhccCCcCCCCC
Q psy13474 67 CGAKHCIPHEK----FAMTLVEQSVCGACGATSE 96 (105)
Q Consensus 67 c~~~~Ci~H~~----F~m~l~Eq~vC~~Cg~~S~ 96 (105)
+-...++.-.+ |..+.-....|..||.+|-
T Consensus 442 w~~~~~~~d~~i~~lf~gQ~ks~Lkc~~cg~~s~ 475 (653)
T KOG1868|consen 442 WLRYLEEEDSKIGDLFVGQLKSYLKCQACGYTST 475 (653)
T ss_pred HHhhccccchHHHHHHHHHHHhheehhhcCCcce
Confidence 44455533333 4444444456999999874
No 53
>PRK15359 type III secretion system chaperone protein SscB; Provisional
Probab=38.69 E-value=36 Score=23.58 Aligned_cols=42 Identities=19% Similarity=0.245 Sum_probs=30.5
Q ss_pred CCCCCChHHHHHHHHhhc-----hhhhhhcccccCcHHHHHHHHHHH
Q psy13474 12 HESALPPDALRRALAEAF-----FDQQRFQLGFMDDAAECFENMLLR 53 (105)
Q Consensus 12 ~~~~l~p~~LR~ALa~~~-----~~~~~Fq~G~M~DA~E~fe~IL~~ 53 (105)
+..-+|.+.+++||+.-. .....++.|..++|.+.|...+..
T Consensus 7 ~~~~~~~~~~~~al~~~p~~~~~~g~~~~~~g~~~~A~~~~~~al~~ 53 (144)
T PRK15359 7 QKNKIPEDILKQLLSVDPETVYASGYASWQEGDYSRAVIDFSWLVMA 53 (144)
T ss_pred cccCCHHHHHHHHHHcCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHc
Confidence 455677888888777521 134678899999999999887654
No 54
>PRK10220 hypothetical protein; Provisional
Probab=38.45 E-value=15 Score=26.12 Aligned_cols=22 Identities=9% Similarity=0.226 Sum_probs=16.2
Q ss_pred hcceehhhhccCCcCCCCCCCC
Q psy13474 78 FAMTLVEQSVCGACGATSEPLP 99 (105)
Q Consensus 78 F~m~l~Eq~vC~~Cg~~S~p~~ 99 (105)
|.-.--+..+|+.|++++.|-.
T Consensus 13 ytY~d~~~~vCpeC~hEW~~~~ 34 (111)
T PRK10220 13 YTYEDNGMYICPECAHEWNDAE 34 (111)
T ss_pred ceEcCCCeEECCcccCcCCccc
Confidence 3334445789999999998764
No 55
>cd02169 Citrate_lyase_ligase Citrate lyase ligase. Citrate lyase ligase, also known as [Citrate (pro-3S)-lyase] ligase, is responsible for acetylation of the (2-(5''-phosphoribosyl)-3'-dephosphocoenzyme-A) prosthetic group of the gamma subunit of citrate lyase, converting the inactive thiol form of this enzyme to the active form. The acetylation of 1 molecule of deacetyl-citrate lyase to enzymatically active citrate lyase requires 6 molecules of ATP. The Adenylylyltranferase activity of the enzyme involves the formation of AMP and and pyrophosphate in the acetylation reaction.
Probab=37.71 E-value=17 Score=29.15 Aligned_cols=27 Identities=15% Similarity=0.292 Sum_probs=23.0
Q ss_pred cCCCCCChHHHHHHHHhhchhhhhhcccccCcHHHHH
Q psy13474 11 SHESALPPDALRRALAEAFFDQQRFQLGFMDDAAECF 47 (105)
Q Consensus 11 s~~~~l~p~~LR~ALa~~~~~~~~Fq~G~M~DA~E~f 47 (105)
..++.++|+.+|++|. .|+++.|.+.|
T Consensus 263 ~~g~~ISST~IR~~l~----------~G~v~~A~~lL 289 (297)
T cd02169 263 YDGQPISASTVRQLLK----------EGNLEEIAKLV 289 (297)
T ss_pred cCCcEEcHHHHHHHHH----------cCCHHHHHHhC
Confidence 3677999999999999 68999988765
No 56
>cd05026 S-100Z S-100Z: S-100Z domain found in proteins similar to S100Z. S100Z is a member of the S100 domain family within the EF-hand Ca2+-binding proteins superfamily. Note that the S-100 hierarchy, to which this S-100Z group belongs, contains only S-100 EF-hand domains, other EF-hands have been modeled separately.S100 proteins exhibit unique patterns of tissue- and cell type-specific expression and have been implicated in the Ca2+-dependent regulation of diverse physiological processes, including cell cycle regulation, differentiation, growth, and metabolic control. S100Z is normally expressed in various tissues, with its highest level of expression being in spleen and leukocytes. The function of S100Z remains unclear. Preliminary structural data suggests that S100Z is homodimer, however a heterodimer with S100P has been reported. S100Z is capable of binding calcium ions. When calcium binds to S110Z, the protein experiences a conformational change, which exposes hydrophobic surfac
Probab=37.39 E-value=71 Score=20.77 Aligned_cols=28 Identities=14% Similarity=0.323 Sum_probs=21.5
Q ss_pred CHHHhhhhhhc-CCC-CCChHHHHHHHHhh
Q psy13474 1 MQELFSQLQSS-HES-ALPPDALRRALAEA 28 (105)
Q Consensus 1 l~~iF~~~~~s-~~~-~l~p~~LR~ALa~~ 28 (105)
++++|..|+.. ... .|+...|+..|.+.
T Consensus 12 ~~~~F~~~dd~dgdg~~Is~~EL~~ll~~~ 41 (93)
T cd05026 12 LIRIFHNYSGKEGDRYKLSKGELKELLQRE 41 (93)
T ss_pred HHHHHHHHHccCCCCCEECHHHHHHHHHHH
Confidence 35679999954 333 59999999999764
No 57
>KOG1863|consensus
Probab=36.72 E-value=42 Score=31.64 Aligned_cols=83 Identities=18% Similarity=0.158 Sum_probs=60.4
Q ss_pred CHHHhhhhhhcCCCCCChHHHHHHHHhhchhhhhhcccccCcHHHHHHHHHHHhhhccCCchhhhccCCCCchhhhhhcc
Q psy13474 1 MQELFSQLQSSHESALPPDALRRALAEAFFDQQRFQLGFMDDAAECFENMLLRIHYHIASEEAEDMCGAKHCIPHEKFAM 80 (105)
Q Consensus 1 l~~iF~~~~~s~~~~l~p~~LR~ALa~~~~~~~~Fq~G~M~DA~E~fe~IL~~lH~~~~~~~~~d~c~~~~Ci~H~~F~m 80 (105)
|+.+|.++|.++.+.|+++.|=+++-... .-.+.=.|+.|-.-.+++.|=..+-..... =..-.+|.-
T Consensus 219 lq~lF~~LQ~s~~k~Vdt~~~~~~~~~~~-----~~~~~QqDvqEf~~~l~d~LE~~~~~~~~~-------~~l~~lf~g 286 (1093)
T KOG1863|consen 219 LQRLFYELQMSKRKYVDTSELTKSLGWDS-----NDSFEQQDVQEFLTKLLDWLEDSMIDAKVE-------NTLQDLFTG 286 (1093)
T ss_pred HHHHHHHHhhcCCCCcCchhhhhhhhccc-----ccHHhhhhHHHHHHHHHHHHHhhccchhhh-------hhhhhhhcC
Confidence 58899999999999999999999988652 334566899998888888876554332110 033446666
Q ss_pred eehhhhccCCcCCCC
Q psy13474 81 TLVEQSVCGACGATS 95 (105)
Q Consensus 81 ~l~Eq~vC~~Cg~~S 95 (105)
.+.....|..|+-+|
T Consensus 287 ~~~~~i~c~~~~~~s 301 (1093)
T KOG1863|consen 287 KMKSVIKCIDVDFES 301 (1093)
T ss_pred CcceEEEEEeeeeec
Confidence 677778888787777
No 58
>cd00213 S-100 S-100: S-100 domain, which represents the largest family within the superfamily of proteins carrying the Ca-binding EF-hand motif. Note that this S-100 hierarchy contains only S-100 EF-hand domains, other EF-hands have been modeled separately. S100 proteins are expressed exclusively in vertebrates, and are implicated in intracellular and extracellular regulatory activities. Intracellularly, S100 proteins act as Ca-signaling or Ca-buffering proteins. The most unusual characteristic of certain S100 proteins is their occurrence in extracellular space, where they act in a cytokine-like manner through RAGE, the receptor for advanced glycation products. Structural data suggest that many S100 members exist within cells as homo- or heterodimers and even oligomers; oligomerization contributes to their functional diversification. Upon binding calcium, most S100 proteins change conformation to a more open structure exposing a hydrophobic cleft. This hydrophobic surface represents th
Probab=36.33 E-value=46 Score=20.87 Aligned_cols=28 Identities=14% Similarity=0.373 Sum_probs=23.8
Q ss_pred CHHHhhhhhh--cCCCCCChHHHHHHHHhh
Q psy13474 1 MQELFSQLQS--SHESALPPDALRRALAEA 28 (105)
Q Consensus 1 l~~iF~~~~~--s~~~~l~p~~LR~ALa~~ 28 (105)
|+.+|..|+. .....|+...|+.++...
T Consensus 10 l~~~F~~~D~~~~~~G~Is~~el~~~l~~~ 39 (88)
T cd00213 10 IIDVFHKYSGKEGDKDTLSKKELKELLETE 39 (88)
T ss_pred HHHHHHHHhhccCCCCcCcHHHHHHHHHHH
Confidence 4678999998 788899999999999753
No 59
>PRK07143 hypothetical protein; Provisional
Probab=35.78 E-value=21 Score=28.47 Aligned_cols=27 Identities=7% Similarity=0.182 Sum_probs=23.3
Q ss_pred CCCCCChHHHHHHHHhhchhhhhhcccccCcHHHHHH
Q psy13474 12 HESALPPDALRRALAEAFFDQQRFQLGFMDDAAECFE 48 (105)
Q Consensus 12 ~~~~l~p~~LR~ALa~~~~~~~~Fq~G~M~DA~E~fe 48 (105)
.+..++|+.+|++|+ .|+|+.|.+.|.
T Consensus 146 ~g~~ISST~IR~~l~----------~G~i~~A~~lLG 172 (279)
T PRK07143 146 NQQKISTSLLKEFIE----------FGDIELLNSLLL 172 (279)
T ss_pred CCcEEcHHHHHHHHH----------cCCHHHHHHHcC
Confidence 566899999999998 799999988764
No 60
>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=35.04 E-value=24 Score=17.91 Aligned_cols=19 Identities=42% Similarity=0.431 Sum_probs=15.7
Q ss_pred hhcccccCcHHHHHHHHHH
Q psy13474 34 RFQLGFMDDAAECFENMLL 52 (105)
Q Consensus 34 ~Fq~G~M~DA~E~fe~IL~ 52 (105)
-.++|+.+.|.++|+..++
T Consensus 11 y~~~~~~~~A~~~~~~a~~ 29 (34)
T PF13181_consen 11 YEQLGDYEEALEYFEKALE 29 (34)
T ss_dssp HHHTTSHHHHHHHHHHHHH
T ss_pred HHHcCCHHHHHHHHHHHHh
Confidence 3568999999999998775
No 61
>COG4871 Uncharacterized protein conserved in archaea [Function unknown]
Probab=34.79 E-value=12 Score=28.61 Aligned_cols=21 Identities=29% Similarity=0.310 Sum_probs=17.2
Q ss_pred cCcHHHHHHHHHHHhhhccCC
Q psy13474 40 MDDAAECFENMLLRIHYHIAS 60 (105)
Q Consensus 40 M~DA~E~fe~IL~~lH~~~~~ 60 (105)
-|+|.|.++.|.+.|...+..
T Consensus 92 edEAkeilgel~d~ineA~~k 112 (193)
T COG4871 92 EDEAKEILGELMDIINEAIAK 112 (193)
T ss_pred HHHHHHHHHHHHHHHHHHHHc
Confidence 478999999999999886644
No 62
>PF08274 PhnA_Zn_Ribbon: PhnA Zinc-Ribbon ; InterPro: IPR013987 The PhnA protein family includes the uncharacterised Escherichia coli protein PhnA and its homologues. The E. coli phnA gene is part of a large operon associated with alkylphosphonate uptake and carbon-phosphorus bond cleavage []. The protein is not related to the characterised phosphonoacetate hydrolase designated PhnA []. This entry represents the N-terminal domain of PhnA, which is predicted to form a zinc-ribbon.; PDB: 2AKL_A.
Probab=34.40 E-value=8.7 Score=21.14 Aligned_cols=13 Identities=38% Similarity=0.611 Sum_probs=9.4
Q ss_pred hhhhccCCcCCCC
Q psy13474 83 VEQSVCGACGATS 95 (105)
Q Consensus 83 ~Eq~vC~~Cg~~S 95 (105)
=+..||..||++.
T Consensus 17 ~~~~vCp~C~~ew 29 (30)
T PF08274_consen 17 GELLVCPECGHEW 29 (30)
T ss_dssp SSSEEETTTTEEE
T ss_pred CCEEeCCcccccC
Confidence 3567899998763
No 63
>TIGR00686 phnA alkylphosphonate utilization operon protein PhnA. The protein family includes an uncharacterized member designated phnA in Escherichia coli, part of a large operon associated with alkylphosphonate uptake and carbon-phosphorus bond cleavage. This protein is not related to the characterized phosphonoacetate hydrolase designated PhnA by Kulakova, et al. (2001, 1997).
Probab=34.24 E-value=17 Score=25.72 Aligned_cols=22 Identities=14% Similarity=0.167 Sum_probs=16.3
Q ss_pred hcceehhhhccCCcCCCCCCCC
Q psy13474 78 FAMTLVEQSVCGACGATSEPLP 99 (105)
Q Consensus 78 F~m~l~Eq~vC~~Cg~~S~p~~ 99 (105)
|.-.-=+..+|+.||+++.+--
T Consensus 12 ytY~dg~~~iCpeC~~EW~~~~ 33 (109)
T TIGR00686 12 YTYHDGTQLICPSCLYEWNENE 33 (109)
T ss_pred ceEecCCeeECccccccccccc
Confidence 4444456789999999997753
No 64
>PF01535 PPR: PPR repeat; InterPro: IPR002885 This entry represents the PPR repeat. Pentatricopeptide repeat (PPR) proteins are characterised by tandem repeats of a degenerate 35 amino acid motif []. Most of PPR proteins have roles in mitochondria or plastid []. PPR repeats were discovered while screening Arabidopsis proteins for those predicted to be targeted to mitochondria or chloroplast [, ]. Some of these proteins have been shown to play a role in post-transcriptional processes within organelles and they are thought to be sequence-specific RNA-binding proteins [, , ]. Plant genomes have between one hundred to five hundred PPR genes per genome whereas non-plant genomes encode two to six PPR proteins. Although no PPR structures are yet known, the motif is predicted to fold into a helix-turn-helix structure similar to those found in the tetratricopeptide repeat (TPR) family (see PDOC50005 from PROSITEDOC) []. The plant PPR protein family has been divided in two subfamilies on the basis of their motif content and organisation [, ]. Examples of PPR repeat-containing proteins include PET309 P32522 from SWISSPROT, which may be involved in RNA stabilisation [], and crp1, which is involved in RNA processing []. The repeat is associated with a predicted plant protein O49549 from SWISSPROT that has a domain organisation similar to the human BRCA1 protein.
Probab=33.17 E-value=22 Score=17.35 Aligned_cols=18 Identities=28% Similarity=0.542 Sum_probs=14.3
Q ss_pred hcccccCcHHHHHHHHHH
Q psy13474 35 FQLGFMDDAAECFENMLL 52 (105)
Q Consensus 35 Fq~G~M~DA~E~fe~IL~ 52 (105)
-+.|+.++|.++|+.+.+
T Consensus 11 ~~~~~~~~a~~~~~~M~~ 28 (31)
T PF01535_consen 11 CKMGQFEEALEVFDEMRE 28 (31)
T ss_pred HccchHHHHHHHHHHHhH
Confidence 357899999999987754
No 65
>PRK00893 aspartate carbamoyltransferase regulatory subunit; Reviewed
Probab=32.92 E-value=18 Score=26.91 Aligned_cols=29 Identities=24% Similarity=0.559 Sum_probs=21.6
Q ss_pred ccCCCCchhh------hhhcceehh--hhccCCcCCC
Q psy13474 66 MCGAKHCIPH------EKFAMTLVE--QSVCGACGAT 94 (105)
Q Consensus 66 ~c~~~~Ci~H------~~F~m~l~E--q~vC~~Cg~~ 94 (105)
-|.+|.||+| ++|-..=-+ ...|.+|+..
T Consensus 107 kC~Np~CITn~~E~v~~~F~v~~~~~~~~rC~YCe~~ 143 (152)
T PRK00893 107 KCPNPNCITNTNEPVESRFYVVDKEPIKLRCKYCEKE 143 (152)
T ss_pred ECCCCCCcCCCCcCcCcEEEEEeCCCCEEEeeCCCCE
Confidence 7999999999 456653233 5789999865
No 66
>PRK05627 bifunctional riboflavin kinase/FMN adenylyltransferase; Reviewed
Probab=32.76 E-value=32 Score=27.66 Aligned_cols=28 Identities=25% Similarity=0.311 Sum_probs=23.7
Q ss_pred cCCCCCChHHHHHHHHhhchhhhhhcccccCcHHHHHH
Q psy13474 11 SHESALPPDALRRALAEAFFDQQRFQLGFMDDAAECFE 48 (105)
Q Consensus 11 s~~~~l~p~~LR~ALa~~~~~~~~Fq~G~M~DA~E~fe 48 (105)
.+++.++|+.+|+.|. .|+|++|.+.|.
T Consensus 156 ~~~~~ISST~IR~~I~----------~G~i~~A~~lLg 183 (305)
T PRK05627 156 EDGERVSSTAIRQALA----------EGDLELANKLLG 183 (305)
T ss_pred cCCCcCchHHHHHHHH----------cCCHHHHHhhhc
Confidence 3567899999999998 799999988654
No 67
>PF13041 PPR_2: PPR repeat family
Probab=31.67 E-value=27 Score=19.68 Aligned_cols=19 Identities=26% Similarity=0.433 Sum_probs=15.9
Q ss_pred hcccccCcHHHHHHHHHHH
Q psy13474 35 FQLGFMDDAAECFENMLLR 53 (105)
Q Consensus 35 Fq~G~M~DA~E~fe~IL~~ 53 (105)
++.|++++|.++|+.+.+.
T Consensus 14 ~~~~~~~~a~~l~~~M~~~ 32 (50)
T PF13041_consen 14 CKAGKFEEALKLFKEMKKR 32 (50)
T ss_pred HHCcCHHHHHHHHHHHHHc
Confidence 5689999999999988754
No 68
>PF12854 PPR_1: PPR repeat
Probab=31.63 E-value=20 Score=19.23 Aligned_cols=14 Identities=36% Similarity=0.608 Sum_probs=11.9
Q ss_pred cccccCcHHHHHHH
Q psy13474 36 QLGFMDDAAECFEN 49 (105)
Q Consensus 36 q~G~M~DA~E~fe~ 49 (105)
+.|.+++|.+.|+.
T Consensus 19 k~G~~~~A~~l~~~ 32 (34)
T PF12854_consen 19 KAGRVDEAFELFDE 32 (34)
T ss_pred HCCCHHHHHHHHHh
Confidence 47999999999874
No 69
>PRK10292 hypothetical protein; Provisional
Probab=31.62 E-value=21 Score=23.36 Aligned_cols=32 Identities=19% Similarity=0.237 Sum_probs=23.3
Q ss_pred ChHHHHHHHHhhchhhhhhcccccCcHHHHHH
Q psy13474 17 PPDALRRALAEAFFDQQRFQLGFMDDAAECFE 48 (105)
Q Consensus 17 ~p~~LR~ALa~~~~~~~~Fq~G~M~DA~E~fe 48 (105)
=.+.||.||++---..+--+.-.|++|.+.|+
T Consensus 37 Ia~vlrTa~a~~r~~rs~~~~qaMe~~i~~L~ 68 (69)
T PRK10292 37 IAGVLRTALANKRIQRSELEKQAMETVINALV 68 (69)
T ss_pred HHHHHHHHHHhcccccCHHHHHHHHHHHHHhc
Confidence 35779999998755556667777888877664
No 70
>cd05029 S-100A6 S-100A6: S-100A6 domain found in proteins similar to S100A6. S100A6 is a member of the S100 domain family within EF-hand Ca2+-binding proteins superfamily. Note that the S-100 hierarchy, to which this S-100A6 group belongs, contains only S-100 EF-hand domains, other EF-hands have been modeled separately. S100 proteins exhibit unique patterns of tissue- and cell type-specific expression and have been implicated in the Ca2+-dependent regulation of diverse physiological processes, including cell cycle regulation, differentiation, growth, and metabolic control . S100A6 is normally expressed in the G1 phase of the cell cycle in neuronal cells. The function of S100A6 remains unclear, but evidence suggests that it is involved in cell cycle regulation and exocytosis. S100A6 may also be involved in tumorigenesis; the protein is overexpressed in several tumors. Ca2+ binding to S100A6 leads to a conformational change in the protein, which exposes a hydrophobic surface for interact
Probab=31.49 E-value=1.3e+02 Score=19.53 Aligned_cols=25 Identities=12% Similarity=0.364 Sum_probs=20.3
Q ss_pred HHhhhhhh-cC-CCCCChHHHHHHHHh
Q psy13474 3 ELFSQLQS-SH-ESALPPDALRRALAE 27 (105)
Q Consensus 3 ~iF~~~~~-s~-~~~l~p~~LR~ALa~ 27 (105)
.||.+|.. +. ...|+.+.||..|.+
T Consensus 14 ~~F~~y~~~~~~~g~Is~~EL~~~l~~ 40 (88)
T cd05029 14 AIFHKYSGREGDKNTLSKKELKELIQK 40 (88)
T ss_pred HHHHHHHccCCCCCEECHHHHHHHHHH
Confidence 57888886 33 569999999999975
No 71
>TIGR00083 ribF riboflavin kinase/FMN adenylyltransferase. multifunctional enzyme: riboflavin kinase (EC 2.7.1.26) (flavokinase) / FMN adenylyltransferase (EC 2.7.7.2) (FAD pyrophosphorylase) (FAD synthetase).
Probab=30.22 E-value=31 Score=27.55 Aligned_cols=26 Identities=23% Similarity=0.296 Sum_probs=23.5
Q ss_pred CCCChHHHHHHHHhhchhhhhhcccccCcHHHHHHH
Q psy13474 14 SALPPDALRRALAEAFFDQQRFQLGFMDDAAECFEN 49 (105)
Q Consensus 14 ~~l~p~~LR~ALa~~~~~~~~Fq~G~M~DA~E~fe~ 49 (105)
+.++|+.+|++|+ .|+++.|.+.|.-
T Consensus 142 ~~ISST~IR~~l~----------~G~i~~A~~lLGr 167 (288)
T TIGR00083 142 IRISSSAIRQALK----------NGDLELANKLLGR 167 (288)
T ss_pred CeECHHHHHHHHH----------cCCHHHHHHhhhh
Confidence 7899999999999 7999999998764
No 72
>cd05025 S-100A1 S-100A1: S-100A1 domain found in proteins similar to S100A1. S100A1 is a calcium-binding protein belonging to a large S100 vertebrate-specific protein family within the EF-hand superfamily of calcium-binding proteins. Note that the S-100 hierarchy, to which this S-100A1 group belongs, contains only S-100 EF-hand domains, other EF-hands have been modeled separately. As is the case with many other members of S100 protein family, S100A1 is implicated in intracellular and extracellular regulatory activities, including interaction with myosin-associated twitchin kinase, actin-capping protein CapZ, sinapsin I, and tubulin. Structural data suggests that S100A1 proteins exist within cells as antiparallel homodimers, while heterodimers with S100A4 and S100B also has been reported. Upon binding calcium S100A1 changes conformation to expose a hydrophobic cleft which is the interaction site of S100A1 with its more that 20 known target proteins.
Probab=29.72 E-value=46 Score=21.27 Aligned_cols=27 Identities=15% Similarity=0.286 Sum_probs=22.2
Q ss_pred CHHHhhhhh-hcCCC-CCChHHHHHHHHh
Q psy13474 1 MQELFSQLQ-SSHES-ALPPDALRRALAE 27 (105)
Q Consensus 1 l~~iF~~~~-~s~~~-~l~p~~LR~ALa~ 27 (105)
|+++|..|+ ..... .|+...|+.+|..
T Consensus 11 l~~~F~~fDd~dg~G~~Is~~El~~~l~~ 39 (92)
T cd05025 11 LINVFHAHSGKEGDKYKLSKKELKDLLQT 39 (92)
T ss_pred HHHHHHHHhcccCCCCeECHHHHHHHHHH
Confidence 468899997 66666 5999999999964
No 73
>PF12688 TPR_5: Tetratrico peptide repeat
Probab=29.55 E-value=67 Score=22.28 Aligned_cols=37 Identities=30% Similarity=0.304 Sum_probs=29.0
Q ss_pred CCCChHHHHHHHHhhchhhhhhcccccCcHHHHHHHHHH
Q psy13474 14 SALPPDALRRALAEAFFDQQRFQLGFMDDAAECFENMLL 52 (105)
Q Consensus 14 ~~l~p~~LR~ALa~~~~~~~~Fq~G~M~DA~E~fe~IL~ 52 (105)
..++....++|+-.+ .+....+|+.++|...|+..+.
T Consensus 30 ~gL~~~~~~~a~i~l--astlr~LG~~deA~~~L~~~~~ 66 (120)
T PF12688_consen 30 AGLSGADRRRALIQL--ASTLRNLGRYDEALALLEEALE 66 (120)
T ss_pred cCCCchHHHHHHHHH--HHHHHHcCCHHHHHHHHHHHHH
Confidence 456666677777665 7777899999999999998765
No 74
>PF13432 TPR_16: Tetratricopeptide repeat; PDB: 3CVP_A 3CVL_A 3CVQ_A 3CV0_A 2GW1_B 3CVN_A 3QKY_A 2PL2_B.
Probab=28.08 E-value=35 Score=19.74 Aligned_cols=21 Identities=29% Similarity=0.330 Sum_probs=15.8
Q ss_pred hhhcccccCcHHHHHHHHHHH
Q psy13474 33 QRFQLGFMDDAAECFENMLLR 53 (105)
Q Consensus 33 ~~Fq~G~M~DA~E~fe~IL~~ 53 (105)
-.++.|..++|.+.|+.+++.
T Consensus 40 ~~~~~g~~~~A~~~~~~a~~~ 60 (65)
T PF13432_consen 40 ILYQQGRYDEALAYYERALEL 60 (65)
T ss_dssp HHHHTT-HHHHHHHHHHHHHH
T ss_pred HHHHcCCHHHHHHHHHHHHHH
Confidence 356789999999999988753
No 75
>KOG0027|consensus
Probab=27.87 E-value=1.4e+02 Score=20.64 Aligned_cols=31 Identities=13% Similarity=0.222 Sum_probs=26.4
Q ss_pred CHHHhhhhhhcCCCCCChHHHHHHHHhhchh
Q psy13474 1 MQELFSQLQSSHESALPPDALRRALAEAFFD 31 (105)
Q Consensus 1 l~~iF~~~~~s~~~~l~p~~LR~ALa~~~~~ 31 (105)
|+++|..|+......++...|+.+|..+...
T Consensus 10 l~~~F~~fD~d~~G~i~~~el~~~lr~lg~~ 40 (151)
T KOG0027|consen 10 LKEAFQLFDKDGDGKISVEELGAVLRSLGQN 40 (151)
T ss_pred HHHHHHHHCCCCCCcccHHHHHHHHHHcCCC
Confidence 4688999999999999999999999886443
No 76
>PRK13376 pyrB bifunctional aspartate carbamoyltransferase catalytic subunit/aspartate carbamoyltransferase regulatory subunit; Provisional
Probab=27.74 E-value=22 Score=31.01 Aligned_cols=30 Identities=23% Similarity=0.552 Sum_probs=23.5
Q ss_pred ccCCCCchhhh--------hhcceehhhhccCCcCCCC
Q psy13474 66 MCGAKHCIPHE--------KFAMTLVEQSVCGACGATS 95 (105)
Q Consensus 66 ~c~~~~Ci~H~--------~F~m~l~Eq~vC~~Cg~~S 95 (105)
.|.+|.||+|. +|-..--....|..|+..-
T Consensus 480 ~C~Np~CIt~~~~~e~~~~~F~~~~~~~~~C~YCe~~~ 517 (525)
T PRK13376 480 RCKNENCITNPAHGENVSASFVRNEKGRFVCEYCETPH 517 (525)
T ss_pred EeCCCCCcCCCCCCCcCCceEEEccCCEEEeeCCCCEe
Confidence 69999999998 4666544568999998753
No 77
>PF09279 EF-hand_like: Phosphoinositide-specific phospholipase C, efhand-like; InterPro: IPR015359 This domain is predominantly found in the enzyme phosphoinositol-specific phospholipase C. It adopts a structure consisting of a core of four alpha helices, in an EF like fold, and is required for functioning of the enzyme []. ; PDB: 3OHM_B 3QR0_A 2ZKM_X 2FJU_B 3QR1_D 1DJW_B 1DJI_B 1DJG_B 1QAS_B 2ISD_B ....
Probab=27.56 E-value=95 Score=19.32 Aligned_cols=27 Identities=26% Similarity=0.530 Sum_probs=23.2
Q ss_pred CHHHhhhhhhcCCCCCChHHHHHHHHhh
Q psy13474 1 MQELFSQLQSSHESALPPDALRRALAEA 28 (105)
Q Consensus 1 l~~iF~~~~~s~~~~l~p~~LR~ALa~~ 28 (105)
++.||..|.. .++.|....+++=|.+.
T Consensus 2 i~~if~~ys~-~~~~mt~~~f~~FL~~e 28 (83)
T PF09279_consen 2 IEEIFRKYSS-DKEYMTAEEFRRFLREE 28 (83)
T ss_dssp HHHHHHHHCT-TSSSEEHHHHHHHHHHT
T ss_pred HHHHHHHHhC-CCCcCCHHHHHHHHHHH
Confidence 4689999955 79999999999999864
No 78
>PF12387 Peptidase_C74: Pestivirus NS2 peptidase; InterPro: IPR022120 The pestivirus NS2 peptidase is responsible for single cleavage between NS2 and NS3 of the Bovine viral diarrhea virus 1 polyprotein, a cleavage that is correlated with cytopathogenicity []. The peptidase is activated by its interaction with 'J-domain protein interacting with viral protein' - Jiv. ; GO: 0003968 RNA-directed RNA polymerase activity, 0004197 cysteine-type endopeptidase activity, 0004252 serine-type endopeptidase activity, 0016817 hydrolase activity, acting on acid anhydrides, 0017111 nucleoside-triphosphatase activity, 0070008 serine-type exopeptidase activity
Probab=27.44 E-value=30 Score=26.74 Aligned_cols=34 Identities=24% Similarity=0.486 Sum_probs=22.2
Q ss_pred ccCCCCchhhhhhcceehhhhccCCcCCCCCCCC
Q psy13474 66 MCGAKHCIPHEKFAMTLVEQSVCGACGATSEPLP 99 (105)
Q Consensus 66 ~c~~~~Ci~H~~F~m~l~Eq~vC~~Cg~~S~p~~ 99 (105)
.--++|||.-.+=--+=-..-.|++||..+.|..
T Consensus 156 Lsk~~hcilCtvCe~r~w~g~~CPKCGr~G~pi~ 189 (200)
T PF12387_consen 156 LSKSKHCILCTVCEGREWKGGNCPKCGRHGKPIT 189 (200)
T ss_pred ccCCCceEEEeeeecCccCCCCCCcccCCCCCee
Confidence 3346789874433333334467999999998864
No 79
>cd05031 S-100A10_like S-100A10_like: S-100A10 domain found in proteins similar to S100A10. S100A10 is a member of the S100 family of EF-hand superfamily of calcium-binding proteins. Note that the S-100 hierarchy, to which this S-100A1_like group belongs, contains only S-100 EF-hand domains, other EF-hands have been modeled separately. S100 proteins are expressed exclusively in vertebrates, and are implicated in intracellular and extracellular regulatory activities. A unique feature of S100A10 is that it contains mutation in both of the calcium binding sites, making it calcium insensitive. S100A10 has been detected in brain, heart, gastrointestinal tract, kidney, liver, lung, spleen, testes, epidermis, aorta, and thymus. Structural data supports the homo- and hetero-dimeric as well as hetero-tetrameric nature of the protein. S100A10 has multiple binding partners in its calcium free state and is therefore involved in many diverse biological functions.
Probab=27.43 E-value=58 Score=20.94 Aligned_cols=27 Identities=11% Similarity=0.289 Sum_probs=22.1
Q ss_pred CHHHhhhhhh-cC-CCCCChHHHHHHHHh
Q psy13474 1 MQELFSQLQS-SH-ESALPPDALRRALAE 27 (105)
Q Consensus 1 l~~iF~~~~~-s~-~~~l~p~~LR~ALa~ 27 (105)
|.++|..|+. .. ...|+.+.|+.+|..
T Consensus 10 l~~~F~~~D~~dg~dG~Is~~El~~~l~~ 38 (94)
T cd05031 10 LILTFHRYAGKDGDKNTLSRKELKKLMEK 38 (94)
T ss_pred HHHHHHHHhccCCCCCeECHHHHHHHHHH
Confidence 4578889987 54 589999999999975
No 80
>PF09976 TPR_21: Tetratricopeptide repeat; InterPro: IPR018704 This domain, found in various hypothetical prokaryotic proteins, has no known function.
Probab=27.34 E-value=47 Score=22.70 Aligned_cols=23 Identities=22% Similarity=0.381 Sum_probs=19.4
Q ss_pred hhhhhcccccCcHHHHHHHHHHH
Q psy13474 31 DQQRFQLGFMDDAAECFENMLLR 53 (105)
Q Consensus 31 ~~~~Fq~G~M~DA~E~fe~IL~~ 53 (105)
.+..|..|+.+.|.+.|+.+++.
T Consensus 55 A~~~~~~g~~~~A~~~l~~~~~~ 77 (145)
T PF09976_consen 55 AKAAYEQGDYDEAKAALEKALAN 77 (145)
T ss_pred HHHHHHCCCHHHHHHHHHHHHhh
Confidence 44567889999999999999984
No 81
>PF01599 Ribosomal_S27: Ribosomal protein S27a; InterPro: IPR002906 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. This family of ribosomal proteins consists mainly of the 40S ribosomal protein S27a which is synthesized as a C-terminal extension of ubiquitin (CEP) (IPR000626 from INTERPRO). The S27a domain compromises the C-terminal half of the protein. The synthesis of ribosomal proteins as extensions of ubiquitin promotes their incorporation into nascent ribosomes by a transient metabolic stabilisation and is required for efficient ribosome biogenesis []. The ribosomal extension protein S27a contains a basic region that is proposed to form a zinc finger; its fusion gene is proposed as a mechanism to maintain a fixed ratio between ubiquitin necessary for degrading proteins and ribosomes a source of proteins [].; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 2K4X_A 3U5C_f 3U5G_f 2XZN_9 2XZM_9.
Probab=27.34 E-value=28 Score=21.04 Aligned_cols=29 Identities=28% Similarity=0.570 Sum_probs=19.4
Q ss_pred hccCCCCchhhhhhcceehhhhccCCcCCC
Q psy13474 65 DMCGAKHCIPHEKFAMTLVEQSVCGACGAT 94 (105)
Q Consensus 65 d~c~~~~Ci~H~~F~m~l~Eq~vC~~Cg~~ 94 (105)
..|.++.|=+-...| .=.++..|++||.|
T Consensus 19 k~CP~~~CG~GvFMA-~H~dR~~CGKCg~T 47 (47)
T PF01599_consen 19 KECPSPRCGAGVFMA-EHKDRHYCGKCGYT 47 (47)
T ss_dssp EE-TSTTTTSSSEEE-E-SSEEEETTTSS-
T ss_pred hcCCCcccCCceEee-ecCCCccCCCcccC
Confidence 588888888754333 33689999999975
No 82
>PF05741 zf-nanos: Nanos RNA binding domain; InterPro: IPR024161 Nanos is a highly conserved RNA-binding protein in higher eukaryotes and functions as a key regulatory protein in translational control using a 3' untranslated region during the development and maintenance of germ cells. Nanos comprises a non-conserved amino-terminus and highly conserved carboxy- terminal regions. The C-terminal region has two conserved Cys-Cys-His-Cys (CCHC)-type zinc-finger motifs that are indispensable for nanos function [, , ]. The structure of the nanos-type zinc finger is composed of two independent zinc-finger (ZF) lobes, the N-terminal ZF1 and the C-terminal ZF2, which are connected by a linker helix []. These lobes create a large cleft. Zinc ions in ZF1 and ZF2 are bound to the CCHC motif by tetrahedral coordination.; PDB: 3ALR_B.
Probab=26.26 E-value=24 Score=21.96 Aligned_cols=14 Identities=43% Similarity=0.961 Sum_probs=5.8
Q ss_pred hhhhccCCcCCCCC
Q psy13474 83 VEQSVCGACGATSE 96 (105)
Q Consensus 83 ~Eq~vC~~Cg~~S~ 96 (105)
.-+.+|+-||+|++
T Consensus 31 Lr~y~Cp~CgAtGd 44 (55)
T PF05741_consen 31 LRKYVCPICGATGD 44 (55)
T ss_dssp GGG---TTT---GG
T ss_pred HhcCcCCCCcCcCc
Confidence 34579999999976
No 83
>PTZ00183 centrin; Provisional
Probab=25.98 E-value=73 Score=21.31 Aligned_cols=28 Identities=18% Similarity=0.424 Sum_probs=23.5
Q ss_pred CHHHhhhhhhcCCCCCChHHHHHHHHhh
Q psy13474 1 MQELFSQLQSSHESALPPDALRRALAEA 28 (105)
Q Consensus 1 l~~iF~~~~~s~~~~l~p~~LR~ALa~~ 28 (105)
++.+|..++.+...-|+...++.+|...
T Consensus 19 ~~~~F~~~D~~~~G~i~~~e~~~~l~~~ 46 (158)
T PTZ00183 19 IREAFDLFDTDGSGTIDPKELKVAMRSL 46 (158)
T ss_pred HHHHHHHhCCCCCCcccHHHHHHHHHHh
Confidence 4678888888888899999999999864
No 84
>PF10825 DUF2752: Protein of unknown function (DUF2752); InterPro: IPR021215 This family is conserved in bacteria. Many members are annotated as being putative membrane proteins.
Probab=25.15 E-value=27 Score=20.99 Aligned_cols=17 Identities=29% Similarity=0.645 Sum_probs=12.4
Q ss_pred chhhhhhcceehhhhccCCcCCC
Q psy13474 72 CIPHEKFAMTLVEQSVCGACGAT 94 (105)
Q Consensus 72 Ci~H~~F~m~l~Eq~vC~~Cg~~ 94 (105)
|.-+.++|+ .|+.||.|
T Consensus 2 C~~~~ltG~------~CPgCG~t 18 (52)
T PF10825_consen 2 CPFKALTGI------PCPGCGMT 18 (52)
T ss_pred CcchhhhCC------CCCCCcHH
Confidence 666666665 49999976
No 85
>PF12994 DUF3878: Domain of unknown function, E. rectale Gene description (DUF3878); InterPro: IPR024538 This entry represents proteins of unknown function found primarily in Firmicutes. The Eubacterium rectale gene appears to be upregulated in the presence of Bacteroides thetaiotaomicron compared to growth in pure culture [].
Probab=24.98 E-value=28 Score=28.55 Aligned_cols=11 Identities=45% Similarity=0.649 Sum_probs=9.7
Q ss_pred ccCcHHHHHHH
Q psy13474 39 FMDDAAECFEN 49 (105)
Q Consensus 39 ~M~DA~E~fe~ 49 (105)
.||||.|+|..
T Consensus 32 lMNDAVEsfLv 42 (299)
T PF12994_consen 32 LMNDAVESFLV 42 (299)
T ss_pred ehhhhhhhhee
Confidence 69999999965
No 86
>TIGR00756 PPR pentatricopeptide repeat domain (PPR motif). This family has a similar consensus to the TPR domain (tetratricopeptide), pfam pfam00515, a 33-residue repeat. It is predicted to form a pair of antiparallel helices similar to that of TPR.
Probab=24.84 E-value=47 Score=16.20 Aligned_cols=18 Identities=33% Similarity=0.516 Sum_probs=14.3
Q ss_pred hcccccCcHHHHHHHHHH
Q psy13474 35 FQLGFMDDAAECFENMLL 52 (105)
Q Consensus 35 Fq~G~M~DA~E~fe~IL~ 52 (105)
.+.|.+++|.++|..+..
T Consensus 11 ~~~~~~~~a~~~~~~M~~ 28 (35)
T TIGR00756 11 CKAGRVEEALELFKEMLE 28 (35)
T ss_pred HHCCCHHHHHHHHHHHHH
Confidence 457899999999988654
No 87
>PF13371 TPR_9: Tetratricopeptide repeat
Probab=23.58 E-value=43 Score=19.63 Aligned_cols=21 Identities=38% Similarity=0.374 Sum_probs=17.7
Q ss_pred hhhcccccCcHHHHHHHHHHH
Q psy13474 33 QRFQLGFMDDAAECFENMLLR 53 (105)
Q Consensus 33 ~~Fq~G~M~DA~E~fe~IL~~ 53 (105)
-.++.|....|.++|+.+++.
T Consensus 38 ~~~~~g~~~~A~~~l~~~l~~ 58 (73)
T PF13371_consen 38 CLFQLGRYEEALEDLERALEL 58 (73)
T ss_pred HHHHhccHHHHHHHHHHHHHH
Confidence 457889999999999999853
No 88
>PF14169 YdjO: Cold-inducible protein YdjO
Probab=23.49 E-value=49 Score=20.95 Aligned_cols=31 Identities=19% Similarity=0.418 Sum_probs=26.7
Q ss_pred hhccCCCCchhhhhhcceehhhhccCCcCCC
Q psy13474 64 EDMCGAKHCIPHEKFAMTLVEQSVCGACGAT 94 (105)
Q Consensus 64 ~d~c~~~~Ci~H~~F~m~l~Eq~vC~~Cg~~ 94 (105)
-+.|++..|..=+-=....-|.-+|+-|+..
T Consensus 18 VW~Ct~e~C~gWmR~nFs~~~~p~CPlC~s~ 48 (59)
T PF14169_consen 18 VWECTSEDCNGWMRDNFSFEEEPVCPLCKSP 48 (59)
T ss_pred eEEeCCCCCCcccccccccCCCccCCCcCCc
Confidence 3699999999988877788899999999864
No 89
>PF09538 FYDLN_acid: Protein of unknown function (FYDLN_acid); InterPro: IPR012644 Members of this family are bacterial proteins with a conserved motif [KR]FYDLN, sometimes flanked by a pair of CXXC motifs, followed by a long region of low complexity sequence in which roughly half the residues are Asp and Glu, including multiple runs of five or more acidic residues. The function of members of this family is unknown.
Probab=23.35 E-value=51 Score=22.89 Aligned_cols=19 Identities=32% Similarity=0.746 Sum_probs=14.6
Q ss_pred ceehhhhccCCcCCCCCCCC
Q psy13474 80 MTLVEQSVCGACGATSEPLP 99 (105)
Q Consensus 80 m~l~Eq~vC~~Cg~~S~p~~ 99 (105)
|+- .-.||++||.+..+.+
T Consensus 22 Lnk-~PivCP~CG~~~~~~~ 40 (108)
T PF09538_consen 22 LNK-DPIVCPKCGTEFPPEP 40 (108)
T ss_pred CCC-CCccCCCCCCccCccc
Confidence 444 5578999999988874
No 90
>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=23.27 E-value=60 Score=18.81 Aligned_cols=23 Identities=35% Similarity=0.403 Sum_probs=19.3
Q ss_pred hhhhhcccccCcHHHHHHHHHHH
Q psy13474 31 DQQRFQLGFMDDAAECFENMLLR 53 (105)
Q Consensus 31 ~~~~Fq~G~M~DA~E~fe~IL~~ 53 (105)
....|+.|+.++|.+.|...++.
T Consensus 10 g~~~~~~~~~~~A~~~~~~ai~~ 32 (69)
T PF13414_consen 10 GQIYFQQGDYEEAIEYFEKAIEL 32 (69)
T ss_dssp HHHHHHTTHHHHHHHHHHHHHHH
T ss_pred HHHHHHcCCHHHHHHHHHHHHHc
Confidence 44568899999999999998886
No 91
>PF12895 Apc3: Anaphase-promoting complex, cyclosome, subunit 3; PDB: 3KAE_D 3Q4A_B 2C2L_D 3Q47_B 3Q49_B 2XPI_A 3ULQ_A.
Probab=22.96 E-value=38 Score=20.84 Aligned_cols=19 Identities=21% Similarity=0.392 Sum_probs=14.1
Q ss_pred hhhhhcccccCcHHHHHHH
Q psy13474 31 DQQRFQLGFMDDAAECFEN 49 (105)
Q Consensus 31 ~~~~Fq~G~M~DA~E~fe~ 49 (105)
..-.+++|+.++|.++|+.
T Consensus 65 a~~~~~l~~y~eAi~~l~~ 83 (84)
T PF12895_consen 65 ARCLLKLGKYEEAIKALEK 83 (84)
T ss_dssp HHHHHHTT-HHHHHHHHHH
T ss_pred HHHHHHhCCHHHHHHHHhc
Confidence 4557888888888888875
No 92
>PRK11788 tetratricopeptide repeat protein; Provisional
Probab=22.59 E-value=1.1e+02 Score=23.54 Aligned_cols=20 Identities=15% Similarity=-0.039 Sum_probs=14.7
Q ss_pred hhcccccCcHHHHHHHHHHH
Q psy13474 34 RFQLGFMDDAAECFENMLLR 53 (105)
Q Consensus 34 ~Fq~G~M~DA~E~fe~IL~~ 53 (105)
..+.|+.++|.+.|+.+++.
T Consensus 292 ~~~~g~~~~A~~~l~~~l~~ 311 (389)
T PRK11788 292 LEEQEGPEAAQALLREQLRR 311 (389)
T ss_pred HHHhCCHHHHHHHHHHHHHh
Confidence 34568888888888877665
No 93
>TIGR00240 ATCase_reg aspartate carbamoyltransferase, regulatory subunit. The presence of this regulatory subunit allows feedback inhibition by CTP on aspartate carbamoyltransferase, the first step in the synthesis of CTP from aspartate. In many species, this regulatory subunit is not present. In Thermotoga maritima, the catalytic and regulatory subunits are encoded by a fused gene and the regulatory region has enough sequence differences to score below the trusted cutoff.
Probab=21.84 E-value=36 Score=25.28 Aligned_cols=29 Identities=28% Similarity=0.531 Sum_probs=21.6
Q ss_pred ccCCCCchhhh-----hhcceehh---hhccCCcCCC
Q psy13474 66 MCGAKHCIPHE-----KFAMTLVE---QSVCGACGAT 94 (105)
Q Consensus 66 ~c~~~~Ci~H~-----~F~m~l~E---q~vC~~Cg~~ 94 (105)
-|.+|.||+|. +|...=-+ ...|..|+.+
T Consensus 105 kC~Np~CIT~~E~v~~~F~v~~~~~~~~lrC~YCe~~ 141 (150)
T TIGR00240 105 KCPNPNCISNAEPVSSKFYVRSEEPDIALRCYYCEKE 141 (150)
T ss_pred ECCCCCCccCCCCCCcEEEEecCCCceEEEEECCCCE
Confidence 89999999984 56554344 3789999865
No 94
>PF13374 TPR_10: Tetratricopeptide repeat; PDB: 3CEQ_B 3EDT_H 3NF1_A.
Probab=21.58 E-value=1e+02 Score=15.73 Aligned_cols=25 Identities=20% Similarity=0.093 Sum_probs=16.2
Q ss_pred hhcccccCcHHHHHHHHHHHhhhcc
Q psy13474 34 RFQLGFMDDAAECFENMLLRIHYHI 58 (105)
Q Consensus 34 ~Fq~G~M~DA~E~fe~IL~~lH~~~ 58 (105)
.+..|+.++|.+.++.+++.--..+
T Consensus 12 ~~~~g~~~~A~~~~~~al~~~~~~~ 36 (42)
T PF13374_consen 12 YRAQGRYEEALELLEEALEIRERLL 36 (42)
T ss_dssp HHHCT-HHHHHHHHHHHHHHH----
T ss_pred HHhhhhcchhhHHHHHHHHHHHHHh
Confidence 4557999999999999887654443
No 95
>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=21.14 E-value=49 Score=19.07 Aligned_cols=19 Identities=37% Similarity=0.487 Sum_probs=13.7
Q ss_pred hcccccCcHHHHHHHHHHH
Q psy13474 35 FQLGFMDDAAECFENMLLR 53 (105)
Q Consensus 35 Fq~G~M~DA~E~fe~IL~~ 53 (105)
++.|+.++|.+.|+.++..
T Consensus 2 l~~~~~~~A~~~~~~~l~~ 20 (68)
T PF14559_consen 2 LKQGDYDEAIELLEKALQR 20 (68)
T ss_dssp HHTTHHHHHHHHHHHHHHH
T ss_pred hhccCHHHHHHHHHHHHHH
Confidence 4567777788888777755
No 96
>PF09723 Zn-ribbon_8: Zinc ribbon domain; InterPro: IPR013429 This entry represents a region of about 41 amino acids found in a number of small proteins in a wide range of bacteria. The region usually begins with the initiator Met and contains two CxxC motifs separated by 17 amino acids. One protein in this entry has been noted as a putative regulatory protein, designated FmdB []. Most proteins in this entry have a C-terminal region containing highly degenerate sequence.
Probab=20.94 E-value=32 Score=19.62 Aligned_cols=8 Identities=38% Similarity=1.095 Sum_probs=3.8
Q ss_pred hccCCcCC
Q psy13474 86 SVCGACGA 93 (105)
Q Consensus 86 ~vC~~Cg~ 93 (105)
..|..||.
T Consensus 27 ~~CP~Cg~ 34 (42)
T PF09723_consen 27 VPCPECGS 34 (42)
T ss_pred CcCCCCCC
Confidence 34555554
No 97
>PF03604 DNA_RNApol_7kD: DNA directed RNA polymerase, 7 kDa subunit; InterPro: IPR006591 DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. Each class of RNA polymerase is assembled from 9 to 15 different polypeptides. Rbp10 (RNA polymerase CX) is a domain found in RNA polymerase subunit 10; present in RNA polymerase I, II and III.; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0006351 transcription, DNA-dependent; PDB: 2PMZ_Z 3HKZ_X 2NVX_L 3S1Q_L 2JA6_L 3S17_L 3HOW_L 3HOV_L 3PO2_L 3HOZ_L ....
Probab=20.94 E-value=47 Score=18.36 Aligned_cols=11 Identities=55% Similarity=1.280 Sum_probs=7.9
Q ss_pred hccCCcCCCCC
Q psy13474 86 SVCGACGATSE 96 (105)
Q Consensus 86 ~vC~~Cg~~S~ 96 (105)
.+|+.||++-+
T Consensus 1 Y~C~~Cg~~~~ 11 (32)
T PF03604_consen 1 YICGECGAEVE 11 (32)
T ss_dssp EBESSSSSSE-
T ss_pred CCCCcCCCeeE
Confidence 36888998766
No 98
>PF06957 COPI_C: Coatomer (COPI) alpha subunit C-terminus; InterPro: IPR010714 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 C terminus (approximately 500 residues) of the eukaryotic coatomer alpha subunit [, ]. This domain is found along with the IPR006692 from INTERPRO domain. More information about these proteins can be found at Protein of the Month: Clathrin [].; GO: 0005198 structural molecule activity, 0005515 protein binding, 0006886 intracellular protein transport, 0016192 vesicle-mediated transport, 0030126 COPI vesicle coat; PDB: 3MKR_B 3MV2_E 3MKQ_B 3MV3_A.
Probab=20.36 E-value=65 Score=27.49 Aligned_cols=31 Identities=23% Similarity=0.380 Sum_probs=24.0
Q ss_pred hhhhhcccccCcHHHHHHHHHHHhhhccCCc
Q psy13474 31 DQQRFQLGFMDDAAECFENMLLRIHYHIASE 61 (105)
Q Consensus 31 ~~~~Fq~G~M~DA~E~fe~IL~~lH~~~~~~ 61 (105)
.-+.|..|...||.++|..||..|=.-+..+
T Consensus 211 gyk~~t~gKF~eA~~~Fr~iL~~i~l~vv~~ 241 (422)
T PF06957_consen 211 GYKLFTAGKFEEAIEIFRSILHSIPLLVVES 241 (422)
T ss_dssp HHHHHHTT-HHHHHHHHHHHHHHHHC--BSS
T ss_pred HHHHHhcCCHHHHHHHHHHHHHHhheeeecC
Confidence 3477999999999999999999987766554
No 99
>smart00834 CxxC_CXXC_SSSS Putative regulatory protein. CxxC_CXXC_SSSS represents a region of about 41 amino acids found in a number of small proteins in a wide range of bacteria. The region usually begins with the initiator Met and contains two CxxC motifs separated by 17 amino acids. One protein in this entry has been noted as a putative regulatory protein, designated FmdB. Most proteins in this entry have a C-terminal region containing highly degenerate sequence.
Probab=20.35 E-value=49 Score=17.94 Aligned_cols=13 Identities=23% Similarity=0.606 Sum_probs=9.5
Q ss_pred hhhhccCCcCCCC
Q psy13474 83 VEQSVCGACGATS 95 (105)
Q Consensus 83 ~Eq~vC~~Cg~~S 95 (105)
-+..+|..||++.
T Consensus 24 ~~~~~CP~Cg~~~ 36 (41)
T smart00834 24 DPLATCPECGGDV 36 (41)
T ss_pred CCCCCCCCCCCcc
Confidence 4567899998854
No 100
>COG5207 UBP14 Isopeptidase T [Posttranslational modification, protein turnover, chaperones]
Probab=20.22 E-value=1.4e+02 Score=27.01 Aligned_cols=74 Identities=19% Similarity=0.225 Sum_probs=55.4
Q ss_pred CCChHHHHHHHHhhchhhhhhcccccCcHHHHHHHHHHHhhhccCCchhhhccCCCCchhhhhhcceehhhhccCCcCCC
Q psy13474 15 ALPPDALRRALAEAFFDQQRFQLGFMDDAAECFENMLLRIHYHIASEEAEDMCGAKHCIPHEKFAMTLVEQSVCGACGAT 94 (105)
Q Consensus 15 ~l~p~~LR~ALa~~~~~~~~Fq~G~M~DA~E~fe~IL~~lH~~~~~~~~~d~c~~~~Ci~H~~F~m~l~Eq~vC~~Cg~~ 94 (105)
.|.|..+..-+.. +-+-|..-+--||-|-|.-+|+.|-....+...++ |+ .+|-+.+=.+..|..|+..
T Consensus 372 gi~p~~fk~~igq---~h~eFg~~~QQDA~EFLlfLL~kirk~~~S~~~~~-------It-~lf~Fe~e~rlsC~~C~~v 440 (749)
T COG5207 372 GISPLDFKMLIGQ---DHPEFGKFAQQDAHEFLLFLLEKIRKGERSYLIPP-------IT-SLFEFEVERRLSCSGCMDV 440 (749)
T ss_pred CcChhhHHHHHcC---CchhhhhhhhhhHHHHHHHHHHHHhhccchhcCCC-------cc-hhhhhhhcceecccccccc
Confidence 4677777776654 66778888889999999999999988544322111 55 7899888888999999987
Q ss_pred CCCCC
Q psy13474 95 SEPLP 99 (105)
Q Consensus 95 S~p~~ 99 (105)
+--.|
T Consensus 441 ~ySye 445 (749)
T COG5207 441 SYSYE 445 (749)
T ss_pred ccccc
Confidence 75443
Done!